SMTL ID : 1f48.2 (1 other biounit)

CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI ARSENITE-TRANSLOCATING ATPASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

12 x SB: ANTIMONY (III) ION(Non-covalent)

SB.1: 6 residues within 4Å: Chain A: C.113, C.172, S.420, C.422 Ligands: SB.2, CL.12 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.113, A:C.172, A:C.422, H2O.1 SB.2: 6 residues within 4Å: Chain A: C.172, H.453, L.457 Ligands: SB.1, CL.12, CL.13 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.172, A:H.453, H2O.1 SB.3: 5 residues within 4Å: Chain A: C.113, H.148, L.152, S.420 Ligands: CL.14 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.113, A:H.148, A:S.420, H2O.4 SB.18: 6 residues within 4Å: Chain B: C.113, C.172, S.420, C.422 Ligands: SB.19, CL.29 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.113, B:C.172, B:C.422, H2O.9 SB.19: 6 residues within 4Å: Chain B: C.172, H.453, L.457 Ligands: SB.18, CL.29, CL.30 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.172, B:H.453, H2O.10 SB.20: 5 residues within 4Å: Chain B: C.113, H.148, L.152, S.420 Ligands: CL.31 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.113, B:H.148, B:S.420, H2O.12 SB.35: 6 residues within 4Å: Chain C: C.113, C.172, S.420, C.422 Ligands: SB.36, CL.46 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.113, C:C.172, C:C.422, H2O.18 SB.36: 6 residues within 4Å: Chain C: C.172, H.453, L.457 Ligands: SB.35, CL.46, CL.47 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.172, C:H.453, H2O.18 SB.37: 5 residues within 4Å: Chain C: C.113, H.148, L.152, S.420 Ligands: CL.48 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.113, C:H.148, C:S.420, H2O.21 SB.52: 6 residues within 4Å: Chain D: C.113, C.172, S.420, C.422 Ligands: SB.53, CL.63 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.113, D:C.172, D:C.422, H2O.26 SB.53: 6 residues within 4Å: Chain D: C.172, H.453, L.457 Ligands: SB.52, CL.63, CL.64 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.172, D:H.453, H2O.26 SB.54: 5 residues within 4Å: Chain D: C.113, H.148, L.152, S.420 Ligands: CL.65 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.113, D:H.148, D:S.420, H2O.29

8 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: T.22, D.45 Ligands: ADP.16 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.22, A:D.45, H2O.8, H2O.8, H2O.9 MG.5: 3 residues within 4Å: Chain A: T.341, D.447 Ligands: ADP.17 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.341, H2O.1, H2O.1, H2O.8, H2O.8 MG.21: 3 residues within 4Å: Chain B: T.22, D.45 Ligands: ADP.33 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.22, B:D.45, H2O.17, H2O.17, H2O.17 MG.22: 3 residues within 4Å: Chain B: T.341, D.447 Ligands: ADP.34 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.341, H2O.10, H2O.10, H2O.17, H2O.17 MG.38: 3 residues within 4Å: Chain C: T.22, D.45 Ligands: ADP.50 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.22, C:D.45, H2O.25, H2O.25, H2O.25 MG.39: 3 residues within 4Å: Chain C: T.341, D.447 Ligands: ADP.51 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.341, H2O.18, H2O.18, H2O.25, H2O.25 MG.55: 3 residues within 4Å: Chain D: T.22, D.45 Ligands: ADP.67 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.22, D:D.45, H2O.33, H2O.33, H2O.34 MG.56: 3 residues within 4Å: Chain D: T.341, D.447 Ligands: ADP.68 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.341, H2O.26, H2O.26, H2O.33, H2O.33

24 x CD: CADMIUM ION(Non-covalent)

