RCSB PDB: Search

1YQ9 \| pdb_00001yq9	Download File View File

Structure of the unready oxidized form of [NiFe] hydrogenase

Volbeda, A., Martin, L., Cavazza, C., Matho, M., Faber, B.W., Roseboom, W., Albracht, S.P., Garcin, E., Rousset, M., Fontecilla-Camps, J.C.

(2005) J Biol Inorg Chem 10: 239-249

Released	2005-04-19
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Megalodesulfovibrio gigas
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, FCO, GOL, H2S, MG, NI, PER, SF4

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1YRQ \| pdb_00001yrq	Download File View File

Structure of the ready oxidized form of [NiFe]-hydrogenase

Volbeda, A., Martin, L., Cavazza, C., Matho, M., Faber, B.W., Roseboom, W., Albracht, S.P., Garcin, E., Rousset, M., Fontecilla-Camps, J.C.

(2005) J Biol Inorg Chem 10: 239-249

Released	2005-04-19
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Solidesulfovibrio fructosivorans
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, FCO, MG, NI, SF4

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1ZLQ \| pdb_00001zlq	Download File View File

Crystallographic and spectroscopic evidence for high affinity binding of Fe EDTA (H2O)- to the periplasmic nickel transporter NikA

Cherrier, M.V., Martin, L., Cavazza, C., Jacquamet, L., Lemaire, D., Gaillard, J., Fontecilla Camps, J.C.

(2005) J Am Chem Soc 127: 10075-10082

Released	2005-08-02
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	ACT, CL, DTT, EDT, FE, GOL, SO4

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2C3M \| pdb_00002c3m	Download File View File

Crystal Structure Of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio africanus

Cavazza, C., Contreras-Martel, C., Pieulle, L., Chabriere, E., Hatchikian, E.C., Fontecilla-Camps, J.C.

(2006) Structure 14: 217

Released	2006-02-15
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Desulfocurvibacter africanus
Macromolecule	PYRUVATE-FERREDOXIN OXIDOREDUCTASE (protein)
Unique Ligands	CA, CL, MG, SF4, TPP

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2C3O \| pdb_00002c3o	Download File View File

CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus

Cavazza, C., Contreras-Martel, C., Pieulle, L., Chabriere, E., Hatchikian, E.C., Fontecilla-Camps, J.C.

(2006) Structure 14: 217

Released	2006-02-15
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Desulfocurvibacter africanus
Macromolecule	PYRUVATE-FERREDOXIN OXIDOREDUCTASE (protein)
Unique Ligands	CA, MG, PYR, SF4, TPP

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2C3P \| pdb_00002c3p	Download File View File

CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus

Cavazza, C., Contreras-Martel, C., Pieulle, L., Chabriere, E., Hatchikian, E.C., Fontecilla-Camps, J.C.

(2006) Structure 14: 217

Released	2006-02-15
Method	X-RAY DIFFRACTION 2.33 Å
Organisms	Desulfocurvibacter africanus
Macromolecule	PYRUVATE-FERREDOXIN OXIDOREDUCTASE (protein)
Unique Ligands	1TP, CA, MG, SF4

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2C3U \| pdb_00002c3u	Download File View File

Crystal Structure Of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio africanus, Oxygen inhibited form

Cavazza, C., Contreras-Martel, C., Pieulle, L., Chabriere, E., Hatchikian, E.C., Fontecilla-Camps, J.C.

(2006) Structure 14: 217

Released	2006-02-15
Method	X-RAY DIFFRACTION 2.32 Å
Organisms	Desulfocurvibacter africanus
Macromolecule	PYRUVATE-FERREDOXIN OXIDOREDUCTASE (protein)
Unique Ligands	2TP, CA, MG, PYR, SF4

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2C3Y \| pdb_00002c3y	Download File View File

CRYSTAL STRUCTURE OF THE RADICAL FORM OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus

Cavazza, C., Contreras-Martel, C., Pieulle, L., Chabriere, E., Hatchikian, E.C., Fontecilla-Camps, J.C.

(2006) Structure 14: 217

Released	2006-02-15
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Desulfocurvibacter africanus
Macromolecule	PYRUVATE-FERREDOXIN OXIDOREDUCTASE (protein)
Unique Ligands	CA, CO2, HTL, MG, SF4

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2C42 \| pdb_00002c42	Download File View File

Crystal Structure Of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio africanus

Cavazza, C., Contreras-Martel, C., Pieulle, L., Chabriere, E., Hatchikian, E.C., Fontecilla-Camps, J.C.

