SMTL ID : 5t2k.1

Geobacillus stearothermophilus HemQ with Manganese-Coproporphyrin III

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-pentamer

Ligands

5 x 76R: [3,3',3'',3'''-(3,8,13,17-tetramethylporphyrin-2,7,12,18-tetrayl-kappa~4~N~21~,N~22~,N~23~,N~24~)tetra(propanoato)(2-)]manganese(Non-covalent)

76R.1: 27 residues within 4Å: Chain A: L.110, S.111, Y.113, L.114, R.130, Y.144, M.146, K.148, W.156, M.168, H.171, G.172, G.175, R.176, Y.178, Q.184, I.186, W.197, V.199, L.201, L.212, V.213, M.216, R.217, S.222, F.228 Chain E: Y.214 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain E, Hydrophobic interactions: A:Q.184, A:I.186, A:W.197, A:V.199, A:V.199, A:L.201, A:L.212 Hydrogen bonds: A:Y.144, A:W.156, A:S.222, A:S.222 Water bridges: A:Y.113, A:G.172, A:Q.184, A:Q.184, A:R.217, E:Y.214 Salt bridges: A:R.130, A:K.148 pi-Cation interactions: A:H.171 Metal complexes: A:H.171 76R.2: 27 residues within 4Å: Chain A: Y.214 Chain B: E.109, S.111, Y.113, R.130, Y.144, M.146, K.148, W.156, M.168, R.169, H.171, G.172, G.175, R.176, Y.178, Q.184, I.186, W.197, V.199, L.201, L.212, V.213, M.216, R.217, S.222, F.228 27 PLIP interactions: 26 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:Q.184, B:I.186, B:I.186, B:W.197, B:W.197, B:V.199, B:L.201, B:L.212 Hydrogen bonds: B:Y.144, B:Y.144, B:W.156, B:Q.184, B:S.222 Water bridges: B:Y.113, B:Y.113, B:R.130, B:R.130, B:H.171, B:M.173, B:M.173, B:R.217, A:Y.214 Salt bridges: B:R.130, B:K.148, B:R.176 pi-Cation interactions: B:H.171 Metal complexes: B:H.171 76R.3: 25 residues within 4Å: Chain C: E.109, S.111, R.130, Y.144, M.146, K.148, W.156, M.168, R.169, H.171, G.172, G.175, R.176, Y.178, Q.184, I.186, W.197, V.199, L.201, L.212, V.213, M.216, R.217, S.222, F.228 29 PLIP interactions: 28 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:Q.184, C:I.186, C:W.197, C:W.197, C:V.199, C:V.199, C:L.201, C:L.212 Hydrogen bonds: C:S.111, C:Y.144, C:W.156, C:Q.184, C:S.222, C:S.222 Water bridges: C:E.109, C:R.130, C:R.130, C:R.130, C:H.171, C:R.176, C:R.176, C:W.197, C:R.217, B:Y.214 Salt bridges: C:R.130, C:K.148, C:R.176 pi-Cation interactions: C:H.171 Metal complexes: C:H.171 76R.4: 26 residues within 4Å: Chain C: Y.214 Chain D: S.111, Y.113, R.130, Y.144, M.146, K.148, W.156, M.168, R.169, H.171, G.172, G.175, R.176, Y.178, Q.184, I.186, W.197, V.199, L.201, L.212, V.213, M.216, R.217, S.222, F.228 25 PLIP interactions: 24 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: D:Q.184, D:I.186, D:I.186, D:W.197, D:V.199, D:L.212 Hydrogen bonds: D:Y.144, D:W.156, D:Q.184, D:S.222, D:S.222 Water bridges: D:S.111, D:Y.113, D:Y.113, D:H.171, D:M.173, D:R.176, D:Q.184, D:R.217, C:Y.214 Salt bridges: D:R.130, D:K.148, D:R.176 pi-Cation interactions: D:H.171 Metal complexes: D:H.171 76R.5: 27 residues within 4Å: Chain D: Y.214 Chain E: S.111, Y.113, L.114, R.130, Y.144, M.146, K.148, W.156, M.168, H.171, G.172, G.175, R.176, Y.178, V.182, Q.184, I.186, W.197, V.199, L.201, L.212, V.213, M.216, R.217, S.222, F.228 22 PLIP interactions: 22 interactions with chain E, Hydrophobic interactions: E:L.114, E:Q.184, E:I.186, E:W.197, E:V.199, E:V.199, E:L.212 Hydrogen bonds: E:Y.144, E:W.156, E:S.222, E:S.222 Water bridges: E:Y.113, E:Y.113, E:H.171, E:G.172, E:Q.184, E:W.197, E:R.217 Salt bridges: E:R.130, E:K.148 pi-Cation interactions: E:H.171 Metal complexes: E:H.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Celis, A.I. et al., Structure-Based Mechanism for Oxidative Decarboxylation Reactions Mediated by Amino Acids and Heme Propionates in Coproheme Decarboxylase (HemQ). J. Am. Chem. Soc. (2017)

Release Date

2017-01-18

Peptides

Putative heme-dependent peroxidase GT50_08830: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Putative heme-dependent peroxidase GT50_08830

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