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Zinc in PDB 6agg: Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase)

Enzymatic activity of Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase)

All present enzymatic activity of Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase):
6.3.4.22;

Protein crystallography data

The structure of Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase), PDB code: 6agg was solved by J.S.Dong, W.M.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.10 / 2.71
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.786, 69.786, 210.822, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 29.8

Other elements in 6agg:

The structure of Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase) (pdb code 6agg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase), PDB code: 6agg:

Zinc binding site 1 out of 1 in 6agg

Go back to Zinc Binding Sites List in 6agg
Zinc binding site 1 out of 1 in the Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase)


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 Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Zn501

b:0.6
occ:1.00
SG Z:CYS370 2.4 99.3 1.0
SG Z:CYS352 2.6 0.1 1.0
SG Z:CYS355 2.6 0.9 1.0
SG Z:CYS373 2.7 0.3 1.0
CB Z:CYS355 2.9 1.0 1.0
N Z:CYS355 3.4 0.7 1.0
CB Z:CYS352 3.8 0.4 1.0
CB Z:CYS370 3.8 88.0 1.0
CA Z:CYS355 3.8 0.4 1.0
CB Z:CYS373 3.9 0.5 1.0
N Z:CYS373 4.2 0.3 1.0
CB Z:SER354 4.2 0.1 1.0
CG Z:LYS372 4.2 0.5 1.0
CB Z:LYS372 4.2 0.2 1.0
OG1 Z:THR375 4.5 0.1 1.0
C Z:SER354 4.5 0.4 1.0
O Z:CYS370 4.6 88.0 1.0
OG Z:SER354 4.6 0.6 1.0
CA Z:CYS373 4.7 0.3 1.0
C Z:LYS372 4.7 0.1 1.0
CA Z:SER354 4.8 0.5 1.0
C Z:CYS355 4.8 0.0 1.0
N Z:GLY356 4.9 0.0 1.0
CA Z:LYS372 4.9 0.6 1.0
N Z:SER354 5.0 1.0 1.0

Reference:

J.Dong, F.Li, F.Gao, J.Wei, Y.Lin, Y.Zhang, J.Lou, G.Liu, Y.Dong, L.Liu, H.Liu, J.Wang, W.Gong. Structure of Trna-Modifying Enzyme Tias and Motions of Its Substrate Binding Zinc Ribbon. J. Mol. Biol. V. 430 4183 2018.
ISSN: ESSN 1089-8638
PubMed: 30121296
DOI: 10.1016/J.JMB.2018.08.015
Page generated: Wed Dec 16 11:29:37 2020

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