Atomistry » Calcium » PDB 4gnb-4gy2 » 4gql
Atomistry »
  Calcium »
    PDB 4gnb-4gy2 »
      4gql »

Calcium in PDB 4gql: Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1, PDB code: 4gql was solved by E.A.Stura, L.Vera, F.Beau, L.Devel, E.Cassar-Lajeunesse, V.Dive, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.60 / 1.15
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.580, 63.390, 36.900, 90.00, 90.00, 90.00
R / Rfree (%) 13.3 / 15.4

Other elements in 4gql:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1 also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1 (pdb code 4gql). 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 the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1, PDB code: 4gql:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4gql

Go back to Calcium Binding Sites List in 4gql
Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1


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 the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:9.5
occ:1.00
O A:HOH417 2.3 17.5 1.0
O A:GLY190 2.3 11.3 1.0
O A:GLY192 2.3 9.9 1.0
O A:ASP158 2.3 8.1 1.0
O A:HOH423 2.4 10.9 1.0
OD2 A:ASP194 2.4 8.4 1.0
O A:HOH648 3.0 52.0 1.0
CG A:ASP194 3.4 9.0 1.0
C A:ASP158 3.5 7.1 1.0
C A:GLY190 3.5 10.8 1.0
C A:GLY192 3.5 9.2 1.0
OD1 A:ASP194 3.8 9.8 1.0
HA A:ILE159 3.9 8.6 1.0
HA A:ASP158 3.9 8.5 1.0
HA A:ILE191 3.9 13.8 1.0
C A:ILE191 3.9 9.5 1.0
HH2 A:TRP109 4.0 13.3 1.0
H A:LEU160 4.0 8.7 0.3
N A:GLY192 4.0 9.5 1.0
H A:LEU160 4.0 8.7 0.7
H A:ASP194 4.1 9.5 1.0
O A:ILE191 4.1 9.4 1.0
HA3 A:GLY193 4.1 10.2 1.0
CA A:ILE191 4.3 11.5 1.0
CA A:ASP158 4.3 7.0 1.0
H A:GLY192 4.3 11.4 1.0
O A:ALA157 4.3 10.7 1.0
N A:ASP194 4.3 7.9 1.0
CA A:GLY192 4.3 9.9 1.0
N A:ILE191 4.3 10.9 1.0
N A:ILE159 4.4 6.8 1.0
N A:GLY190 4.4 12.1 1.0
CA A:GLY190 4.4 12.0 1.0
O A:GLY188 4.4 11.7 1.0
N A:GLY193 4.5 8.5 1.0
HB2 A:LEU160 4.5 12.8 0.3
H A:GLY190 4.5 14.5 1.0
CA A:ILE159 4.6 7.1 1.0
HA3 A:GLY192 4.6 11.9 1.0
CA A:GLY193 4.6 8.5 1.0
HA2 A:GLY190 4.6 14.3 1.0
CB A:ASP194 4.7 7.5 1.0
N A:LEU160 4.7 7.2 0.3
N A:LEU160 4.7 7.2 0.7
C A:GLY193 4.7 7.5 1.0
HB2 A:LEU160 4.7 12.8 0.7
HA A:ASP194 4.7 9.2 1.0
O A:HOH650 4.8 34.4 1.0
C A:SER189 4.8 12.0 1.0
O A:HOH409 4.8 12.4 1.0
CA A:ASP194 4.9 7.7 1.0
CH2 A:TRP109 4.9 11.1 1.0
HB2 A:ASP194 5.0 9.0 1.0

Calcium binding site 2 out of 3 in 4gql

Go back to Calcium Binding Sites List in 4gql
Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1


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 the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:9.3
occ:1.00
O A:GLU199 2.4 9.0 1.0
OE2 A:GLU199 2.4 9.5 1.0
O A:HOH424 2.4 14.0 1.0
OD2 A:ASP124 2.4 9.9 1.0
O A:HOH436 2.4 13.6 1.0
O A:GLU201 2.4 9.5 1.0
OD1 A:ASP124 2.6 11.2 1.0
CG A:ASP124 2.8 9.9 1.0
HG3 A:GLU199 3.3 10.9 1.0
HA A:PHE202 3.4 11.0 1.0
CD A:GLU199 3.5 9.8 1.0
C A:GLU199 3.5 8.1 1.0
C A:GLU201 3.6 9.4 1.0
HD1 A:TRP203 3.6 9.4 1.0
HG1 A:THR122 3.7 11.2 1.0
HA A:GLU199 3.8 9.3 1.0
CG A:GLU199 3.9 9.1 1.0
H A:TRP203 4.1 10.6 1.0
HD1 A:PHE202 4.1 17.4 1.0
OG1 A:THR122 4.1 9.3 1.0
CA A:GLU199 4.2 7.8 1.0
CA A:PHE202 4.2 9.2 1.0
HA A:ASP200 4.3 10.8 1.0
CD1 A:TRP203 4.3 7.9 1.0
N A:PHE202 4.4 9.1 1.0
CB A:ASP124 4.4 10.2 1.0
HD2 A:PRO123 4.4 15.3 1.0
N A:GLU201 4.4 8.6 1.0
O A:HOH575 4.5 45.7 1.0
O A:HOH450 4.5 33.8 1.0
C A:ASP200 4.5 9.7 1.0
N A:ASP200 4.5 8.7 1.0
OE1 A:GLU199 4.6 9.7 1.0
O A:HOH582 4.6 36.7 1.0
H A:GLU201 4.6 10.3 1.0
O A:HOH466 4.6 23.9 1.0
HE1 A:TRP203 4.6 9.6 1.0
O A:HOH487 4.6 21.4 1.0
CB A:GLU199 4.6 8.3 1.0
HG2 A:GLU199 4.6 10.9 1.0
HG2 A:PRO123 4.7 16.1 1.0
CA A:GLU201 4.7 8.6 1.0
CA A:ASP200 4.7 9.0 1.0
HB2 A:ASP124 4.7 12.2 1.0
HB3 A:ASP124 4.8 12.2 1.0
N A:TRP203 4.8 8.8 1.0
H A:ASP124 4.8 12.6 1.0
NE1 A:TRP203 4.8 8.0 1.0
O A:HOH412 4.9 19.8 1.0
CD1 A:PHE202 4.9 14.5 1.0
O A:ASP200 5.0 11.2 1.0

