SMTL ID : 2nya.1 (1 other biounit)

Crystal structure of the periplasmic nitrate reductase (NAP) from Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 11 residues within 4Å: Chain A: C.10, F.12, C.13, T.15, G.16, C.17, C.45, K.47, G.48, P.185, I.186 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.10, A:C.13, A:C.17, A:C.45

1 x 6MO: MOLYBDENUM(VI) ION(Non-covalent)

6MO.2: 3 residues within 4Å: Chain A: C.143 Ligands: MGD.3, MGD.4 No protein-ligand interaction detected (PLIP)

2 x MGD: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE(Non-covalent)

MGD.3: 38 residues within 4Å: Chain A: R.11, Q.114, N.139, H.142, C.143, M.336, Q.340, Q.374, C.444, T.445, N.446, N.447, A.450, S.472, D.473, P.474, Y.475, T.477, T.489, A.490, M.491, K.495, D.522, T.682, G.683, R.684, W.689, H.690, T.691, S.693, M.694, F.758, V.765, N.766, F.782, K.783 Ligands: 6MO.2, MGD.4 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:R.11, A:Q.114, A:N.139, A:Q.340, A:C.444, A:N.446, A:A.450, A:S.472, A:K.495, A:T.682, A:T.682, A:R.684, A:T.691, A:S.693, A:S.693, A:N.766, A:N.766, A:K.783 Water bridges: A:N.447, A:W.492, A:W.492, A:T.691, A:S.693 Salt bridges: A:D.473, A:D.522, A:H.690, A:H.690 pi-Stacking: A:F.758, A:F.782 MGD.4: 36 residues within 4Å: Chain A: C.13, K.47, C.143, W.176, G.177, A.178, N.179, E.182, M.183, S.207, T.208, Y.209, H.211, F.223, P.225, Q.226, D.228, T.335, M.336, G.337, F.338, G.373, Q.374, S.681, G.683, R.684, V.685, L.686, H.688, W.689, H.690, Y.755, K.783, K.784 Ligands: 6MO.2, MGD.3 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:K.47, A:W.176, A:N.179, A:E.182, A:M.183, A:S.207, A:T.208, A:Q.226, A:T.335, A:M.336, A:R.684, A:R.684, A:R.684, A:H.688, A:H.690, A:H.690 Water bridges: A:T.335, A:T.335, A:K.784, A:K.784 Salt bridges: A:D.228, A:R.684, A:K.783 pi-Stacking: A:F.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jepson, B.J. et al., Spectropotentiometric and structural analysis of the periplasmic nitrate reductase from Escherichia coli. J.Biol.Chem. (2007)

Release Date

2006-12-05

Peptides

Periplasmic nitrate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Periplasmic nitrate reductase

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