SMTL ID : 3w1b.1

Crystal Structure of Human DNA ligase IV-Artemis Complex (Mercury Derivative)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Covalent)

AMP.1: 4 residues within 4Å: Chain A: K.274, K.450, K.452 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.274, A:K.450, A:K.452

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

SO4.2: 4 residues within 4Å: Chain A: R.33, V.199, S.200, T.203 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.200, A:T.203, A:T.203 Water bridges: A:S.200 Salt bridges: A:R.33 SO4.3: 5 residues within 4Å: Chain A: G.277, E.278, R.279, R.294, E.332 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.279 Water bridges: A:R.279, A:K.346 Salt bridges: A:R.294, A:K.346 SO4.4: 5 residues within 4Å: Chain A: S.293, R.294, N.295, Y.297, Y.299 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.293, A:S.293, A:R.294, A:N.295, A:N.295 SO4.5: 4 residues within 4Å: Chain A: N.298, Y.299, D.301, Q.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.301, A:Q.302 SO4.6: 2 residues within 4Å: Chain A: K.321, A.322 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.322 Water bridges: A:T.395 SO4.7: 3 residues within 4Å: Chain A: R.26, R.38, H.39 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.26, A:R.38, A:H.39 SO4.8: 6 residues within 4Å: Chain A: L.251, A.252, R.294, R.444, K.450 Ligands: AMP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.252 Salt bridges: A:R.294, A:R.444, A:K.450 SO4.9: 1 residues within 4Å: Chain A: R.164 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.164 SO4.10: 4 residues within 4Å: Chain A: F.530, H.531, R.532, K.533 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.532, A:K.533 Salt bridges: A:H.531 SO4.11: 1 residues within 4Å: Chain A: R.164 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.164

9 x HG: MERCURY (II) ION(Non-covalent)

HG.12: 2 residues within 4Å: Chain A: C.138, Q.140 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.138, H2O.9 HG.13: 4 residues within 4Å: Chain A: M.69, L.222, V.225, C.226 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.226 HG.14: 5 residues within 4Å: Chain A: F.343, C.364, Y.365, C.366, E.402 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.364, A:C.366 HG.15: 4 residues within 4Å: Chain A: T.340, M.344, C.511, Y.517 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.511 HG.16: 3 residues within 4Å: Chain A: M.480, C.511 Ligands: HG.20 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.511 HG.17: 2 residues within 4Å: Chain A: C.553, N.554 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.553 HG.18: 3 residues within 4Å: Chain A: F.530, I.539, C.541 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.541 HG.19: 4 residues within 4Å: Chain A: T.573, C.575, L.600, R.604 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.575 HG.20: 4 residues within 4Å: Chain A: S.509, C.511, L.516 Ligands: HG.16 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.511

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ochi, T. et al., Structure of the catalytic region of DNA ligase IV in complex with an artemis fragment sheds light on double-strand break repair. Structure (2013)

Release Date

2013-04-03

Peptides

DNA ligase 4: A
Artemis-derived peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA ligase 4

Artemis-derived peptide

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