SMTL ID : 3g0r.1

Complex of Mth0212 and an 8bp dsDNA with distorted ends

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: L.126, D.130, W.180 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.130, A:W.180 GOL.2: 7 residues within 4Å: Chain A: L.4, D.32, I.33, T.75, K.76, V.77, F.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.32, A:T.75, A:K.76, A:V.77 GOL.3: 10 residues within 4Å: Chain A: D.191, T.192, F.193, R.220, D.222, Y.223, F.224, W.238, I.239, I.251 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.191, A:D.191, A:T.192, A:F.193, A:R.220, A:F.224, A:W.238 GOL.4: 11 residues within 4Å: Chain A: T.61, P.62, E.84, F.91, D.92, T.93, E.94, G.95, R.96, I.97 Ligands: PG4.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.62, A:E.94, A:G.95, A:R.96, A:I.97 GOL.5: 6 residues within 4Å: Chain A: H.156, I.185, V.190, D.191, R.194, M.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.156, A:D.191 GOL.6: 6 residues within 4Å: Chain A: K.20, Y.208, G.245, S.246 Chain D: T.4, G.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.20, A:Y.208 GOL.7: 5 residues within 4Å: Chain A: H.156, R.157, R.178, A.179, D.182 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.157, A:R.178 GOL.8: 5 residues within 4Å: Chain A: E.29, W.238, I.239, L.240, V.243 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.238 Water bridges: A:R.236, A:S.241 GOL.9: 4 residues within 4Å: Chain A: N.137, R.140, D.141, N.187 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.137, A:R.140, A:D.141 GOL.13: 10 residues within 4Å: Chain B: F.193, R.220, D.222, Y.223, F.224, S.237, W.238, I.239, I.251, G.252 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.220, B:R.220, B:S.237, B:W.238, B:G.252 Water bridges: B:F.224 GOL.14: 2 residues within 4Å: Chain B: D.130, W.180 2 PLIP interactions: 2 interactions with chain B Water bridges: B:W.180, B:K.183 GOL.15: 5 residues within 4Å: Chain B: G.55, Y.56, R.57, K.76, P.78 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.55, B:R.57 Water bridges: B:Y.56

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.10: 8 residues within 4Å: Chain A: A.42, E.44, Q.45, P.62, A.63, E.64, K.66 Ligands: GOL.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.92 PG4.11: 7 residues within 4Å: Chain A: R.51, H.52, V.53, G.55, Y.56, R.57, S.58 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.52, A:G.55, A:S.58, A:S.58 Water bridges: A:V.53 PG4.12: 9 residues within 4Å: Chain A: W.9, V.17, K.20, G.21, F.22, W.25, D.242, V.243, M.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.17, A:M.244

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

NA.16: 4 residues within 4Å: Chain C: C.5, G.6 Chain D: G.5, U.6 No protein-ligand interaction detected (PLIP) NA.17: 4 residues within 4Å: Chain C: G.4, C.5 Chain D: U.6, G.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lakomek, K. et al., Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA. J.Mol.Biol. (2010)

Release Date

2010-03-09

Peptides

Exodeoxyribonuclease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Exodeoxyribonuclease

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