SMTL ID : 7vuk.1

Crystal Structure of the core region of Thermus thermophilus MutS2 complexed with ADP.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.38 Å

Oligo State

homo-dimer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.322, D.394, E.395 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.322 MG.2: 2 residues within 4Å: Chain A: E.418 Chain B: K.485 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain A: W.350 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain B: T.322, D.394, E.395 Ligands: ADP.28 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.322 MG.19: 2 residues within 4Å: Chain B: Q.443, G.463 No protein-ligand interaction detected (PLIP)

8 x NA: SODIUM ION(Non-functional Binders)

NA.4: 2 residues within 4Å: Chain A: A.51, A.267 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.51 NA.5: 1 residues within 4Å: Chain A: D.272 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.272 NA.6: 1 residues within 4Å: Chain A: Q.410 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.410 NA.7: 1 residues within 4Å: Chain A: H.428 No protein-ligand interaction detected (PLIP) NA.8: 3 residues within 4Å: Chain A: E.9, H.291, K.326 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.9, A:K.326 NA.20: 2 residues within 4Å: Chain B: Q.336, V.354 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.336, B:V.354 NA.21: 3 residues within 4Å: Chain B: G.315, K.433, G.466 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.433, B:K.433 NA.22: 3 residues within 4Å: Chain B: E.9, I.294, K.326 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.9 Water bridges: B:K.326

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 3 residues within 4Å: Chain A: R.475, E.481, K.485 Ligand excluded by PLIP CL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain B: R.122, D.239, L.240 Ligand excluded by PLIP

10 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 7 residues within 4Å: Chain A: M.1, R.2, L.5, P.35, Q.336, R.353, V.354 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.336, A:Q.336 PEG.12: 4 residues within 4Å: Chain A: A.303, N.308, Q.443, L.462 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.303 PEG.13: 4 residues within 4Å: Chain A: E.9, R.12, L.16, L.293 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.9 PEG.14: 4 residues within 4Å: Chain A: E.42, P.278, A.279, F.280 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.42, A:F.280 PEG.15: 6 residues within 4Å: Chain A: E.403 Chain B: S.430, K.433, Q.437, G.466, R.467 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.433, B:Q.437, B:G.466, B:R.467 PEG.16: 1 residues within 4Å: Chain A: N.219 No protein-ligand interaction detected (PLIP) PEG.24: 4 residues within 4Å: Chain B: L.25, E.28, L.29, E.255 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.28, B:E.28 PEG.25: 3 residues within 4Å: Chain B: R.158, V.175, L.177 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.158, B:V.175, B:V.175 PEG.26: 4 residues within 4Å: Chain B: N.317, S.398, G.399, L.429 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.317 PEG.27: 3 residues within 4Å: Chain B: E.66, E.81, K.84 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.66, B:K.84

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.17: 13 residues within 4Å: Chain A: I.294, A.297, V.298, P.316, N.317, M.318, G.319, G.320, K.321, T.322, A.323, Y.458 Ligands: MG.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:V.298, A:V.298, A:P.316, A:N.317, A:M.318, A:G.320, A:K.321, A:T.322, A:T.322 ADP.28: 13 residues within 4Å: Chain B: I.294, A.297, V.298, N.317, M.318, G.319, G.320, K.321, T.322, A.323, E.395, Y.458 Ligands: MG.18 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:V.298, B:V.298, B:G.319, B:G.320, B:K.321, B:T.322, B:A.323, B:E.395

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukui, K. et al., Structural and functional insights into the mechanism by which MutS2 recognizes a DNA junction. Structure (2022)

Release Date

2022-04-06

Peptides

Endonuclease MutS2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Endonuclease MutS2

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