SMTL ID : 2j5w.1

Ceruloplasmin revisited: structural and functional roles of various metal cation binding sites

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: K.128, Q.143, D.146, D.147 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:K.128, A:D.146, A:D.147, H2O.1, H2O.2

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

NA.2: 6 residues within 4Å: Chain A: Y.55, G.64, Y.67, S.256, N.257, M.259 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.64, A:G.64 Water bridges: A:I.63 NA.3: 5 residues within 4Å: Chain A: F.408, G.417, Y.420, S.617, M.620 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.417, A:Y.420, A:S.617 NA.4: 5 residues within 4Å: Chain A: F.767, G.776, Y.779, S.955, M.958 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.767, A:G.776

7 x CU: COPPER (II) ION(Non-covalent)

CU.5: 5 residues within 4Å: Chain A: V.294, H.295, C.338, H.343, L.348 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.295, A:C.338, A:H.343 CU.6: 5 residues within 4Å: Chain A: H.182, H.999, L.1037, H.1039 Ligands: OXY.13 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.182, A:H.999, A:H.1039, H2O.13 CU.7: 4 residues within 4Å: Chain A: H.122, H.180, H.1041 Ligands: OXY.13 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.122, A:H.180, A:H.1041 CU.8: 6 residues within 4Å: Chain A: H.120, H.122, H.997, H.999 Ligands: O.9, OXY.13 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.120, A:H.997, O.9, H2O.13 CU.10: 5 residues within 4Å: Chain A: V.655, H.656, C.699, H.704, M.709 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.656, A:C.699, A:H.704 CU.11: 6 residues within 4Å: Chain A: L.993, H.994, C.1040, V.1042, H.1045, M.1050 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.994, A:C.1040, A:H.1045 CU.12: 3 residues within 4Å: Chain A: E.291, H.959, D.1044 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.959, A:D.1044, H2O.12, H2O.12, H2O.13

1 x O: OXYGEN ATOM(Non-covalent)

O.9: 6 residues within 4Å: Chain A: H.120, S.121, Y.126, H.997, H.999 Ligands: CU.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.123

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.13: 11 residues within 4Å: Chain A: H.120, H.122, H.180, H.182, H.997, H.999, H.1039, H.1041 Ligands: CU.6, CU.7, CU.8 No protein-ligand interaction detected (PLIP)

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.14: 2 residues within 4Å: Chain A: N.138, I.1035 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.1035 Hydrogen bonds: A:N.138 Water bridges: A:N.138 NAG.15: 1 residues within 4Å: Chain A: N.397 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 7 residues within 4Å: Chain A: Y.665, W.667, R.672, T.674, A.675, N.676, L.683 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.665, A:N.676, A:N.676 GOL.17: 9 residues within 4Å: Chain A: P.186, I.189, A.190, V.223, V.224, D.225, M.288, G.289, T.1043 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.223, A:D.225, A:T.1043, A:T.1043 Water bridges: A:S.222, A:N.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bento, I. et al., Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation-Binding Sites. Acta Crystallogr.,Sect.D (2007)

Release Date

2007-02-06

Peptides

CERULOPLASMIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CERULOPLASMIN

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