SMTL ID : 8s0a.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.1: 13 residues within 4Å: Chain C: 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 19 PLIP interactions: 14 interactions with chain C, 5 interactions with chain G 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:Q.531, C:N.631, C:N.631, G:R.529, G:E.622 Salt bridges: C:K.529, C:K.529, G:R.619, G:R.619, G:R.619

5 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.8: 3 residues within 4Å: Chain C: E.605 Chain F: S.388 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.388 MG.11: 2 residues within 4Å: Chain G: S.403 Ligands: ADP.10 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.403 MG.14: 2 residues within 4Å: Chain H: S.388 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:S.388

5 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 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.172, F:C.175, F:C.197 ZN.12: 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.15: 5 residues within 4Å: Chain H: C.184, C.187, C.206, S.208, C.211 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.184, H:C.187, H:C.206, H:C.211

4 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.4: 17 residues within 4Å: Chain D: S.308, H.310, D.348, P.349, S.350, V.351, A.352, K.353, S.354, Q.355, V.503 Chain F: R.371, E.463, Q.464, R.611, E.614 Ligands: MG.5 17 PLIP interactions: 12 interactions with chain D, 5 interactions with chain F Hydrogen bonds: D:H.310, D:H.310, D:D.348, 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:Q.464, F:R.611, F:E.614 Salt bridges: D:K.353, F:R.611 ADP.7: 15 residues within 4Å: Chain C: H.511, R.656, V.764, R.765, E.768 Chain F: I.343, F.344, G.384, T.385, A.386, K.387, S.388, Q.389, L.532 Ligands: MG.8 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:F.344, F:F.344, F:G.384, F:T.385, F:A.386, F:K.387, F:S.388, F:S.388, F:Q.389, F:Q.389, C:H.511 Salt bridges: F:K.387 ADP.10: 13 residues within 4Å: Chain E: R.497, E.592, R.732, E.735 Chain G: H.359, P.398, S.399, T.400, A.401, K.402, S.403, Q.404 Ligands: MG.11 12 PLIP interactions: 4 interactions with chain E, 8 interactions with chain G Hydrogen bonds: E:R.497, E:R.497, G:H.359, G:H.359, G:S.399, G:T.400, G:K.402, G:S.403, G:Q.404 Salt bridges: E:R.732, E:R.732, G:K.402 ADP.13: 15 residues within 4Å: Chain D: A.617, R.618, E.621 Chain H: E.343, I.344, Y.345, G.384, V.385, A.386, K.387, S.388, Q.389, L.533, I.537 Ligands: MG.14 13 PLIP interactions: 3 interactions with chain D, 10 interactions with chain H Hydrogen bonds: D:R.480, H:Y.345, H:Y.345, H:G.384, H:V.385, H:A.386, H:K.387, H:S.388, H:Q.389, H:Q.389 Salt bridges: D:R.618, D:R.618, H:K.387

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weissmann, F. et al., MCM double hexamer loading visualized with human proteins. Nature (2024)

Release Date

2024-10-02

Peptides

DNA replication licensing factor MCM2: C
DNA replication licensing factor MCM3: D
DNA replication licensing factor MCM4: E
DNA replication licensing factor MCM5: F
DNA replication licensing factor MCM6: G
DNA replication licensing factor MCM7: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
2

D
3

E
4

F
5

G
6

H
7

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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