SMTL ID : 7utd.1

The 2.19-angstrom CryoEM structure of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis - Complex minus stalk

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-8-4-mer

Ligands

8 x 3NI: NICKEL (III) ION(Non-covalent)

3NI.1: 6 residues within 4Å: Chain A: C.59, I.61, C.62, C.507, C.510 Ligands: FCO.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.59, A:C.62, A:C.507, A:C.510 3NI.8: 6 residues within 4Å: Chain C: C.59, I.61, C.62, C.507, C.510 Ligands: FCO.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.59, C:C.62, C:C.507, C:C.510 3NI.15: 6 residues within 4Å: Chain E: C.59, I.61, C.62, C.507, C.510 Ligands: FCO.16 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.59, E:C.62, E:C.507, E:C.510 3NI.22: 6 residues within 4Å: Chain G: C.59, I.61, C.62, C.507, C.510 Ligands: FCO.23 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.59, G:C.62, G:C.507, G:C.510 3NI.29: 6 residues within 4Å: Chain I: C.59, I.61, C.62, C.507, C.510 Ligands: FCO.30 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.59, I:C.62, I:C.507, I:C.510 3NI.36: 6 residues within 4Å: Chain K: C.59, I.61, C.62, C.507, C.510 Ligands: FCO.37 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.59, K:C.62, K:C.507, K:C.510 3NI.43: 6 residues within 4Å: Chain M: C.59, I.61, C.62, C.507, C.510 Ligands: FCO.44 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.59, M:C.62, M:C.507, M:C.510 3NI.50: 6 residues within 4Å: Chain O: C.59, I.61, C.62, C.507, C.510 Ligands: FCO.51 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.59, O:C.62, O:C.507, O:C.510

8 x FCO: CARBONMONOXIDE-(DICYANO) IRON(Non-covalent)

FCO.2: 11 residues within 4Å: Chain A: C.62, H.66, A.438, A.439, R.440, L.443, P.462, T.463, C.507, C.510 Ligands: 3NI.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.440, A:R.440, A:T.463, A:T.463 Metal complexes: A:C.62, A:C.510 FCO.9: 11 residues within 4Å: Chain C: C.62, H.66, A.438, A.439, R.440, L.443, P.462, T.463, C.507, C.510 Ligands: 3NI.8 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.440, C:R.440, C:T.463, C:T.463 Metal complexes: C:C.62, C:C.510 FCO.16: 11 residues within 4Å: Chain E: C.62, H.66, A.438, A.439, R.440, L.443, P.462, T.463, C.507, C.510 Ligands: 3NI.15 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:R.440, E:R.440, E:T.463, E:T.463 Metal complexes: E:C.62, E:C.510 FCO.23: 11 residues within 4Å: Chain G: C.62, H.66, A.438, A.439, R.440, L.443, P.462, T.463, C.507, C.510 Ligands: 3NI.22 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:R.440, G:R.440, G:T.463, G:T.463 Metal complexes: G:C.62, G:C.510 FCO.30: 11 residues within 4Å: Chain I: C.62, H.66, A.438, A.439, R.440, L.443, P.462, T.463, C.507, C.510 Ligands: 3NI.29 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:R.440, I:R.440, I:T.463, I:T.463 Metal complexes: I:C.62, I:C.510 FCO.37: 11 residues within 4Å: Chain K: C.62, H.66, A.438, A.439, R.440, L.443, P.462, T.463, C.507, C.510 Ligands: 3NI.36 6 PLIP interactions: 6 interactions with chain K Hydrogen bonds: K:R.440, K:R.440, K:T.463, K:T.463 Metal complexes: K:C.62, K:C.510 FCO.44: 11 residues within 4Å: Chain M: C.62, H.66, A.438, A.439, R.440, L.443, P.462, T.463, C.507, C.510 Ligands: 3NI.43 6 PLIP interactions: 6 interactions with chain M Hydrogen bonds: M:R.440, M:R.440, M:T.463, M:T.463 Metal complexes: M:C.62, M:C.510 FCO.51: 11 residues within 4Å: Chain O: C.62, H.66, A.438, A.439, R.440, L.443, P.462, T.463, C.507, C.510 Ligands: 3NI.50 6 PLIP interactions: 6 interactions with chain O Hydrogen bonds: O:R.440, O:R.440, O:T.463, O:T.463 Metal complexes: O:C.62, O:C.510

