SMTL ID : 3ml1.1

Crystal Structure of the Periplasmic Nitrate Reductase from Cupriavidus necator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: C.19, F.21, C.22, T.24, G.25, C.26, N.53, C.54, K.56, G.57, P.194, I.195 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.19, A:C.22, A:C.26, A:C.54

1 x MOS: DIOXOTHIOMOLYBDENUM(VI) ION(Non-covalent)

MOS.2: 6 residues within 4Å: Chain A: C.152, Q.384, A.387, R.694 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: 37 residues within 4Å: Chain A: R.20, Q.123, N.148, H.151, C.152, M.346, Q.350, Q.384, V.454, N.455, N.456, N.457, A.460, S.482, D.483, A.484, Y.485, T.487, S.499, A.500, M.501, K.505, D.532, T.692, G.693, R.694, W.699, H.700, S.701, S.703, M.704, W.768, N.776, F.792, K.793 Ligands: MOS.2, MGD.4 34 PLIP interactions: 34 interactions with chain A Hydrogen bonds: A:R.20, A:Q.123, A:Q.123, A:N.148, A:Q.350, A:V.454, A:N.455, A:N.456, A:N.456, A:A.460, A:S.482, A:A.484, A:S.499, A:K.505, A:K.505, A:T.692, A:T.692, A:R.694, A:R.694, A:S.701, A:S.703, A:S.703, A:N.776, A:N.776, A:K.793 Water bridges: A:W.502, A:S.703 Salt bridges: A:D.483, A:D.532, A:H.700, A:H.700 pi-Stacking: A:W.768, A:F.792 pi-Cation interactions: A:W.768 MGD.4: 35 residues within 4Å: Chain A: C.22, K.56, C.152, W.185, G.186, S.187, N.188, E.191, M.192, S.216, T.217, F.218, H.220, F.232, P.234, Q.235, D.237, T.345, M.346, G.347, F.348, G.383, Q.384, V.691, G.693, R.694, V.695, L.696, H.698, W.699, H.700, K.793, K.794 Ligands: MOS.2, MGD.3 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:W.185, A:N.188, A:E.191, A:M.192, A:S.216, A:T.217, A:T.217, A:Q.235, A:T.345, A:M.346, A:R.694, A:R.694, A:R.694, A:H.698, A:H.700, A:H.700, A:K.794 Water bridges: A:K.56, A:K.56, A:H.193, A:G.347, A:G.347 Salt bridges: A:D.237, A:R.694, A:K.793

2 x HEC: HEME C(Covalent)

HEC.5: 16 residues within 4Å: Chain B: P.41, T.42, I.43, P.44, H.45, I.47, Y.50, R.58, C.59, C.62, H.63, A.73, I.74, C.99, H.103 Ligands: HEC.6 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:I.43, B:I.43, B:P.44, B:I.47, B:Y.50, B:Y.50, B:R.58 Hydrogen bonds: B:I.74 Metal complexes: B:H.45, B:H.63 HEC.6: 24 residues within 4Å: Chain A: L.52, N.53, Y.58 Chain B: M.38, Q.39, P.40, P.41, N.57, C.59, M.60, H.63, I.74, P.75, V.76, S.77, T.79, H.80, R.96, Y.97, F.98, C.99, C.102, H.103 Ligands: HEC.5 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:P.40, B:P.41, B:H.63, B:I.74, B:V.76, B:R.96, A:L.52, A:Y.58, A:Y.58 Hydrogen bonds: B:P.75, B:S.77, B:T.79 Salt bridges: B:H.80 pi-Cation interactions: B:R.96 Metal complexes: B:H.80, B:H.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Coelho, C. et al., The crystal structure of Cupriavidus necator nitrate reductase in oxidized and partially reduced states. J.Mol.Biol. (2011)

Release Date

2011-04-06

Peptides

Periplasmic nitrate reductase: A
Diheme cytochrome c napB: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Periplasmic nitrate reductase

Diheme cytochrome c napB

Related Entries With Identical Sequence