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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

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