(2006) Structure 14: 217

Released	2006-12-20
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Desulfocurvibacter africanus
Macromolecule	PYRUVATE-FERREDOXIN OXIDOREDUCTASE (protein)
Unique Ligands	CA, MG, PYR, SF4, TPP

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2Q0M \| pdb_00002q0m	Download File View File

Tricarbonylmanganese(I)-lysozyme complex : a structurally characterized organometallic protein

Razavet, M., Artero, V., Cavazza, C., Oudart, Y., Fontecilla-Camps, J.C., Fontecave, M.

(2007) Chem Commun (Camb) 2805-2807

Released	2007-12-11
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Gallus gallus
Macromolecule	Lysozyme C (protein)
Unique Ligands	CL, CMO, MN, NA, TFS

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2UZA \| pdb_00002uza	Download File View File

CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS

Chabriere, E., Cavazza, C., Contreras-Martel, C., Fontecilla-Camps, J.C.

(2006) Structure 14: 217-224

Released	2008-05-20
Method	X-RAY DIFFRACTION 2.42 Å
Organisms	Desulfocurvibacter africanus
Macromolecule	PYRUVATE FERREDOXIN OXIDOREDUCTASE (protein)
Unique Ligands	CA, CO2, HTL, MG, SF4

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3DP8 \| pdb_00003dp8	Download File View File

Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (nickel butane-1,2,4-tricarboxylate form)

Cherrier, M.V., Cavazza, C., Bochot, C., Lemaire, D., Fontecilla-Camps, J.C.

(2008) Biochemistry 47: 9937-9943

Released	2008-09-16
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli K-12
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	ACT, CL, GOL, HCT, NI, SO4

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3E3K \| pdb_00003e3k	Download File View File

Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (butane-1,2,4-tricarboxylate without nickel form)

Cherrier, M.V., Cavazza, C., Bochot, C., Lemaire, D., Fontecilla-Camps, J.C.

(2008) Biochemistry 47: 9937-9943

Released	2008-09-16
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Escherichia coli K-12
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	ACT, CL, GOL, HCT, SO4

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3MVW \| pdb_00003mvw	Download File View File

X-ray structure of a "NikA+Iron complex" hybrid, NikA/1

Cavazza, C., Bochot, C., Rousselot-Pailley, P., Carpentier, P., Cherrier, M.V., Martin, L., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S.

(2010) Nat Chem 2: 1069-1076

Released	2011-02-09
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Escherichia coli K-12
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	ACT, BHZ, CL, FE, GOL, SO4

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3MVX \| pdb_00003mvx	Download File View File

X-ray structure of the reduced NikA/1 hybrid, NikA/1-Red

Cavazza, C., Bochot, C., Rousselot-Pailley, P., Carpentier, P., Cherrier, M.V., Martin, L., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S.

(2010) Nat Chem 2: 1069-1076

Released	2011-02-09
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Escherichia coli K-12
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	ACT, BHZ, CL, DTU, DTV, FE2, GOL, SO4

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3MVY \| pdb_00003mvy	Download File View File

X-ray structure of the diatomic oxo-intermediate NikA/1-Int', prior hydroxylation

Cavazza, C., Bochot, C., Rousselot-Pailley, P., Carpentier, P., Cherrier, M.V., Martin, L., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S.

(2010) Nat Chem 2: 1069-1076

Released	2011-02-09
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli K-12
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	ACT, BHZ, CL, FE, GOL, PER, SO4

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3MVZ \| pdb_00003mvz	Download File View File

X-ray structure of the (hydro)peroxo intermediate NikA/1-Int", after monohydroxylation of the iron complex

Cavazza, C., Bochot, C., Rousselot-Pailley, P., Carpentier, P., Cherrier, M.V., Martin, L., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S.

(2010) Nat Chem 2: 1069-1076

Released	2011-02-09
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Escherichia coli K-12
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	ACT, BHN, FE, GOL, PER, SO4

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3MW0 \| pdb_00003mw0	Download File View File

X-ray structure of the doubly hydroxylated iron complex-NikA species, NikA1/O2

Cavazza, C., Bochot, C., Rousselot-Pailley, P., Carpentier, P., Cherrier, M.V., Martin, L., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S.

