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Calcium in PDB 3nqx: Crystal Structure of Vibriolysin Mcp-02 Mature Enzyme, A Zinc Metalloprotease From M4 Family

Enzymatic activity of Crystal Structure of Vibriolysin Mcp-02 Mature Enzyme, A Zinc Metalloprotease From M4 Family

All present enzymatic activity of Crystal Structure of Vibriolysin Mcp-02 Mature Enzyme, A Zinc Metalloprotease From M4 Family:
3.4.24.25;

Protein crystallography data

The structure of Crystal Structure of Vibriolysin Mcp-02 Mature Enzyme, A Zinc Metalloprotease From M4 Family, PDB code: 3nqx was solved by X.Gao, J.Wang, J.-W.Wu, Y.-Z.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.45 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.801, 73.792, 91.421, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 21.7

Other elements in 3nqx:

The structure of Crystal Structure of Vibriolysin Mcp-02 Mature Enzyme, A Zinc Metalloprotease From M4 Family also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Vibriolysin Mcp-02 Mature Enzyme, A Zinc Metalloprotease From M4 Family (pdb code 3nqx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Vibriolysin Mcp-02 Mature Enzyme, A Zinc Metalloprotease From M4 Family, PDB code: 3nqx:

Calcium binding site 1 out of 1 in 3nqx

Go back to Calcium Binding Sites List in 3nqx
Calcium binding site 1 out of 1 in the Crystal Structure of Vibriolysin Mcp-02 Mature Enzyme, A Zinc Metalloprotease From M4 Family


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Vibriolysin Mcp-02 Mature Enzyme, A Zinc Metalloprotease From M4 Family within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca511

b:11.1
occ:1.00
 OE1 A:GLU377 2.3 11.0 1.0
O A:LEU390 2.4 12.9 1.0
OE1 A:GLU380 2.4 11.2 1.0
OD1 A:ASP341 2.4 10.6 1.0
OD2 A:ASP388 2.5 11.4 1.0
O A:HOH512 2.5 20.3 1.0
OE2 A:GLU380 2.7 11.6 1.0
CD A:GLU380 2.9 11.1 1.0
CD A:GLU377 3.3 9.4 1.0
CG A:ASP341 3.5 9.1 1.0
CG A:ASP388 3.5 12.3 1.0
OE2 A:GLU377 3.5 9.9 1.0
C A:LEU390 3.5 11.6 1.0
OD1 A:ASP388 3.8 13.9 1.0
CB A:ASP341 4.0 9.0 1.0
N A:LEU390 4.0 11.5 1.0
O A:HOH68 4.3 13.0 1.0
CA A:LEU390 4.3 11.4 1.0
CG A:GLU380 4.4 10.2 1.0
O A:HOH15 4.4 9.4 1.0
OD2 A:ASP341 4.4 9.5 1.0
N A:VAL391 4.5 10.4 1.0
CA A:VAL391 4.5 9.7 1.0
N A:GLY392 4.6 9.2 1.0
O A:HOH707 4.6 28.6 1.0
N A:TRP389 4.6 11.5 1.0
O A:HOH35 4.7 10.6 1.0
N A:ASP388 4.7 9.7 1.0
CG A:GLU377 4.7 9.6 1.0
CB A:LEU390 4.7 12.4 1.0
CB A:ASP388 4.8 11.8 1.0
O A:HOH624 4.9 24.3 1.0
C A:TRP389 5.0 11.9 1.0

Reference:

X.Gao, J.Wang, D.-Q.Yu, F.Bian, B.-B.Xie, X.-L.Chen, B.-C.Zhou, L.-H.Lai, Z.-X.Wang, J.-W.Wu, Y.-Z.Zhang. Structural Basis For the Autoprocessing of Zinc Metalloproteases in the Thermolysin Family Proc.Natl.Acad.Sci.Usa V. 107 17569 2010.
ISSN: ISSN 0027-8424
PubMed: 20876133
DOI: 10.1073/PNAS.1005681107
Page generated: Tue Jul 8 14:58:51 2025

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