SMTL ID : 3ovs.1

How the CCA-adding Enzyme Selects Adenine over Cytosine in Position 76 of tRNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

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

CTP.1: 14 residues within 4Å: Chain A: G.46, S.47, R.50, D.61, T.130, H.133, K.152, Y.161, Y.173, R.224 Chain C: A.32, C.33, C.34 Ligands: CA.9 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.47, A:S.47, A:S.47, A:R.50, A:R.50, A:H.133, A:R.224 Water bridges: A:G.46, A:H.134, A:K.152, A:G.172, A:G.172 Salt bridges: A:K.152, A:K.152 CTP.10: 14 residues within 4Å: Chain B: G.46, S.47, R.50, D.61, T.130, H.133, K.152, Y.161, S.171, Y.173, R.224 Chain D: A.32, C.33, C.34 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.47, B:S.47, B:R.50, B:R.50, B:D.61, B:T.130, B:H.133, B:S.171, B:R.224 Salt bridges: B:K.152, B:K.152

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

SO4.2: 3 residues within 4Å: Chain A: R.299, R.302, K.303 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.299, A:R.302, A:K.303 SO4.3: 2 residues within 4Å: Chain A: W.136, R.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.135 Salt bridges: A:R.140 SO4.4: 4 residues within 4Å: Chain A: V.40, E.41, L.65, F.66 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.41 SO4.5: 4 residues within 4Å: Chain A: R.168, L.230, S.231, L.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.232 Salt bridges: A:R.168 SO4.6: 5 residues within 4Å: Chain A: R.93, Y.94, I.288, V.289, N.292 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.289, A:N.292 Salt bridges: A:R.93 SO4.11: 3 residues within 4Å: Chain B: R.299, R.302, K.303 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.299, B:R.302, B:K.303

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 1 residues within 4Å: Chain A: R.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.140 EDO.8: 5 residues within 4Å: Chain A: N.312, F.342, R.343 Chain B: M.314, Q.334 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.312, A:R.343, A:R.343 EDO.12: 1 residues within 4Å: Chain B: Q.348 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.348, A:R.197

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 3 residues within 4Å: Chain A: E.59, D.61 Ligands: CTP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.59, A:D.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, B. et al., How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA. Science (2010)

Release Date

2010-12-01

Peptides

CCA-Adding Enzyme: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CCA-Adding Enzyme