SMTL ID : 7mc6.1

Crystal structure of the SARS-CoV-2 ExoN-nsp10 complex containing Mg2+ ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.209, C.212, C.228, H.231 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.209, A:C.212, A:C.228, A:H.231 ZN.2: 4 residues within 4Å: Chain A: H.259, C.263, H.266, C.281 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.259, A:C.263, A:H.266, A:C.281 ZN.12: 4 residues within 4Å: Chain B: C.75, C.78, H.84, C.91 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.75, B:C.78, B:H.84, B:C.91 ZN.13: 4 residues within 4Å: Chain B: C.118, C.121, C.129, C.131 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.118, B:C.121, B:C.129, B:C.131

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: T.252, S.257, N.258, L.261 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.252, A:S.257 EDO.4: 3 residues within 4Å: Chain A: H.84, R.86, S.180 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.180 EDO.5: 5 residues within 4Å: Chain A: S.220, A.222, S.223, G.234, F.235 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.220, A:S.223, A:S.223 Water bridges: A:T.225 EDO.6: 3 residues within 4Å: Chain A: H.266, G.267, C.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.267 EDO.7: 6 residues within 4Å: Chain A: F.62, K.63, M.64, F.75, H.190, L.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.64, A:M.64 EDO.8: 6 residues within 4Å: Chain A: S.173, D.174, W.229, H.230, H.231, S.232 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.230, A:S.232 Water bridges: A:V.169, A:S.173 EDO.9: 3 residues within 4Å: Chain A: A.189, H.190, G.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.189, A:G.191 EDO.14: 7 residues within 4Å: Chain A: L.40 Chain B: K.44, M.45, L.46, C.47, H.49, E.67 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:C.47, B:C.47, B:E.67 Water bridges: B:E.67, B:E.67 EDO.15: 6 residues within 4Å: Chain B: I.39, T.40, N.41, C.42, N.106, P.108 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.41, B:C.42, B:N.106

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

CL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 3 residues within 4Å: Chain A: D.92, E.94, D.275 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.92, A:E.94, A:D.275, H2O.2, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moeller, N.H. et al., Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2021-05-05

Peptides

Proofreading exoribonuclease: A
Non-structural protein 10: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
M

Proofreading exoribonuclease

Non-structural protein 10

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