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: E.40, E.300, V.459, H.513 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.40, A:V.459, A:H.513 MG.10: 4 residues within 4Å: Chain C: E.40, E.300, V.459, H.513 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.40, C:V.459, C:H.513 MG.17: 4 residues within 4Å: Chain E: E.40, E.300, V.459, H.513 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.40, E:V.459, E:H.513 MG.24: 4 residues within 4Å: Chain G: E.40, E.300, V.459, H.513 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.40, G:V.459, G:H.513 MG.31: 4 residues within 4Å: Chain I: E.40, E.300, V.459, H.513 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.40, I:V.459, I:H.513 MG.38: 4 residues within 4Å: Chain K: E.40, E.300, V.459, H.513 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.40, K:V.459, K:H.513 MG.45: 4 residues within 4Å: Chain M: E.40, E.300, V.459, H.513 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:E.40, M:V.459, M:H.513 MG.52: 4 residues within 4Å: Chain O: E.40, E.300, V.459, H.513 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:E.40, O:V.459, O:H.513

8 x MQ9: MENAQUINONE-9(Non-covalent)

MQ9.4: 15 residues within 4Å: Chain B: K.258, Q.259, S.260, C.272, F.274, Y.275, M.333, P.335, Y.347, M.348, G.349, A.352, R.355 Chain Q: G.43, D.44 9 PLIP interactions: 1 interactions with chain Q, 8 interactions with chain B Hydrophobic interactions: Q:D.44, B:K.258, B:K.258, B:F.274, B:F.274, B:Y.275, B:Y.275, B:R.355 pi-Stacking: B:Y.275 MQ9.11: 15 residues within 4Å: Chain D: F.255, K.258, Q.259, S.260, C.272, F.274, Y.275, M.333, P.335, Y.347, M.348, A.352, R.355 Chain R: A.53, L.57 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain R Hydrophobic interactions: D:F.255, D:K.258, D:K.258, D:F.274, D:F.274, D:Y.275, D:Y.275, D:Y.275, D:M.348, D:A.352, D:R.355, R:L.57, R:L.57 Hydrogen bonds: D:Y.347 pi-Stacking: D:Y.275 MQ9.18: 15 residues within 4Å: Chain F: K.258, Q.259, S.260, C.272, F.274, Y.275, M.333, P.335, Y.347, M.348, G.349, A.352, R.355 Chain R: G.43, D.44 9 PLIP interactions: 1 interactions with chain R, 8 interactions with chain F Hydrophobic interactions: R:D.44, F:K.258, F:K.258, F:F.274, F:F.274, F:Y.275, F:Y.275, F:R.355 pi-Stacking: F:Y.275 MQ9.25: 15 residues within 4Å: Chain H: F.255, K.258, Q.259, S.260, C.272, F.274, Y.275, M.333, P.335, Y.347, M.348, A.352, R.355 Chain S: A.53, L.57 15 PLIP interactions: 13 interactions with chain H, 2 interactions with chain S Hydrophobic interactions: H:F.255, H:K.258, H:K.258, H:F.274, H:F.274, H:Y.275, H:Y.275, H:Y.275, H:M.348, H:A.352, H:R.355, S:L.57, S:L.57 Hydrogen bonds: H:Y.347 pi-Stacking: H:Y.275 MQ9.32: 15 residues within 4Å: Chain J: K.258, Q.259, S.260, C.272, F.274, Y.275, M.333, P.335, Y.347, M.348, G.349, A.352, R.355 Chain T: G.43, D.44 9 PLIP interactions: 1 interactions with chain T, 8 interactions with chain J Hydrophobic interactions: T:D.44, J:K.258, J:K.258, J:F.274, J:F.274, J:Y.275, J:Y.275, J:R.355 pi-Stacking: J:Y.275 MQ9.39: 15 residues within 4Å: Chain L: K.258, Q.259, S.260, C.272, F.274, Y.275, M.333, P.335, Y.347, M.348, G.349, A.352, R.355 Chain S: G.43, D.44 9 PLIP interactions: 1 interactions with chain S, 8 interactions with chain L Hydrophobic interactions: S:D.44, L:K.258, L:K.258, L:F.274, L:F.274, L:Y.275, L:Y.275, L:R.355 pi-Stacking: L:Y.275 MQ9.46: 15 residues within 4Å: Chain N: F.255, K.258, Q.259, S.260, C.272, F.274, Y.275, M.333, P.335, Y.347, M.348, A.352, R.355 Chain T: A.53, L.57 15 PLIP interactions: 13 interactions with chain N, 2 interactions with chain T Hydrophobic interactions: N:F.255, N:K.258, N:K.258, N:F.274, N:F.274, N:Y.275, N:Y.275, N:Y.275, N:M.348, N:A.352, N:R.355, T:L.57, T:L.57 Hydrogen bonds: N:Y.347 pi-Stacking: N:Y.275 MQ9.53: 15 residues within 4Å: Chain P: F.255, K.258, Q.259, S.260, C.272, F.274, Y.275, M.333, P.335, Y.347, M.348, A.352, R.355 Chain Q: A.53, L.57 15 PLIP interactions: 13 interactions with chain P, 2 interactions with chain Q Hydrophobic interactions: P:F.255, P:K.258, P:K.258, P:F.274, P:F.274, P:Y.275, P:Y.275, P:Y.275, P:M.348, P:A.352, P:R.355, Q:L.57, Q:L.57 Hydrogen bonds: P:Y.347 pi-Stacking: P:Y.275

