SMTL ID : 3o5a.1

Crystal Structure of partially reduced Periplasmic Nitrate Reductase from Cupriavidus necator using Ionic Liquids

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 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 32 PLIP interactions: 32 interactions with chain A Hydrogen bonds: A:R.20, A:Q.123, A:N.148, A:Q.350, A:V.454, A:N.456, A:N.456, A:A.460, A:S.482, A:A.484, A:S.499, A:W.502, 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: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 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:K.56, 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: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:T.345, A:G.347 Salt bridges: A:D.237, A:R.694, A:K.793

19 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 4 residues within 4Å: Chain A: A.157, F.397, H.399, R.400 Ligand excluded by PLIP FMT.6: 7 residues within 4Å: Chain A: L.241, N.242, A.245, F.303, M.360, N.363, L.364 Ligand excluded by PLIP FMT.7: 5 residues within 4Å: Chain A: S.15, K.16, H.520, Y.587 Ligands: FMT.17 Ligand excluded by PLIP FMT.8: 5 residues within 4Å: Chain A: R.150, H.399, I.786, S.787, L.788 Ligand excluded by PLIP FMT.9: 7 residues within 4Å: Chain A: D.167, E.168, R.392, E.393, D.404, H.616, W.632 Ligand excluded by PLIP FMT.10: 3 residues within 4Å: Chain A: R.734, G.735, V.736 Ligand excluded by PLIP FMT.11: 1 residues within 4Å: Chain A: R.734 Ligand excluded by PLIP FMT.12: 2 residues within 4Å: Chain A: A.627, R.628 Ligand excluded by PLIP FMT.13: 4 residues within 4Å: Chain A: G.229, I.230, I.231, K.325 Ligand excluded by PLIP FMT.14: 2 residues within 4Å: Chain A: R.203, H.207 Ligand excluded by PLIP FMT.15: 3 residues within 4Å: Chain A: R.733, R.734, T.753 Ligand excluded by PLIP FMT.16: 5 residues within 4Å: Chain A: A.525, G.527, E.528, A.529, R.530 Ligand excluded by PLIP FMT.17: 2 residues within 4Å: Chain A: E.626 Ligands: FMT.7 Ligand excluded by PLIP FMT.21: 4 residues within 4Å: Chain B: G.49, Y.50, Q.51, R.58 Ligand excluded by PLIP FMT.22: 4 residues within 4Å: Chain A: R.746 Chain B: A.14, N.15, E.16 Ligand excluded by PLIP FMT.23: 3 residues within 4Å: Chain A: P.709 Chain B: G.114, N.115 Ligand excluded by PLIP FMT.24: 4 residues within 4Å: Chain A: D.68, P.486 Chain B: L.3, V.4 Ligand excluded by PLIP FMT.25: 6 residues within 4Å: Chain A: L.491 Chain B: V.4, D.5, R.8, G.9, T.11 Ligand excluded by PLIP FMT.26: 3 residues within 4Å: Chain B: H.45, Y.50 Ligands: HEC.19 Ligand excluded by PLIP

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.18: 6 residues within 4Å: Chain A: S.772, L.774, K.777 Chain B: R.8, N.15, P.17 Ligand excluded by PLIP

2 x HEC: HEME C(Non-covalent)(Covalent)

HEC.19: 17 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.20, FMT.26 12 PLIP interactions: 12 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, B:I.74 Hydrogen bonds: B:I.74 Water bridges: B:T.42 Metal complexes: B:H.45, B:H.63 HEC.20: 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.19 15 PLIP interactions: 12 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, A:L.52, A:Y.58, A:Y.58 Hydrogen bonds: B:S.77, B:T.79 Water bridges: B:P.75 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

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