SMTL ID : 9cq5.1

Mn-bound RuBisCO from spinach with CABP inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-8-8-mer

Ligands

8 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: T.173, K.201, D.203, E.204, H.294 Ligands: CAP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.203, A:E.204 MN.3: 8 residues within 4Å: Chain A: N.123 Chain B: K.175, K.177, K.201, D.203, E.204, H.294 Ligands: CAP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.203, B:E.204 MN.5: 8 residues within 4Å: Chain C: K.175, K.177, K.201, D.203, E.204, H.294 Chain D: N.123 Ligands: CAP.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.203, C:E.204 MN.7: 7 residues within 4Å: Chain C: N.123 Chain D: T.173, K.201, D.203, E.204, H.294 Ligands: CAP.8 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.203, D:E.204 MN.9: 7 residues within 4Å: Chain E: K.177, K.201, D.203, E.204, H.294 Chain F: N.123 Ligands: CAP.10 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.203, E:E.204 MN.11: 7 residues within 4Å: Chain E: N.123 Chain F: K.177, K.201, D.203, E.204, H.294 Ligands: CAP.12 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.203, F:E.204 MN.13: 8 residues within 4Å: Chain G: K.175, K.177, K.201, D.203, E.204, H.294 Chain H: N.123 Ligands: CAP.14 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.203, G:E.204 MN.15: 7 residues within 4Å: Chain G: N.123 Chain H: K.177, K.201, D.203, E.204, H.294 Ligands: CAP.16 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.203, H:E.204

8 x CAP: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE(Non-covalent)

CAP.2: 22 residues within 4Å: Chain A: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, G.329, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Chain B: E.60, T.65, W.66, N.123 Ligands: MN.1 26 PLIP interactions: 22 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.173, A:K.175, A:G.329, A:S.379, A:S.379, A:G.380, A:G.381, A:G.403, A:G.404, B:T.65, B:T.65, B:N.123 Water bridges: A:R.295, A:R.295, A:R.295, A:H.298, A:H.298, A:G.405, B:N.123 Salt bridges: A:K.175, A:K.175, A:K.177, A:R.295, A:H.327, A:K.334, A:K.334 CAP.4: 22 residues within 4Å: Chain A: E.60, T.65, W.66, N.123 Chain B: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.298, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Ligands: MN.3 22 PLIP interactions: 19 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.175, B:S.379, B:S.379, B:S.379, B:G.380, B:G.381, B:G.403, B:G.404, A:T.65, A:T.65, A:N.123 Water bridges: B:I.382, B:G.405 Salt bridges: B:K.175, B:K.175, B:K.177, B:H.294, B:R.295, B:H.298, B:H.327, B:K.334, B:K.334 CAP.6: 23 residues within 4Å: Chain C: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.298, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Chain D: E.60, T.65, W.66, N.123 Ligands: MN.5 22 PLIP interactions: 19 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:T.173, C:K.175, C:S.379, C:S.379, C:G.380, C:G.381, C:G.403, C:G.404, D:T.65, D:T.65, D:N.123 Water bridges: C:R.295, C:G.329, C:G.405 Salt bridges: C:K.175, C:K.175, C:K.177, C:R.295, C:H.298, C:H.327, C:K.334, C:K.334 CAP.8: 21 residues within 4Å: Chain C: E.60, T.65, W.66, N.123 Chain D: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Ligands: MN.7 20 PLIP interactions: 17 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:K.175, D:G.329, D:S.379, D:G.381, D:G.403, D:G.404, C:T.65, C:T.65, C:N.123 Water bridges: D:R.295, D:R.295, D:H.298, D:G.380 Salt bridges: D:K.175, D:K.175, D:K.177, D:R.295, D:H.327, D:K.334, D:K.334 CAP.10: 22 residues within 4Å: Chain E: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.298, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Chain F: E.60, T.65, W.66, N.123 Ligands: MN.9 22 PLIP interactions: 19 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:T.173, E:T.173, E:K.175, E:H.298, E:S.379, E:G.380, E:G.381, E:G.403, E:G.404, F:T.65, F:T.65, F:N.123 Water bridges: E:R.295, E:R.295, E:G.329 Salt bridges: E:K.175, E:K.175, E:K.177, E:R.295, E:H.327, E:K.334, E:K.334 CAP.12: 22 residues within 4Å: Chain E: E.60, T.65, W.66, N.123 Chain F: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.298, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Ligands: MN.11 20 PLIP interactions: 17 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:K.175, F:H.298, F:S.379, F:S.379, F:G.380, F:G.381, F:G.403, F:G.404, E:T.65, E:T.65, E:N.123 Water bridges: F:S.379, F:S.379 Salt bridges: F:K.175, F:K.175, F:K.177, F:R.295, F:H.327, F:K.334, F:K.334 CAP.14: 23 residues within 4Å: Chain G: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.298, H.327, K.334, L.335, S.379, G.380, G.381, Q.401, G.403, G.404 Chain H: E.60, T.65, W.66, N.123 Ligands: MN.13 25 PLIP interactions: 22 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:T.173, G:K.175, G:H.298, G:S.379, G:S.379, G:G.380, G:G.381, G:G.403, G:G.404, H:T.65, H:T.65, H:N.123 Water bridges: G:T.173, G:T.173, G:G.329, G:G.329, G:G.405, G:G.405 Salt bridges: G:K.175, G:K.175, G:K.177, G:R.295, G:H.327, G:K.334, G:K.334 CAP.16: 22 residues within 4Å: Chain G: E.60, T.65, W.66, N.123 Chain H: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Ligands: MN.15 20 PLIP interactions: 17 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:T.173, H:K.175, H:S.379, H:G.380, H:G.381, H:G.403, H:G.404, G:T.65, G:T.65, G:N.123 Water bridges: H:R.295, H:H.298 Salt bridges: H:K.175, H:K.175, H:K.177, H:H.294, H:R.295, H:H.327, H:K.334, H:K.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Voland, R.W. et al., The structure of Mn(II)-bound Rubisco from Spinacia oleracea. J.Inorg.Biochem. (2024)

Release Date

2025-02-05

Peptides

Ribulose bisphosphate carboxylase large chain: ABCDEFGH
Ribulose bisphosphate carboxylase small subunit, chloroplastic 2: IJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Ribulose bisphosphate carboxylase large chain

Ribulose bisphosphate carboxylase small subunit, chloroplastic 2

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