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

F3S.5: 13 residues within 4Å: Chain A: R.57, H.163 Chain B: A.57, C.58, G.60, N.61, E.118, G.157, D.158, C.159, G.206, C.207, P.208 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.58, B:C.159, B:C.207 F3S.6: 12 residues within 4Å: Chain A: Q.160 Chain B: T.245, T.284, S.286, C.288, W.293, K.299, C.306, L.307, G.308, C.309, T.310 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.288, B:C.306, B:C.309 F3S.7: 12 residues within 4Å: Chain B: Q.246, C.249, R.251, V.252, F.255, C.272, L.273, F.274, C.279, G.281, P.282, T.300 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.249, B:C.272, B:C.279 F3S.12: 13 residues within 4Å: Chain C: R.57, H.163 Chain D: A.57, C.58, G.60, N.61, E.118, G.157, D.158, C.159, G.206, C.207, P.208 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.58, D:C.159, D:C.207 F3S.13: 12 residues within 4Å: Chain C: Q.160 Chain D: T.245, T.284, S.286, C.288, W.293, K.299, C.306, L.307, G.308, C.309, T.310 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.288, D:C.306, D:C.309 F3S.14: 12 residues within 4Å: Chain D: Q.246, C.249, R.251, V.252, F.255, C.272, L.273, F.274, C.279, G.281, P.282, T.300 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.249, D:C.272, D:C.279 F3S.19: 13 residues within 4Å: Chain E: R.57, H.163 Chain F: A.57, C.58, G.60, N.61, E.118, G.157, D.158, C.159, G.206, C.207, P.208 3 PLIP interactions: 3 interactions with chain F, Metal complexes: F:C.58, F:C.159, F:C.207 F3S.20: 12 residues within 4Å: Chain E: Q.160 Chain F: T.245, T.284, S.286, C.288, W.293, K.299, C.306, L.307, G.308, C.309, T.310 3 PLIP interactions: 3 interactions with chain F, Metal complexes: F:C.288, F:C.306, F:C.309 F3S.21: 12 residues within 4Å: Chain F: Q.246, C.249, R.251, V.252, F.255, C.272, L.273, F.274, C.279, G.281, P.282, T.300 3 PLIP interactions: 3 interactions with chain F, Metal complexes: F:C.249, F:C.272, F:C.279 F3S.26: 13 residues within 4Å: Chain G: R.57, H.163 Chain H: A.57, C.58, G.60, N.61, E.118, G.157, D.158, C.159, G.206, C.207, P.208 3 PLIP interactions: 3 interactions with chain H, Metal complexes: H:C.58, H:C.159, H:C.207 F3S.27: 12 residues within 4Å: Chain G: Q.160 Chain H: T.245, T.284, S.286, C.288, W.293, K.299, C.306, L.307, G.308, C.309, T.310 3 PLIP interactions: 3 interactions with chain H, Metal complexes: H:C.288, H:C.306, H:C.309 F3S.28: 12 residues within 4Å: Chain H: Q.246, C.249, R.251, V.252, F.255, C.272, L.273, F.274, C.279, G.281, P.282, T.300 3 PLIP interactions: 3 interactions with chain H, Metal complexes: H:C.249, H:C.272, H:C.279 F3S.33: 13 residues within 4Å: Chain I: R.57, H.163 Chain J: A.57, C.58, G.60, N.61, E.118, G.157, D.158, C.159, G.206, C.207, P.208 3 PLIP interactions: 3 interactions with chain J, Metal complexes: J:C.58, J:C.159, J:C.207 F3S.34: 12 residues within 4Å: Chain I: Q.160 Chain J: T.245, T.284, S.286, C.288, W.293, K.299, C.306, L.307, G.308, C.309, T.310 