SMTL ID : 8s09.1

H. sapiens MCM2-7 double hexamer bound to double stranded DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-mer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.1: 15 residues within 4Å: Chain C: S.484, I.485, Y.486, P.525, G.526, T.527, A.528, K.529, S.530, Q.531, N.631, L.675 Chain G: R.619, E.622 Ligands: MG.2 18 PLIP interactions: 3 interactions with chain G, 15 interactions with chain C Salt bridges: G:R.619, G:R.619, G:R.619, C:K.529, C:K.529 Hydrogen bonds: C:Y.486, C:Y.486, C:G.526, C:T.527, C:T.527, C:T.527, C:A.528, C:K.529, C:S.530, C:S.530, C:Q.531, C:N.631, C:N.631 ATP.15: 15 residues within 4Å: Chain I: S.484, I.485, Y.486, P.525, G.526, T.527, A.528, K.529, S.530, Q.531, N.631, L.675 Chain M: R.619, E.622 Ligands: MG.16 19 PLIP interactions: 3 interactions with chain M, 16 interactions with chain I Salt bridges: M:R.619, M:R.619, M:R.619, I:K.529, I:K.529 Hydrogen bonds: I:Y.486, I:Y.486, I:G.526, I:T.527, I:T.527, I:T.527, I:A.528, I:K.529, I:S.530, I:S.530, I:S.530, I:Q.531, I:N.631, I:N.631

8 x MG: MAGNESIUM ION

MG.2: 3 residues within 4Å: Chain C: S.530, D.587 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.530 MG.5: 3 residues within 4Å: Chain D: S.354 Chain F: E.463 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.354 MG.10: 3 residues within 4Å: Chain G: S.403, D.460 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.403 MG.13: 5 residues within 4Å: Chain D: H.425 Chain H: S.388, D.445, E.446 Ligands: ADP.12 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:S.388 MG.16: 3 residues within 4Å: Chain I: S.530, D.587 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:S.530 MG.19: 3 residues within 4Å: Chain J: S.354 Chain L: E.463 Ligands: ADP.18 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.354 MG.24: 3 residues within 4Å: Chain M: S.403, D.460 Ligands: ADP.21 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:S.403 MG.27: 5 residues within 4Å: Chain J: H.425 Chain N: S.388, D.445, E.446 Ligands: ADP.26 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:S.388

10 x ZN: ZINC ION

ZN.3: 4 residues within 4Å: Chain C: C.329, C.332, C.352, C.355 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.329, C:C.332, C:C.352, C:C.355 ZN.6: 4 residues within 4Å: Chain E: C.306, C.309, C.328, C.331 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.306, E:C.309, E:C.328, E:C.331 ZN.9: 5 residues within 4Å: Chain F: C.172, S.174, C.175, C.197, C.207 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.172, F:C.175, F:C.197, F:C.207 ZN.11: 4 residues within 4Å: Chain G: C.158, C.161, C.180, C.185 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.158, G:C.161, G:C.180, G:C.185 ZN.14: 5 residues within 4Å: Chain H: C.184, C.187, C.206, S.208, C.211 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:C.184, H:C.187, H:C.206, H:S.208, H:C.211 ZN.17: 4 residues within 4Å: Chain I: C.329, C.332, C.352, C.355 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.329, I:C.332, I:C.352, I:C.355 ZN.20: 4 residues within 4Å: Chain K: C.306, C.309, C.328, C.331 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.306, K:C.309, K:C.328, K:C.331 ZN.23: 5 residues within 4Å: Chain L: C.172, S.174, C.175, C.197, C.207 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.172, L:C.175, L:C.197, L:C.207 ZN.25: 4 residues within 4Å: Chain M: C.158, C.161, C.180, C.185 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.158, M:C.161, M:C.180, M:C.185 ZN.28: 5 residues within 4Å: Chain N: C.184, C.187, C.206, S.208, C.211 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:C.184, N:C.187, N:C.206, N:S.208, N:C.211