Calcium binding site 3 out of 3 in 4gql

Go back to Calcium Binding Sites List in 4gql
Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1


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 the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:8.2
occ:1.00
OE2 A:GLU201 2.2 12.2 1.0
O A:GLY176 2.3 9.8 1.0
OD2 A:ASP175 2.3 9.4 1.0
OD1 A:ASP198 2.3 9.1 1.0
O A:ILE180 2.3 8.9 1.0
O A:GLY178 2.3 10.8 1.0
CG A:ASP198 3.4 7.7 1.0
C A:ILE180 3.5 8.4 1.0
CD A:GLU201 3.5 11.1 1.0
H A:ASP175 3.5 11.7 1.0
CG A:ASP175 3.5 10.4 1.0
C A:GLY178 3.5 10.2 1.0
C A:GLY176 3.5 9.9 1.0
HG23 A:ILE180 3.7 13.4 1.0
H A:GLY178 3.8 14.5 1.0
N A:GLY178 3.8 12.1 1.0
HA A:LEU181 3.8 8.9 1.0
HB3 A:ASP198 3.9 8.0 1.0
H A:ILE180 3.9 11.3 1.0
N A:ILE180 4.0 9.4 1.0
HA A:LYS177 4.0 15.4 1.0
OD1 A:ASP175 4.1 10.6 1.0
HG22 A:ILE180 4.1 13.4 1.0
CB A:ASP198 4.1 6.6 1.0
N A:GLY176 4.1 9.3 1.0
C A:LYS177 4.1 12.0 1.0
HB2 A:ASP198 4.1 8.0 1.0
HD23 A:LEU181 4.1 13.5 1.0
OE1 A:GLU201 4.2 12.9 1.0
H A:GLY176 4.2 11.2 1.0
HB3 A:PHE174 4.2 9.1 1.0
CA A:GLY178 4.3 11.9 1.0
N A:ASP175 4.3 9.7 1.0
CA A:ILE180 4.3 9.1 1.0
CG2 A:ILE180 4.3 11.2 1.0
C A:ASP175 4.3 10.2 1.0
OD2 A:ASP198 4.3 8.2 1.0
HG2 A:GLU201 4.3 11.1 1.0
C A:GLY179 4.4 9.0 1.0
CA A:GLY176 4.4 10.2 1.0
N A:LEU181 4.4 7.4 1.0
HA3 A:GLY179 4.4 11.3 1.0
N A:LYS177 4.4 11.4 1.0
CA A:LYS177 4.4 12.8 1.0
N A:GLY179 4.5 10.4 1.0
CG A:GLU201 4.5 9.3 1.0
HB2 A:ASP200 4.5 11.3 1.0
CA A:LEU181 4.6 7.4 1.0
CA A:ASP175 4.6 10.2 1.0
CB A:ASP175 4.7 9.8 1.0
CA A:GLY179 4.7 9.4 1.0
O A:HOH634 4.7 38.9 1.0
HA2 A:GLY178 4.7 14.3 1.0
O A:LYS177 4.7 14.3 1.0
O A:ASP175 4.8 11.4 1.0
HG3 A:GLU201 4.8 11.1 1.0
HA2 A:GLY176 4.9 12.2 1.0
O A:GLY179 4.9 9.9 1.0
CB A:ILE180 4.9 9.9 1.0

Reference:

B.Czarny, E.A.Stura, L.Devel, L.Vera, E.Cassar-Lajeunesse, F.Beau, V.Calderone, M.Fragai, C.Luchinat, V.Dive. Molecular Determinants of A Selective Matrix Metalloprotease-12 Inhibitor: Insights From Crystallography and Thermodynamic Studies. J.Med.Chem. V. 56 1149 2013.
ISSN: ISSN 0022-2623
PubMed: 23343195
DOI: 10.1021/JM301574D
Page generated: Sat Dec 12 04:48:40 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