3 PLIP interactions: 3 interactions with chain J, Metal complexes: J:C.288, J:C.306, J:C.309 F3S.35: 12 residues within 4Å: Chain J: Q.246, C.249, R.251, V.252, F.255, C.272, L.273, F.274, C.279, G.281, P.282, T.300 3 PLIP interactions: 3 interactions with chain J, Metal complexes: J:C.249, J:C.272, J:C.279 F3S.40: 13 residues within 4Å: Chain K: R.57, H.163 Chain L: A.57, C.58, G.60, N.61, E.118, G.157, D.158, C.159, G.206, C.207, P.208 3 PLIP interactions: 3 interactions with chain L, Metal complexes: L:C.58, L:C.159, L:C.207 F3S.41: 12 residues within 4Å: Chain K: Q.160 Chain L: T.245, T.284, S.286, C.288, W.293, K.299, C.306, L.307, G.308, C.309, T.310 3 PLIP interactions: 3 interactions with chain L, Metal complexes: L:C.288, L:C.306, L:C.309 F3S.42: 12 residues within 4Å: Chain L: Q.246, C.249, R.251, V.252, F.255, C.272, L.273, F.274, C.279, G.281, P.282, T.300 3 PLIP interactions: 3 interactions with chain L, Metal complexes: L:C.249, L:C.272, L:C.279 F3S.47: 13 residues within 4Å: Chain M: R.57, H.163 Chain N: A.57, C.58, G.60, N.61, E.118, G.157, D.158, C.159, G.206, C.207, P.208 3 PLIP interactions: 3 interactions with chain N, Metal complexes: N:C.58, N:C.159, N:C.207 F3S.48: 12 residues within 4Å: Chain M: Q.160 Chain N: T.245, T.284, S.286, C.288, W.293, K.299, C.306, L.307, G.308, C.309, T.310 3 PLIP interactions: 3 interactions with chain N, Metal complexes: N:C.288, N:C.306, N:C.309 F3S.49: 12 residues within 4Å: Chain N: Q.246, C.249, R.251, V.252, F.255, C.272, L.273, F.274, C.279, G.281, P.282, T.300 3 PLIP interactions: 3 interactions with chain N, Metal complexes: N:C.249, N:C.272, N:C.279 F3S.54: 13 residues within 4Å: Chain O: R.57, H.163 Chain P: A.57, C.58, G.60, N.61, E.118, G.157, D.158, C.159, G.206, C.207, P.208 3 PLIP interactions: 3 interactions with chain P, Metal complexes: P:C.58, P:C.159, P:C.207 F3S.55: 12 residues within 4Å: Chain O: Q.160 Chain P: T.245, T.284, S.286, C.288, W.293, K.299, C.306, L.307, G.308, C.309, T.310 3 PLIP interactions: 3 interactions with chain P, Metal complexes: P:C.288, P:C.306, P:C.309 F3S.56: 12 residues within 4Å: Chain P: Q.246, C.249, R.251, V.252, F.255, C.272, L.273, F.274, C.279, G.281, P.282, T.300 3 PLIP interactions: 3 interactions with chain P, Metal complexes: P:C.249, P:C.272, P:C.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grinter, R. et al., Structural basis for bacterial energy extraction from atmospheric hydrogen. Nature (2023)

Release Date

2023-01-04

Peptides

Hydrogenase-2, large subunit: ACEGIKMO
Hydrogenase-2, small subunit: BDFHJLNP
Type 2 [NiFe]-hydrogenase Huc membrane adapter subunit: QRST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

M
M

O
O

B
B

D
D

F
F

H
H

J
J

L
L

N
N

P
P

Q
Q

R
R

S
S

T
T

Hydrogenase-2, large subunit

Hydrogenase-2, small subunit

Type 2 [NiFe]-hydrogenase Huc membrane adapter subunit

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