8 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.4: 18 residues within 4Å: Chain D: S.308, I.309, H.310, D.348, P.349, S.350, V.351, A.352, K.353, S.354, Q.355 Chain F: R.371, E.463, Q.464, R.513, R.611, E.614 Ligands: MG.5 19 PLIP interactions: 11 interactions with chain D, 8 interactions with chain F Hydrogen bonds: D:H.310, D:H.310, D:S.350, D:V.351, D:A.352, D:K.353, D:S.354, D:S.354, D:Q.355, D:Q.355, F:R.371, F:R.371, F:E.463, F:Q.464, F:R.611, F:E.614 Salt bridges: D:K.353, F:R.513, F:R.611 ADP.7: 13 residues within 4Å: Chain E: R.497, E.592, R.643, R.732, E.735 Chain G: T.357, I.358, H.359, S.399, A.401, K.402, S.403 Ligands: MG.10 12 PLIP interactions: 8 interactions with chain G, 4 interactions with chain E Hydrogen bonds: G:H.359, G:H.359, G:S.399, G:A.401, G:K.402, G:S.403, G:S.403, E:R.497, E:R.497, E:R.643 Salt bridges: G:K.402, E:R.732 ADP.8: 13 residues within 4Å: Chain C: H.511, R.765, E.768 Chain F: S.342, I.343, F.344, G.384, T.385, A.386, K.387, S.388, Q.389, H.535 16 PLIP interactions: 13 interactions with chain F, 3 interactions with chain C Hydrogen bonds: F:F.344, F:F.344, F:G.384, F:T.385, F:T.385, F:A.386, F:K.387, F:S.388, F:S.388, F:S.388, F:Q.389, F:Q.389, C:H.511 Salt bridges: F:K.387, C:R.765, C:R.765 ADP.12: 16 residues within 4Å: Chain D: H.425, A.617, R.618, E.621 Chain H: I.344, Y.345, G.384, V.385, A.386, K.387, S.388, Q.389, E.446, L.533, I.537 Ligands: MG.13 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain D Hydrogen bonds: H:Y.345, H:Y.345, H:G.384, H:A.386, H:K.387, H:S.388, H:S.388, H:Q.389, H:Q.389 Salt bridges: H:K.387, D:R.618 ADP.18: 18 residues within 4Å: Chain J: S.308, I.309, H.310, D.348, P.349, S.350, V.351, A.352, K.353, S.354, Q.355 Chain L: R.371, E.463, Q.464, R.513, R.611, E.614 Ligands: MG.19 19 PLIP interactions: 11 interactions with chain J, 8 interactions with chain L Hydrogen bonds: J:H.310, J:H.310, J:S.350, J:V.351, J:A.352, J:K.353, J:S.354, J:S.354, J:Q.355, J:Q.355, L:R.371, L:R.371, L:E.463, L:Q.464, L:R.611, L:E.614 Salt bridges: J:K.353, L:R.513, L:R.611 ADP.21: 13 residues within 4Å: Chain K: R.497, E.592, R.643, R.732, E.735 Chain M: T.357, I.358, H.359, S.399, A.401, K.402, S.403 Ligands: MG.24 12 PLIP interactions: 8 interactions with chain M, 4 interactions with chain K Hydrogen bonds: M:H.359, M:H.359, M:S.399, M:A.401, M:K.402, M:S.403, M:S.403, K:R.497, K:R.497, K:R.643 Salt bridges: M:K.402, K:R.732 ADP.22: 13 residues within 4Å: Chain I: H.511, R.765, E.768 Chain L: S.342, I.343, F.344, G.384, T.385, A.386, K.387, S.388, Q.389, H.535 16 PLIP interactions: 13 interactions with chain L, 3 interactions with chain I Hydrogen bonds: L:F.344, L:F.344, L:G.384, L:T.385, L:T.385, L:A.386, L:K.387, L:S.388, L:S.388, L:S.388, L:Q.389, L:Q.389, I:H.511 Salt bridges: L:K.387, I:R.765, I:R.765 ADP.26: 16 residues within 4Å: Chain J: H.425, A.617, R.618, E.621 Chain N: I.344, Y.345, G.384, V.385, A.386, K.387, S.388, Q.389, E.446, L.533, I.537 Ligands: MG.27 11 PLIP interactions: 10 interactions with chain N, 1 interactions with chain J Hydrogen bonds: N:Y.345, N:Y.345, N:G.384, N:A.386, N:K.387, N:S.388, N:S.388, N:Q.389, N:Q.389 Salt bridges: N:K.387, J:R.618

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weissmann, F. et al., MCM Double Hexamer Loading Visualised with Human Proteins. Nature (2024)

Release Date

2024-10-02

Peptides

DNA replication licensing factor MCM2: CI
DNA replication licensing factor MCM3: DJ
DNA replication licensing factor MCM4: EK
DNA replication licensing factor MCM5: FL
DNA replication licensing factor MCM6: GM
DNA replication licensing factor MCM7: HN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
2

I
A

D
3

J
B

E
4

K
C

F
5

L
D

G
6

M
E

H
7

N
F

DNA replication licensing factor MCM2

DNA replication licensing factor MCM3

DNA replication licensing factor MCM4

DNA replication licensing factor MCM5

DNA replication licensing factor MCM6

DNA replication licensing factor MCM7

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