CD.6: 1 residues within 4Å: Chain A: H.585 Ligand excluded by PLIP CD.7: 1 residues within 4Å: Chain A: D.321 Ligand excluded by PLIP CD.8: 3 residues within 4Å: Chain A: H.584, H.586 Chain C: E.326 Ligand excluded by PLIP CD.9: 1 residues within 4Å: Chain A: H.397 Ligand excluded by PLIP CD.10: 5 residues within 4Å: Chain A: D.386, H.388 Chain B: D.386, H.388 Ligands: CD.27 Ligand excluded by PLIP CD.11: 1 residues within 4Å: Chain A: H.520 Ligand excluded by PLIP CD.23: 1 residues within 4Å: Chain B: H.585 Ligand excluded by PLIP CD.24: 1 residues within 4Å: Chain B: D.321 Ligand excluded by PLIP CD.25: 3 residues within 4Å: Chain B: H.584, H.586 Chain D: E.326 Ligand excluded by PLIP CD.26: 1 residues within 4Å: Chain B: H.397 Ligand excluded by PLIP CD.27: 5 residues within 4Å: Chain A: D.386, H.388 Chain B: D.386, H.388 Ligands: CD.10 Ligand excluded by PLIP CD.28: 1 residues within 4Å: Chain B: H.520 Ligand excluded by PLIP CD.40: 1 residues within 4Å: Chain C: H.585 Ligand excluded by PLIP CD.41: 1 residues within 4Å: Chain C: D.321 Ligand excluded by PLIP CD.42: 3 residues within 4Å: Chain A: E.326 Chain C: H.584, H.586 Ligand excluded by PLIP CD.43: 1 residues within 4Å: Chain C: H.397 Ligand excluded by PLIP CD.44: 5 residues within 4Å: Chain C: D.386, H.388 Chain D: D.386, H.388 Ligands: CD.61 Ligand excluded by PLIP CD.45: 1 residues within 4Å: Chain C: H.520 Ligand excluded by PLIP CD.57: 1 residues within 4Å: Chain D: H.585 Ligand excluded by PLIP CD.58: 1 residues within 4Å: Chain D: D.321 Ligand excluded by PLIP CD.59: 3 residues within 4Å: Chain B: E.326 Chain D: H.584, H.586 Ligand excluded by PLIP CD.60: 1 residues within 4Å: Chain D: H.397 Ligand excluded by PLIP CD.61: 5 residues within 4Å: Chain C: D.386, H.388 Chain D: D.386, H.388 Ligands: CD.44 Ligand excluded by PLIP CD.62: 1 residues within 4Å: Chain D: H.520 Ligand excluded by PLIP

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

CL.12: 8 residues within 4Å: Chain A: G.111, A.112, C.113, C.172, H.453 Ligands: SB.1, SB.2, CL.13 Ligand excluded by PLIP CL.13: 7 residues within 4Å: Chain A: Q.108, G.111, C.113, T.114, H.453 Ligands: SB.2, CL.12 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: C.113, I.117, H.148, L.152 Ligands: SB.3 Ligand excluded by PLIP CL.29: 8 residues within 4Å: Chain B: G.111, A.112, C.113, C.172, H.453 Ligands: SB.18, SB.19, CL.30 Ligand excluded by PLIP CL.30: 7 residues within 4Å: Chain B: Q.108, G.111, C.113, T.114, H.453 Ligands: SB.19, CL.29 Ligand excluded by PLIP CL.31: 5 residues within 4Å: Chain B: C.113, I.117, H.148, L.152 Ligands: SB.20 Ligand excluded by PLIP CL.46: 8 residues within 4Å: Chain C: G.111, A.112, C.113, C.172, H.453 Ligands: SB.35, SB.36, CL.47 Ligand excluded by PLIP CL.47: 7 residues within 4Å: Chain C: Q.108, G.111, C.113, T.114, H.453 Ligands: SB.36, CL.46 Ligand excluded by PLIP CL.48: 5 residues within 4Å: Chain C: C.113, I.117, H.148, L.152 Ligands: SB.37 Ligand excluded by PLIP CL.63: 8 residues within 4Å: Chain D: G.111, A.112, C.113, C.172, H.453 Ligands: SB.52, SB.53, CL.64 Ligand excluded by PLIP CL.64: 7 residues within 4Å: Chain D: Q.108, G.111, C.113, T.114, H.453 Ligands: SB.53, CL.63 Ligand excluded by PLIP CL.65: 5 residues within 4Å: Chain D: C.113, I.117, H.148, L.152 Ligands: SB.54 Ligand excluded by PLIP

4 x SBO: TRIHYDROXYANTIMONITE(III)(Non-covalent)

SBO.15: 6 residues within 4Å: Chain A: G.18, R.206, L.277, E.500, R.543 Ligands: ADP.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.206, A:R.206, A:R.543 SBO.32: 6 residues within 4Å: Chain B: G.18, R.206, L.277, E.500, R.543 Ligands: ADP.33 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.206, B:R.206, B:R.543 SBO.49: 6 residues within 4Å: Chain C: G.18, R.206, L.277, E.500, R.543 Ligands: ADP.50 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.206, C:R.206, C:R.543 SBO.66: 6 residues within 4Å: Chain D: G.18, R.206, L.277, E.500, R.543 Ligands: ADP.67 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.206, D:R.206, D:R.543

