SMTL ID : 1r89.1

Crystal Structures of an Archaeal Class I CCA-Adding Enzyme and Its Nucleotide Complexes

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: D.61 Ligands: MG.6, CTP.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.61, H2O.1 MN.2: 3 residues within 4Å: Chain A: H.396, H.398 Ligands: CTP.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.396, A:H.398 MN.4: 5 residues within 4Å: Chain A: E.59, R.93, H.101, V.109, D.110 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.101, A:D.110, H2O.10 MN.9: 3 residues within 4Å: Chain B: D.61 Ligands: MG.14, CTP.15 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.61, H2O.13 MN.10: 3 residues within 4Å: Chain B: H.396, H.398 Ligands: CTP.16 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.396, B:H.398 MN.12: 5 residues within 4Å: Chain B: E.59, R.93, H.101, V.109, D.110 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.101, B:D.110, H2O.23

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

NA.3: 2 residues within 4Å: Chain A: S.391, T.395 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.391, A:T.395 NA.11: 2 residues within 4Å: Chain B: S.391, T.395 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.391

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

CL.5: 6 residues within 4Å: Chain A: V.45, G.46, R.50, T.130, H.134 Ligands: CTP.7 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain B: V.45, G.46, R.50, T.130, H.134 Ligands: CTP.15 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain A: E.59, D.61, D.110 Ligands: MN.1, CTP.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.61, A:D.110, H2O.1 MG.14: 5 residues within 4Å: Chain B: E.59, D.61, D.110 Ligands: MN.9, CTP.15 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.61, B:D.110, H2O.13

4 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.7: 13 residues within 4Å: Chain A: G.46, S.47, R.50, D.61, A.126, T.130, H.133, K.152, Y.161, G.172 Ligands: MN.1, CL.5, MG.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.47, A:S.47, A:R.50, A:H.133, A:Y.161 Water bridges: A:K.152, A:K.152, A:G.172, A:G.172, A:G.172, A:G.172 Salt bridges: A:K.152, A:K.152 CTP.8: 7 residues within 4Å: Chain A: K.303, R.310, Y.392, H.396, H.398, T.399 Ligands: MN.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.310, A:Y.392, A:T.399, A:T.399 Water bridges: A:K.303, A:K.303, A:K.303, A:R.310, A:R.310 Salt bridges: A:K.303, A:K.303, A:R.310, A:H.396, A:H.396, A:H.396, A:H.398, A:H.398 CTP.15: 13 residues within 4Å: Chain B: G.46, S.47, R.50, D.61, A.126, T.130, H.133, K.152, Y.161, G.172 Ligands: MN.9, CL.13, MG.14 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.47, B:S.47, B:R.50, B:T.130, B:H.133, B:Y.161, B:Y.161 Water bridges: B:E.59, B:K.152, B:K.152, B:G.172, B:G.172, B:G.172, B:G.172 Salt bridges: B:K.152, B:K.152 CTP.16: 7 residues within 4Å: Chain B: K.303, R.310, Y.392, H.396, H.398, T.399 Ligands: MN.10 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:T.399 Water bridges: B:K.303, B:K.303, B:K.303, B:R.310, B:R.310, B:R.310, B:R.310 Salt bridges: B:K.303, B:K.303, B:R.310, B:H.396, B:H.396, B:H.396, B:H.398, B:H.398

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, Y. et al., Crystal structures of an archaeal class I CCA-adding enzyme and its nucleotide complexes. Mol.Cell (2003)

Release Date

2003-12-16

Peptides

tRNA nucleotidyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

tRNA nucleotidyltransferase

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