SMTL ID : 1r8b.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: D.61 Ligands: MG.4, ATP.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.61 MN.2: 3 residues within 4Å: Chain A: H.396, H.398 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.396, A:H.398 MN.9: 3 residues within 4Å: Chain B: D.61 Ligands: MG.12, ATP.15 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.61 MN.10: 3 residues within 4Å: Chain B: H.396, H.398 Ligands: ATP.16 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.396, B:H.398

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: E.59, R.93, H.101, D.110 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.59, A:H.101, A:D.110, A:D.110, H2O.5 MG.4: 5 residues within 4Å: Chain A: E.59, D.61, D.110 Ligands: MN.1, ATP.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.59, A:D.61, H2O.6, H2O.7 MG.11: 4 residues within 4Å: Chain B: E.59, R.93, H.101, D.110 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.59, B:H.101, B:D.110, B:D.110, H2O.17 MG.12: 5 residues within 4Å: Chain B: E.59, D.61, D.110 Ligands: MN.9, ATP.15 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.59, B:D.61, H2O.19, H2O.20

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

NA.5: 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.13: 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.6: 3 residues within 4Å: Chain A: H.133, Y.173, R.224 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: H.133, Y.173, R.224 Ligand excluded by PLIP

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.7: 13 residues within 4Å: Chain A: G.46, S.47, D.61, F.63, A.95, E.96, T.130, H.133, K.152, Y.161, G.172 Ligands: MN.1, MG.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.47, A:S.47, A:E.96, A:H.133 Water bridges: A:T.52, A:T.130, A:K.152, A:G.172, A:G.172, A:G.172, A:G.172 Salt bridges: A:K.152, A:K.152 ATP.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 Water bridges: A:R.299, A:R.299, A:K.303, A:K.303, A:K.303, A:R.310, A:T.399 Salt bridges: A:K.303, A:K.303, A:R.310, A:H.396, A:H.396, A:H.396 pi-Cation interactions: A:R.310 ATP.15: 13 residues within 4Å: Chain B: G.46, S.47, D.61, F.63, A.95, E.96, T.130, H.133, K.152, Y.161, G.172 Ligands: MN.9, MG.12 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.47, B:S.47, B:E.96, B:T.130, B:Y.161 Water bridges: B:T.52, B:T.130, B:K.152, B:G.172, B:G.172, B:G.172, B:G.172 Salt bridges: B:K.152, B:K.152 ATP.16: 7 residues within 4Å: Chain B: K.303, R.310, Y.392, H.396, H.398, T.399 Ligands: MN.10 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:R.310 Water bridges: B:R.299, B:K.303, B:K.303, B:K.303, B:R.310, B:T.399, B:T.399 Salt bridges: B:K.303, B:K.303, B:R.310, B:H.396, B:H.396, B:H.396 pi-Cation interactions: B:R.310

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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