SMTL ID : 6dhw.2 (1 other biounit)

Crystal structure of primase iron-sulfur domain (266-457)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 11 residues within 4Å: Chain A: P.20, P.21, C.22, C.102, I.105, C.119, P.120, F.121, Q.156, C.159, P.179 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.22, A:C.102, A:C.119, A:C.159 SF4.6: 12 residues within 4Å: Chain B: P.20, P.21, C.22, C.102, I.105, C.119, P.120, F.121, Q.156, C.159, L.176, P.179 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.22, B:C.102, B:C.119, B:C.159

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

SO4.2: 6 residues within 4Å: Chain A: Q.64, E.65 Chain B: H.35, R.37, H.38, R.41 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.38, A:E.65 Salt bridges: B:R.37, B:R.41 SO4.3: 5 residues within 4Å: Chain A: H.35, R.37, H.38, R.41 Chain B: Q.64 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.38, B:Q.64 Salt bridges: A:H.35, A:R.41 SO4.4: 2 residues within 4Å: Chain A: S.87, F.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.88 SO4.5: 3 residues within 4Å: Chain A: T.16, R.24, Y.136 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.24 SO4.7: 4 residues within 4Å: Chain B: T.16, R.24, K.28, Y.136 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.24 SO4.8: 4 residues within 4Å: Chain B: H.34, W.62, D.77, Y.80 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.77, B:Y.80 Salt bridges: B:H.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holt, M.E. et al., Functional and structural similarity of human DNA primase [4Fe4S] cluster domain constructs. PLoS ONE (2018)

Release Date

2018-12-19

Peptides

DNA primase large subunit: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

DNA primase large subunit

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