SMTL ID : 7b04.7 (7 other biounits)

Structure of Nitrite oxidoreductase (Nxr) from the anammox bacterium Kuenenia stuttgartiensis.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.97 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: C.45, W.49, W.60, N.61, I.174, C.235, I.236, A.237, C.238, T.256, C.258 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.45, A:C.235, A:C.238, A:C.258 SF4.2: 12 residues within 4Å: Chain A: C.175, N.176, H.177, C.178, P.181, G.182, C.183, C.218, Y.220, K.222, P.223, K.234 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.175, A:C.178, A:C.183, A:C.218 SF4.3: 14 residues within 4Å: Chain A: C.35, I.36, A.37, C.38, Q.39, T.40, C.41, V.63, Q.172, C.262, V.263, G.264, I.266, R.267 5 PLIP interactions: 5 interactions with chain A, pi-Cation interactions: A:F.30 Metal complexes: A:C.35, A:C.38, A:C.41, A:C.262 SF4.8: 12 residues within 4Å: Chain B: C.67, P.69, D.71, H.73, A.74, C.75, I.77, M.114, C.115, K.117, G.118, W.926 8 PLIP interactions: 8 interactions with chain B, Salt bridges: B:D.71, B:D.71, B:D.71 Metal complexes: B:C.67, B:D.71, B:D.71, B:C.75, B:C.115

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.4: 11 residues within 4Å: Chain A: C.187, I.192, I.203, C.208, R.209, G.210, Y.211, R.212, K.213, C.214, S.232 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.187, A:C.208, A:C.214

2 x MD1: PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER(Non-covalent)

MD1.5: 33 residues within 4Å: Chain B: N.70, R.124, K.236, H.273, D.275, H.531, T.652, N.653, V.654, N.655, N.659, K.661, T.680, D.681, I.682, T.685, A.697, N.698, W.700, F.703, D.734, T.915, K.917, V.922, H.923, S.924, Q.925, H.1020, Q.1057, T.1060, P.1098 Ligands: MD1.6, MO.7 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:R.124, B:K.236, B:K.236, B:H.531, B:N.653, B:N.653, B:N.655, B:N.659, B:N.659, B:K.661, B:T.680, B:T.915, B:K.917, B:S.924, B:S.924, B:Q.925, B:Q.925, B:Q.1057, B:Q.1057 Water bridges: B:N.70, B:N.70 Salt bridges: B:H.273, B:D.734, B:H.923, B:H.923 pi-Stacking: B:H.1020 MD1.6: 40 residues within 4Å: Chain B: N.70, D.71, K.117, D.275, T.305, G.306, K.307, N.308, E.311, N.312, K.313, M.314, I.333, T.334, P.335, E.336, S.338, I.350, N.352, N.353, D.355, G.526, E.527, G.528, V.529, Y.532, W.562, A.563, G.564, V.914, P.916, K.917, S.918, R.919, T.921, V.922, H.923, K.1099 Ligands: MD1.5, MO.7 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:K.117, B:G.306, B:K.307, B:N.308, B:N.312, B:N.312, B:I.333, B:N.352, B:N.353, B:E.527, B:G.528, B:Y.532, B:K.917, B:R.919, B:H.923, B:H.923 Salt bridges: B:K.307, B:D.355, B:K.1099

1 x MO: MOLYBDENUM ATOM(Non-covalent)

MO.7: 4 residues within 4Å: Chain B: D.275, G.564 Ligands: MD1.5, MD1.6 Ligand excluded by PLIP

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.9: 28 residues within 4Å: Chain A: P.188, R.189, R.209, Y.211 Chain C: Q.84, K.86, A.87, A.135, L.136, M.137, R.154, M.155, L.164, H.166, F.241, G.242, T.243, L.244, N.290, M.291, A.292, W.294, R.301, N.302, G.303, K.305, I.307, S.308 23 PLIP interactions: 16 interactions with chain C, 7 interactions with chain A, Hydrophobic interactions: C:Q.84, C:K.86, C:A.87, C:M.137, C:R.154, C:H.166, C:F.241, C:L.244, C:A.292, C:W.294, C:N.302, C:K.305, C:I.307, A:P.188, A:R.189, A:Y.211 Hydrogen bonds: C:G.242, C:L.244, A:Y.211, A:Y.211 Salt bridges: C:H.166, A:R.189, A:R.209

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 5 residues within 4Å: Chain C: D.117, T.119, N.121, D.132, N.295 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.117, C:D.117, C:T.119, C:D.132, C:D.132 CA.11: 6 residues within 4Å: Chain C: D.235, Q.247, H.249, D.251, D.275, D.278 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.235, C:H.249, C:D.251, C:D.278, C:D.278

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chicano, T.M. et al., Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex. Nat Microbiol (2021)

Release Date

2021-07-14

Peptides

Nitrite oxidoreductase subunit B: A
Nitrite oxidoreductase subunit A: B
Nitrite oxidoreductase subunit C: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
T

C
U

Nitrite oxidoreductase subunit B

Nitrite oxidoreductase subunit A

Nitrite oxidoreductase subunit C

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