8 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.16: 21 residues within 4Å: Chain A: K.16, G.17, G.18, V.19, G.20, K.21, T.22, S.23, N.235, G.236, F.276, L.277, Q.278, N.281, M.282, L.291, T.501, T.502, R.543 Ligands: MG.4, SBO.15 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:G.18, A:G.20, A:K.21, A:T.22, A:S.23, A:S.23, A:N.235, A:G.236, A:F.276, A:Q.278, A:M.282, A:M.282, A:T.501, A:T.502 Water bridges: A:K.21, A:K.21, A:T.22, A:N.49, A:N.49, A:T.502 Salt bridges: A:K.21 pi-Cation interactions: A:R.206 ADP.17: 19 residues within 4Å: Chain A: Q.208, S.210, G.336, G.337, V.338, G.339, K.340, T.341, T.342, N.527, N.528, P.566, V.567, L.568, S.570, E.571, P.572, L.581 Ligands: MG.5 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:Q.208, A:S.210, A:S.210, A:G.337, A:V.338, A:G.339, A:K.340, A:T.341, A:T.341, A:T.342, A:T.342, A:N.527, A:N.528, A:N.528, A:P.566, A:L.568 Water bridges: A:K.340, A:K.340, A:K.340, A:T.341, A:D.364, A:D.364 Salt bridges: A:K.340 ADP.33: 21 residues within 4Å: Chain B: K.16, G.17, G.18, V.19, G.20, K.21, T.22, S.23, N.235, G.236, F.276, L.277, Q.278, N.281, M.282, L.291, T.501, T.502, R.543 Ligands: MG.21, SBO.32 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:G.18, B:G.20, B:K.21, B:T.22, B:S.23, B:S.23, B:D.45, B:N.235, B:G.236, B:F.276, B:Q.278, B:M.282, B:M.282, B:T.501, B:T.502 Water bridges: B:K.21, B:K.21, B:T.22, B:N.49, B:N.49, B:T.502 Salt bridges: B:K.21 pi-Cation interactions: B:R.206 ADP.34: 19 residues within 4Å: Chain B: Q.208, S.210, G.336, G.337, V.338, G.339, K.340, T.341, T.342, N.527, N.528, P.566, V.567, L.568, S.570, E.571, P.572, L.581 Ligands: MG.22 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:Q.208, B:S.210, B:S.210, B:G.337, B:V.338, B:G.339, B:K.340, B:T.341, B:T.341, B:T.342, B:T.342, B:N.527, B:N.528, B:N.528, B:P.566, B:L.568 Water bridges: B:K.340, B:K.340, B:K.340, B:T.341, B:D.364, B:D.364 Salt bridges: B:K.340 ADP.50: 21 residues within 4Å: Chain C: K.16, G.17, G.18, V.19, G.20, K.21, T.22, S.23, N.235, G.236, F.276, L.277, Q.278, N.281, M.282, L.291, T.501, T.502, R.543 Ligands: MG.38, SBO.49 24 PLIP interactions: 24 interactions with chain C Hydrogen bonds: C:G.18, C:G.20, C:K.21, C:T.22, C:T.22, C:S.23, C:S.23, C:D.45, C:N.235, C:G.236, C:F.276, C:Q.278, C:M.282, C:M.282, C:T.501, C:T.501 Water bridges: C:K.21, C:K.21, C:T.22, C:N.49, C:T.502, C:T.502 Salt bridges: C:K.21 pi-Cation interactions: C:R.206 ADP.51: 19 residues within 4Å: Chain C: Q.208, S.210, G.336, G.337, V.338, G.339, K.340, T.341, T.342, N.527, N.528, P.566, V.567, L.568, S.570, E.571, P.572, L.581 Ligands: MG.39 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:Q.208, C:S.210, C:S.210, C:G.337, C:V.338, C:G.339, C:K.340, C:T.341, C:T.342, C:T.342, C:N.527, C:N.528, C:N.528, C:P.566, C:L.568 Water bridges: C:K.340, C:K.340, C:K.340, C:K.340, C:T.341, C:T.341, C:D.364, C:D.447, C:E.571 Salt bridges: C:K.340 ADP.67: 21 residues within 4Å: Chain D: K.16, G.17, G.18, V.19, G.20, K.21, T.22, S.23, N.235, G.236, F.276, L.277, Q.278, N.281, M.282, L.291, T.501, T.502, R.543 Ligands: MG.55, SBO.66 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:G.18, D:G.20, D:K.21, D:T.22, D:T.22, D:S.23, D:S.23, D:N.235, D:G.236, D:F.276, D:Q.278, D:M.282, D:M.282, D:T.501, D:T.501 Water bridges: D:K.21, D:K.21, D:T.22, D:N.49, D:T.502, D:T.502 Salt bridges: D:K.21 pi-Cation interactions: D:R.206 ADP.68: 19 residues within 4Å: Chain D: Q.208, S.210, G.336, G.337, V.338, G.339, K.340, T.341, T.342, N.527, N.528, P.566, V.567, L.568, S.570, E.571, P.572, L.581 Ligands: MG.56 22 PLIP interactions: 22 interactions with chain D Hydrogen bonds: D:Q.208, D:S.210, D:S.210, D:G.337, D:V.338, D:G.339, D:K.340, D:T.341, D:T.342, D:T.342, D:N.527, D:N.528, D:N.528, D:P.566, D:L.568 Water bridges: D:K.340, D:K.340, D:K.340, D:T.341, D:D.364, D:E.571 Salt bridges: D:K.340

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Structure of the ArsA ATPase: the catalytic subunit of a heavy metal resistance pump. EMBO J. (2000)

Release Date

2000-09-13

Peptides

ARSENITE-TRANSLOCATING ATPASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

ARSENITE-TRANSLOCATING ATPASE

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