Atomistry » Calcium » PDB 5cv4-5d63 » 5czm
Atomistry »
  Calcium »
    PDB 5cv4-5d63 »
      5czm »

Calcium in PDB 5czm: Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470

Enzymatic activity of Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470

All present enzymatic activity of Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470, PDB code: 5czm was solved by C.Rouanet-Mehouas, L.Roselia, L.Devel, V.Dive, E.A.Stura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.45 / 1.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.970, 63.290, 35.910, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 17.4

Other elements in 5czm:

The structure of Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Bromine (Br) 1 atom
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470 (pdb code 5czm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470, PDB code: 5czm:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5czm

Go back to Calcium Binding Sites List in 5czm
Calcium binding site 1 out of 3 in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470


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 A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:12.2
occ:1.00
O A:GLY192 2.3 12.0 1.0
O A:GLY190 2.3 13.6 1.0
O A:HOH420 2.3 18.3 1.0
O A:ASP158 2.3 10.1 1.0
OD2 A:ASP194 2.4 11.1 1.0
O A:HOH441 2.4 12.5 1.0
CG A:ASP194 3.3 10.0 1.0
C A:GLY192 3.5 11.2 1.0
C A:ASP158 3.5 9.5 1.0
C A:GLY190 3.5 13.5 1.0
OD1 A:ASP194 3.8 10.7 1.0
C A:ILE191 4.0 12.7 1.0
N A:GLY192 4.0 12.6 1.0
O A:ILE191 4.2 12.4 1.0
N A:ASP194 4.2 10.0 1.0
CA A:GLY192 4.3 11.8 1.0
O A:ALA157 4.3 11.8 1.0
CA A:ASP158 4.3 9.8 1.0
CA A:ILE191 4.3 13.9 1.0
N A:ILE191 4.4 13.7 1.0
O A:GLY188 4.4 16.1 1.0
N A:GLY190 4.4 15.1 1.0
N A:ILE159 4.4 8.5 1.0
N A:GLY193 4.4 10.6 1.0
CA A:GLY190 4.4 14.2 1.0
CA A:ILE159 4.5 8.9 1.0
CA A:GLY193 4.5 10.6 1.0
N A:LEU160 4.5 8.7 1.0
CB A:ASP194 4.6 10.2 1.0
C A:GLY193 4.6 10.5 1.0
O A:HOH636 4.7 28.6 1.0
CA A:ASP194 4.7 9.7 1.0
O A:HOH447 4.7 20.5 1.0
C A:SER189 4.7 16.1 1.0
O A:HOH434 4.9 13.9 1.0
CH2 A:TRP109 5.0 13.1 1.0

Calcium binding site 2 out of 3 in 5czm

Go back to Calcium Binding Sites List in 5czm
Calcium binding site 2 out of 3 in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:11.9
occ:1.00
O A:HOH564 2.4 17.0 1.0
O A:GLU199 2.4 10.3 1.0
O A:GLU201 2.4 12.0 1.0
O A:HOH533 2.4 17.1 1.0
OD2 A:ASP124 2.4 11.9 1.0
OE2 A:GLU199 2.4 12.2 1.0
OD1 A:ASP124 2.6 13.7 1.0
CG A:ASP124 2.9 12.3 1.0
CD A:GLU199 3.5 11.7 1.0
C A:GLU199 3.5 9.7 1.0
C A:GLU201 3.6 11.1 1.0
CG A:GLU199 3.9 10.7 1.0
OG1 A:THR122 4.1 12.1 1.0
CA A:GLU199 4.2 9.2 1.0
CA A:PHE202 4.2 11.3 1.0
CD1 A:TRP203 4.3 9.9 1.0
N A:PHE202 4.3 10.9 1.0
CB A:ASP124 4.4 12.6 1.0
N A:GLU201 4.4 10.7 1.0
O A:HOH497 4.4 27.6 1.0
O A:HOH619 4.4 32.7 1.0
C A:ASP200 4.5 10.8 1.0
N A:ASP200 4.5 10.2 1.0
OE1 A:GLU199 4.6 12.1 1.0
O A:HOH458 4.6 21.4 1.0
O A:HOH409 4.6 24.0 1.0
CB A:GLU199 4.6 9.7 1.0
CA A:GLU201 4.6 10.6 1.0
CA A:ASP200 4.7 10.9 1.0
N A:TRP203 4.7 10.8 1.0
NE1 A:TRP203 4.8 9.7 1.0
CD1 A:PHE202 4.9 17.1 1.0
O A:HOH655 4.9 22.3 1.0
O A:ASP200 5.0 12.1 1.0

Calcium binding site 3 out of 3 in 5czm

Go back to Calcium Binding Sites List in 5czm
Calcium binding site 3 out of 3 in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:10.5
occ:1.00
OE2 A:GLU201 2.2 14.6 1.0
O A:GLY176 2.3 12.1 1.0
OD1 A:ASP198 2.3 9.2 1.0
O A:GLY178 2.3 12.2 1.0
O A:ILE180 2.3 10.3 1.0
OD2 A:ASP175 2.3 10.8 1.0
CG A:ASP198 3.4 8.4 1.0
CD A:GLU201 3.5 13.4 1.0
C A:ILE180 3.5 10.1 1.0
C A:GLY178 3.5 11.8 1.0
C A:GLY176 3.5 11.4 1.0
CG A:ASP175 3.5 11.3 1.0
N A:GLY178 3.8 13.4 1.0
N A:ILE180 4.0 10.4 1.0
CB A:ASP198 4.1 8.4 1.0
OD1 A:ASP175 4.1 12.6 1.0
N A:GLY176 4.1 11.8 1.0
C A:LYS177 4.1 14.0 1.0
OE1 A:GLU201 4.2 14.7 1.0
CG2 A:ILE180 4.2 15.6 1.0
CA A:GLY178 4.2 12.9 1.0
N A:ASP175 4.3 9.9 1.0
CA A:ILE180 4.3 11.0 1.0
C A:ASP175 4.3 11.0 1.0
OD2 A:ASP198 4.3 9.2 1.0
C A:GLY179 4.3 10.4 1.0
CA A:LYS177 4.4 13.9 1.0
CA A:GLY176 4.4 11.5 1.0
N A:LYS177 4.4 13.2 1.0
N A:LEU181 4.4 10.1 1.0
CG A:GLU201 4.5 11.5 1.0
N A:GLY179 4.5 11.2 1.0
CA A:LEU181 4.6 9.6 1.0
CA A:ASP175 4.6 10.4 1.0
CA A:GLY179 4.7 10.5 1.0
CB A:ASP175 4.7 10.8 1.0
O A:HOH436 4.7 26.9 1.0
O A:ASP175 4.8 12.7 1.0
O A:LYS177 4.8 15.8 1.0
O A:GLY179 4.8 11.1 1.0
CB A:ILE180 4.9 14.2 1.0

Reference:

C.Rouanet-Mehouas, B.Czarny, F.Beau, E.Cassar-Lajeunesse, E.A.Stura, V.Dive, L.Devel. Zinc-Metalloproteinase Inhibitors: Evaluation of the Complex Role Played By the Zinc-Binding Group on Potency and Selectivity. J. Med. Chem. V. 60 403 2017.
ISSN: ISSN 1520-4804
PubMed: 27996256
DOI: 10.1021/ACS.JMEDCHEM.6B01420
Page generated: Sat Dec 12 05:20:45 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy