SMTL ID : 6ipk.1

Binary Complex of Human DNA Polymerase Mu with Mn8oxodGTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: D.204, D.206 Ligands: MN.2, 8DG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, H2O.1 MN.2: 5 residues within 4Å: Chain A: D.204, D.206, D.280 Ligands: MN.1, 8DG.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, A:D.280, H2O.2, H2O.2

1 x 8DG: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

8DG.3: 19 residues within 4Å: Chain A: G.193, G.194, R.197, K.199, Q.201, G.202, H.203, D.204, D.206, R.261, G.295, W.296, G.298, S.299, K.300, S.320 Ligands: MN.1, MN.2, EPE.10 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.194, A:H.203, A:D.204, A:R.261, A:S.299, A:S.320, A:S.320 Water bridges: A:R.197, A:R.197, A:K.199, A:K.199, A:K.199, A:K.199 Salt bridges: A:R.197, A:K.199, A:K.199, A:H.203, A:H.203 pi-Stacking: A:W.296, A:W.296

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: G.121, V.122, K.123, T.124 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.121, A:G.121, A:K.123, A:T.124 SO4.5: 1 residues within 4Å: Chain A: R.103 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.103 SO4.6: 4 residues within 4Å: Chain A: F.118, G.119, H.203, R.278 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.119 Water bridges: A:F.118, A:V.120, A:R.278 Salt bridges: A:H.203, A:R.278 SO4.7: 2 residues within 4Å: Chain A: R.196, P.351 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.196 Salt bridges: A:R.196 SO4.8: 2 residues within 4Å: Chain A: M.12 Ligands: SO4.9 No protein-ligand interaction detected (PLIP) SO4.9: 5 residues within 4Å: Chain A: L.63, P.64, S.65, Q.72 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.65, A:S.65, A:Q.72

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.10: 7 residues within 4Å: Chain A: A.258, F.259, R.261, R.307, N.319, H.321 Ligands: 8DG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.307 Salt bridges: A:R.261, A:H.321

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, Y.K. et al., Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions. J.Am.Chem.Soc. (2019)

Release Date

2019-05-29

Peptides

DNA-directed DNA/RNA polymerase mu: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-directed DNA/RNA polymerase mu

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