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Zinc in PDB 4jiv: VCA0105 Paar-Repeat Protein From Vibrio Cholerae in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5

Enzymatic activity of VCA0105 Paar-Repeat Protein From Vibrio Cholerae in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5

All present enzymatic activity of VCA0105 Paar-Repeat Protein From Vibrio Cholerae in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5:
3.2.1.17;

Protein crystallography data

The structure of VCA0105 Paar-Repeat Protein From Vibrio Cholerae in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5, PDB code: 4jiv was solved by S.A.Buth, P.G.Leiman, M.M.Shneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.40 / 1.90
Space group P 42 2 2
Cell size a, b, c (Å), α, β, γ (°) 113.703, 113.703, 76.897, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 20.8

Other elements in 4jiv:

The structure of VCA0105 Paar-Repeat Protein From Vibrio Cholerae in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the VCA0105 Paar-Repeat Protein From Vibrio Cholerae in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 (pdb code 4jiv). 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 VCA0105 Paar-Repeat Protein From Vibrio Cholerae in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5, PDB code: 4jiv:

Zinc binding site 1 out of 1 in 4jiv

Go back to Zinc Binding Sites List in 4jiv
Zinc binding site 1 out of 1 in the VCA0105 Paar-Repeat Protein From Vibrio Cholerae in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of VCA0105 Paar-Repeat Protein From Vibrio Cholerae in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn101

b:45.5
occ:1.00
 NE2 D:HIS54 2.0 43.0 1.0
NE2 D:HIS14 2.1 48.5 1.0
NE2 D:HIS46 2.2 39.2 1.0
SG D:CYS81 2.3 48.2 1.0
CD2 D:HIS54 3.0 43.5 1.0
CE1 D:HIS54 3.0 41.8 1.0
CD2 D:HIS14 3.1 48.3 1.0
CE1 D:HIS14 3.1 50.6 1.0
CE1 D:HIS46 3.1 38.6 1.0
CB D:CYS81 3.2 49.6 1.0
CD2 D:HIS46 3.2 38.6 1.0
NE D:ARG56 3.9 42.4 1.0
O D:CYS81 4.1 50.8 1.0
ND1 D:HIS54 4.1 41.5 1.0
CG D:HIS54 4.1 42.9 1.0
C D:CYS81 4.1 50.1 1.0
ND1 D:HIS14 4.2 50.7 1.0
CG D:HIS14 4.2 49.7 1.0
ND1 D:HIS46 4.3 37.6 1.0
CA D:CYS81 4.3 50.0 1.0
CG D:HIS46 4.3 37.6 1.0
CG D:ARG56 4.4 42.5 1.0
CD D:ARG56 4.4 41.9 1.0
CB D:PHE17 4.5 48.1 1.0
CZ D:ARG56 4.6 43.0 1.0
CG D:PHE17 4.6 49.2 1.0
N D:GLY82 4.7 49.5 1.0
O D:HOH234 4.7 52.5 1.0
NH2 D:ARG56 4.7 42.6 1.0
O D:GLY82 4.9 47.6 1.0
CD2 D:PHE17 4.9 48.8 1.0
CD1 D:PHE17 5.0 50.7 1.0

Reference:

M.M.Shneider, S.A.Buth, B.T.Ho, M.Basler, J.J.Mekalanos, P.G.Leiman. Paar-Repeat Proteins Sharpen and Diversify the Type VI Secretion System Spike. Nature V. 500 350 2013.
ISSN: ISSN 0028-0836
PubMed: 23925114
DOI: 10.1038/NATURE12453
Page generated: Wed Dec 16 05:26:26 2020

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