Atomistry » Zinc » PDB 3wod-3wyl » 3wqz
Atomistry »
  Zinc »
    PDB 3wod-3wyl »
      3wqz »

Zinc in PDB 3wqz: Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with A Trna(Ala) Variant Having A3.U70

Enzymatic activity of Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with A Trna(Ala) Variant Having A3.U70

All present enzymatic activity of Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with A Trna(Ala) Variant Having A3.U70:
6.1.1.7;

Protein crystallography data

The structure of Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with A Trna(Ala) Variant Having A3.U70, PDB code: 3wqz was solved by M.Naganuma, S.Sekine, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.74 / 3.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.609, 169.676, 176.649, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 27.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with A Trna(Ala) Variant Having A3.U70 (pdb code 3wqz). 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 Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with A Trna(Ala) Variant Having A3.U70, PDB code: 3wqz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3wqz

Go back to Zinc Binding Sites List in 3wqz
Zinc binding site 1 out of 2 in the Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with A Trna(Ala) Variant Having A3.U70


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 Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with A Trna(Ala) Variant Having A3.U70 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:0.9
occ:1.00
NE2 A:HIS604 2.4 84.7 1.0
SG A:CYS703 2.6 0.3 1.0
CE1 A:HIS604 3.2 85.6 1.0
CD2 A:HIS604 3.4 86.0 1.0
CB A:CYS703 3.4 0.5 1.0
ND1 A:HIS604 4.3 86.3 1.0
NE2 A:HIS707 4.3 0.4 1.0
CG A:HIS604 4.4 84.0 1.0
ND1 A:HIS600 4.5 0.3 1.0
CA A:CYS703 4.5 0.8 1.0
NE2 A:GLN701 4.7 99.6 1.0
CE1 A:HIS707 4.8 0.2 1.0
O A:HIS600 5.0 93.8 1.0
CD A:GLN701 5.0 0.9 1.0

Zinc binding site 2 out of 2 in 3wqz

Go back to Zinc Binding Sites List in 3wqz
Zinc binding site 2 out of 2 in the Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with A Trna(Ala) Variant Having A3.U70


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 Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with A Trna(Ala) Variant Having A3.U70 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:0.7
occ:1.00
NE2 B:HIS604 2.2 75.8 1.0
NE2 B:HIS600 2.3 0.4 1.0
SG B:CYS703 2.3 91.4 1.0
CE1 B:HIS604 2.8 74.3 1.0
CD2 B:HIS600 3.1 97.7 1.0
CD2 B:HIS604 3.3 89.2 1.0
CE1 B:HIS600 3.3 0.6 1.0
CB B:CYS703 3.7 0.0 1.0
ND1 B:HIS604 3.9 77.2 1.0
NE2 B:GLN701 4.0 92.2 1.0
CG B:HIS604 4.2 80.0 1.0
CG B:HIS600 4.3 97.5 1.0
ND1 B:HIS600 4.4 0.3 1.0
CD B:GLN701 4.6 78.1 1.0
NE2 B:HIS707 4.6 0.7 1.0
CE1 B:HIS707 4.8 0.1 1.0
OE1 B:GLN701 4.9 68.7 1.0
CA B:CYS703 4.9 0.1 1.0

Reference:

M.Naganuma, S.Sekine, Y.E.Chong, M.Guo, X.L.Yang, H.Gamper, Y.M.Hou, P.Schimmel, S.Yokoyama. The Selective Trna Aminoacylation Mechanism Based on A Single G.U Pair Nature V. 510 507 2014.
ISSN: ISSN 0028-0836
PubMed: 24919148
DOI: 10.1038/NATURE13440
Page generated: Wed Dec 16 04:57:56 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