SMTL ID : 3ova.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

2 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.1: 16 residues within 4Å: Chain A: G.44, S.45, R.48, E.57, D.59, T.128, H.131, K.150, Y.159, A.161, Y.171, R.222 Chain B: A.32, C.33, C.34 Ligands: MG.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:S.45, A:S.45, A:S.45, A:R.48, A:R.48, A:E.57, A:T.128, A:Y.159, A:Y.171, A:R.222 Water bridges: A:G.44, A:T.50, A:L.52, A:S.55, A:E.57, A:D.59, A:D.108, A:H.132, A:S.169, A:S.169, A:G.170 Salt bridges: A:K.150 APC.7: 16 residues within 4Å: Chain C: G.44, S.45, R.48, E.57, D.59, T.128, H.131, K.150, Y.159, A.161, Y.171, R.222 Chain D: A.32, C.33, C.34 Ligands: MG.9 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:S.45, C:S.45, C:S.45, C:R.48, C:R.48, C:H.131, C:Y.171, C:R.222 Water bridges: C:G.44, C:Y.46, C:L.52, C:S.55, C:E.57, C:H.132, C:K.150, C:S.169, C:S.169, C:G.170 Salt bridges: C:K.150

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

SO4.2: 3 residues within 4Å: Chain A: R.297, R.300, K.301 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.297, A:R.300, A:K.301 SO4.8: 3 residues within 4Å: Chain C: R.297, R.300, K.301 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:R.297, C:R.300, C:K.301

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.45, E.57, D.59 Ligands: APC.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.57 MG.9: 4 residues within 4Å: Chain C: S.45, E.57, D.59 Ligands: APC.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.57

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

EDO.4: 5 residues within 4Å: Chain A: V.38, E.39, L.62, L.63, F.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.39, A:L.63 EDO.5: 2 residues within 4Å: Chain A: R.138, V.178 No protein-ligand interaction detected (PLIP) EDO.6: 4 residues within 4Å: Chain A: I.121, K.122, S.123, A.124 No protein-ligand interaction detected (PLIP) EDO.10: 5 residues within 4Å: Chain C: V.38, E.39, L.62, L.63, F.64 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.39, C:L.63 EDO.11: 2 residues within 4Å: Chain C: R.138, V.178 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain C: I.121, K.122, S.123, A.124 No protein-ligand interaction detected (PLIP)

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: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

CCA-adding enzyme