(2010) Nat Chem 2: 1069-1076

Released	2011-02-09
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Escherichia coli K-12
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	BHR, DTD, FE

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3MZ9 \| pdb_00003mz9	Download File View File

X-ray structure of NikA in complex with HBED

Cavazza, C., Bochot, C., Rousselot-Pailley, P., Carpentier, P., Cherrier, M.V., Martin, L., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S.

(2010) Nat Chem 2: 1069-1076

Released	2011-02-09
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli K-12
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	ACT, BHN, CL, DTD, FE, GOL, SO4

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3MZB \| pdb_00003mzb	Download File View File

X-ray structure of NikA in complex with the doubly hydroxylated iron complex, 1-O2

Cavazza, C., Bochot, C., Rousselot-Pailley, P., Carpentier, P., Cherrier, M.V., Martin, L., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S.

(2010) Nat Chem 2: 1069-1076

Released	2011-02-09
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Escherichia coli K-12
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	ACT, BHR, CL, DTD, FE, GOL, SO4

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3QIM \| pdb_00003qim	Download File View File

Histidine 416 of the periplamsic binding protein NikA is essential for nickel uptake in Escherichia coli

Cavazza, C., Martin, L., Laffly, E., Lebrette, H., Cherrier, M.V., Zeppieri, L., Richaud, P., Carriere, M., Fontecilla-Camps, J.C.

(2011) FEBS Lett 585: 711-715

Released	2011-03-02
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli K-12
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	ACT, GOL, SO4

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4DCX \| pdb_00004dcx	Download File View File

X-ray structure of NikA in complex with Fe(1R,2R)-N,N'-Bis(2-pyridylmethyl)-N,N'-dicarboxymethyl-1,2-cyclohexanediamine

Cherrier, M.V., Girgenti, E., Amara, P., Iannello, M., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S., Cavazza, C.

(2012) J Biol Inorg Chem 17: 817-829

Released	2012-05-09
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli K-12
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	ACT, GOL, L2D, SO4

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4DCY \| pdb_00004dcy	Download File View File

X-ray structure of NikA in complex with Fe(1S,2S)-N,N-kappa-Bis(2-pyridylmethyl)-N-carboxymethyl-N-kappa-methyl-1,2-cyclohexanediamine

Cherrier, M.V., Girgenti, E., Amara, P., Iannello, M., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S., Cavazza, C.

(2012) J Biol Inorg Chem 17: 817-829

Released	2012-05-09
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli K-12
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	ACT, GOL, L2M, SO4, UNX

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4I8C \| pdb_00004i8c	Download File View File

X-ray structure of NikA in complex with Ni-(L-His)2

Lebrette, H., Iannello, M., Fontecilla-Camps, J.C., Cavazza, C.

(2012) J Inorg Biochem 121C: 16-18

Released	2013-01-30
Method	X-RAY DIFFRACTION 2.503 Å
Organisms	Escherichia coli K-12
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	ACT, CL, GOL, HIS, NI, SO4

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4I9D \| pdb_00004i9d	Download File View File

X-ray structure of NikA in complex with Fe-N,N'-Bis(2-pyridylmethyl)-N-carboxymethyl-N'-methyl

Cherrier, M.V., Amara, P., Iannello, M., Cavazza, C.

(2013) Angew Chem Int Ed Engl 52: 3922-3925

Released	2013-04-17
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Escherichia coli BL21(DE3)
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	ACT, GOL, L4D, SO4

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

1YQ9 | pdb_00001yq9

1YRQ | pdb_00001yrq

1ZLQ | pdb_00001zlq

2C3M | pdb_00002c3m

2C3O | pdb_00002c3o

2C3P | pdb_00002c3p

2C3U | pdb_00002c3u

2C3Y | pdb_00002c3y

2C42 | pdb_00002c42

2Q0M | pdb_00002q0m

2UZA | pdb_00002uza

3DP8 | pdb_00003dp8

3E3K | pdb_00003e3k

3MVW | pdb_00003mvw

3MVX | pdb_00003mvx

3MVY | pdb_00003mvy

3MVZ | pdb_00003mvz

3MW0 | pdb_00003mw0

3MZ9 | pdb_00003mz9

3MZB | pdb_00003mzb

3QIM | pdb_00003qim

4DCX | pdb_00004dcx

4DCY | pdb_00004dcy

4I8C | pdb_00004i8c

4I9D | pdb_00004i9d