Zinc in PDB 5v6x: Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Mutant (32A Ntd) Bound to Trna(Pyl)

Enzymatic activity of Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Mutant (32A Ntd) Bound to Trna(Pyl)

All present enzymatic activity of Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Mutant (32A Ntd) Bound to Trna(Pyl):
6.1.1.26;

Protein crystallography data

The structure of Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Mutant (32A Ntd) Bound to Trna(Pyl), PDB code: 5v6x was solved by T.Suzuki, D.Soll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.33 / 2.76
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 72.620, 72.620, 238.580, 90.00, 90.00, 120.00
R / Rfree (%) 20.6 / 24.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Mutant (32A Ntd) Bound to Trna(Pyl) (pdb code 5v6x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Mutant (32A Ntd) Bound to Trna(Pyl), PDB code: 5v6x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5v6x

Go back to Zinc Binding Sites List in 5v6x
Zinc binding site 1 out of 2 in the Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Mutant (32A Ntd) Bound to Trna(Pyl)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Mutant (32A Ntd) Bound to Trna(Pyl) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn200

b:74.3
occ:1.00
ND1 A:HIS24 2.0 71.4 1.0
SG A:CYS69 2.3 79.4 1.0
SG A:CYS42 2.4 70.3 1.0
SG A:CYS72 2.4 70.9 1.0
CE1 A:HIS24 2.9 70.5 1.0
CB A:CYS69 3.0 77.2 1.0
CG A:HIS24 3.1 68.6 1.0
CB A:CYS42 3.2 77.2 1.0
CB A:HIS24 3.5 66.3 1.0
CB A:CYS72 3.7 72.4 1.0
NE2 A:HIS24 4.0 69.7 1.0
CD2 A:HIS24 4.1 67.6 1.0
CA A:HIS24 4.1 68.9 1.0
N A:CYS42 4.3 81.5 1.0
CB A:MET40 4.4 77.2 1.0
CA A:CYS42 4.4 84.4 1.0
N A:CYS72 4.4 91.2 1.0
CA A:CYS69 4.5 78.5 1.0
CA A:CYS72 4.6 86.7 1.0
CG A:MET40 4.8 77.9 1.0

Zinc binding site 2 out of 2 in 5v6x

Go back to Zinc Binding Sites List in 5v6x
Zinc binding site 2 out of 2 in the Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Mutant (32A Ntd) Bound to Trna(Pyl)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Trna Binding Domain of Pyrrolysyl-Trna Synthetase Mutant (32A Ntd) Bound to Trna(Pyl) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn200

b:74.8
occ:1.00
ND1 B:HIS24 2.1 66.0 1.0
SG B:CYS69 2.4 76.3 1.0
SG B:CYS72 2.4 95.0 1.0
SG B:CYS42 2.4 75.7 1.0
CB B:CYS42 3.0 77.1 1.0
CE1 B:HIS24 3.0 63.7 1.0
CB B:CYS69 3.1 73.7 1.0
CG B:HIS24 3.2 62.2 1.0
CB B:HIS24 3.5 60.6 1.0
CB B:CYS72 3.6 92.6 1.0
NE2 B:HIS24 4.2 62.3 1.0
CA B:CYS42 4.2 77.8 1.0
CA B:HIS24 4.2 63.9 1.0
N B:CYS42 4.2 74.2 1.0
N B:CYS72 4.2 91.7 1.0
CD2 B:HIS24 4.3 60.7 1.0
CA B:CYS72 4.4 92.1 1.0
CB B:MET40 4.5 77.1 1.0
CA B:CYS69 4.6 78.9 1.0
N B:LYS25 5.0 65.6 1.0

Reference:

T.Suzuki, C.Miller, L.T.Guo, J.M.L.Ho, D.I.Bryson, Y.S.Wang, D.R.Liu, D.Soll. Crystal Structures Reveal An Elusive Functional Domain of Pyrrolysyl-Trna Synthetase. Nat. Chem. Biol. V. 13 1261 2017.
ISSN: ESSN 1552-4469
PubMed: 29035363
DOI: 10.1038/NCHEMBIO.2497
Page generated: Wed Dec 16 11:07:49 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy