Atomistry » Calcium » PDB 5ckm-5cxl » 5cxa
Atomistry »
  Calcium »
    PDB 5ckm-5cxl »
      5cxa »

Calcium in PDB 5cxa: Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470, PDB code: 5cxa was solved by C.Rouanet-Mehouas, 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) 36.62 / 1.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.230, 63.700, 36.620, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 18.1

Other elements in 5cxa:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 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 A Carboxylate Inhibitor Related to RXP470 (pdb code 5cxa). 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 A Carboxylate Inhibitor Related to RXP470, PDB code: 5cxa:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5cxa

Go back to Calcium Binding Sites List in 5cxa
Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to 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 the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:11.3
occ:1.00
 O A:GLY190 2.3 14.0 1.0
O A:GLY192 2.3 12.2 1.0
O A:ASP158 2.3 10.3 1.0
O A:HOH420 2.4 14.6 1.0
OD1 A:ASP194 2.4 10.7 1.0
O A:HOH423 2.4 12.8 1.0
CG A:ASP194 3.4 10.0 1.0
C A:ASP158 3.5 9.4 1.0
C A:GLY190 3.5 13.7 1.0
C A:GLY192 3.5 11.8 1.0
OD2 A:ASP194 3.8 11.3 1.0
C A:ILE191 4.0 12.6 1.0
N A:GLY192 4.1 12.9 1.0
O A:ILE191 4.2 11.9 1.0
N A:ASP194 4.2 9.9 1.0
O A:ALA157 4.3 13.5 1.0
CA A:GLY192 4.3 13.0 1.0
CA A:ASP158 4.4 10.2 1.0
CA A:ILE191 4.4 15.3 1.0
O A:GLY188 4.4 14.8 1.0
N A:ILE191 4.4 14.0 1.0
N A:ILE159 4.4 8.9 1.0
CA A:GLY190 4.4 14.1 1.0
N A:GLY190 4.4 14.6 1.0
N A:GLY193 4.5 11.3 1.0
O A:HOH634 4.5 41.3 1.0
CA A:ILE159 4.5 9.3 1.0
CA A:GLY193 4.5 10.0 1.0
O A:HOH417 4.6 31.1 1.0
C A:GLY193 4.6 10.3 1.0
CB A:ASP194 4.6 10.5 1.0
N A:LEU160 4.6 8.8 1.0
CA A:ASP194 4.8 9.4 1.0
C A:SER189 4.8 16.0 1.0
CH2 A:TRP109 4.9 11.4 1.0
O A:HOH443 4.9 14.0 1.0

Calcium binding site 2 out of 3 in 5cxa

Go back to Calcium Binding Sites List in 5cxa
Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to 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 the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:12.1
occ:1.00
 OD2 A:ASP124 2.4 11.3 1.0
OE2 A:GLU199 2.4 11.7 1.0
O A:HOH555 2.4 16.4 1.0
O A:GLU201 2.4 12.2 1.0
O A:GLU199 2.4 10.9 1.0
O A:HOH586 2.4 15.5 1.0
OD1 A:ASP124 2.6 13.5 1.0
CG A:ASP124 2.8 11.6 1.0
CD A:GLU199 3.5 11.4 1.0
C A:GLU199 3.6 10.1 1.0
C A:GLU201 3.6 11.2 1.0
CG A:GLU199 3.9 12.5 1.0
OG1 A:THR122 4.1 11.4 1.0
CA A:GLU199 4.2 10.1 1.0
CA A:PHE202 4.3 11.9 1.0
CD1 A:TRP203 4.3 12.4 1.0
CB A:ASP124 4.4 13.2 1.0
N A:PHE202 4.4 11.8 1.0
O A:HOH635 4.5 29.9 1.0
N A:GLU201 4.5 10.3 1.0
OE1 A:GLU199 4.6 11.9 1.0
C A:ASP200 4.6 11.8 1.0
N A:ASP200 4.6 10.4 1.0
O A:HOH419 4.6 21.6 1.0
CB A:GLU199 4.6 11.5 1.0
O A:HOH518 4.7 27.9 1.0
CA A:GLU201 4.7 11.6 1.0
O A:HOH449 4.7 36.6 1.0
CA A:ASP200 4.7 11.3 1.0
N A:TRP203 4.8 11.4 1.0
NE1 A:TRP203 4.8 10.6 1.0
O A:HOH670 4.9 19.6 1.0
CD1 A:PHE202 4.9 16.4 1.0

Calcium binding site 3 out of 3 in 5cxa

Go back to Calcium Binding Sites List in 5cxa
Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to 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 the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:10.3
occ:1.00
 O A:GLY176 2.3 13.0 1.0
O A:ILE180 2.3 12.4 1.0
O A:GLY178 2.3 12.8 1.0
OE2 A:GLU201 2.3 17.4 1.0
OD2 A:ASP198 2.3 10.7 1.0
OD1 A:ASP175 2.4 11.8 1.0
C A:ILE180 3.4 11.3 1.0
CG A:ASP198 3.4 9.6 1.0
C A:GLY178 3.5 12.6 1.0
C A:GLY176 3.5 12.2 1.0
CG A:ASP175 3.5 10.6 1.0
CD A:GLU201 3.6 14.9 1.0
N A:GLY178 3.8 12.7 1.0
N A:ILE180 3.9 10.9 1.0
N A:GLY176 4.1 11.5 1.0
OD2 A:ASP175 4.1 12.8 1.0
CA A:ILE180 4.1 11.0 1.0
CB A:ASP198 4.1 9.2 1.0
C A:LYS177 4.2 13.4 1.0
C A:GLY179 4.2 11.3 1.0
CA A:GLY178 4.2 13.5 1.0
N A:ASP175 4.3 11.3 1.0
C A:ASP175 4.3 11.1 1.0
OD1 A:ASP198 4.4 10.3 1.0
CG A:GLU201 4.4 11.9 1.0
CA A:LYS177 4.4 13.3 1.0
OE1 A:GLU201 4.4 16.0 1.0
N A:LYS177 4.4 12.7 1.0
CA A:GLY176 4.4 12.3 1.0
CB A:ILE180 4.5 12.3 1.0
N A:LEU181 4.5 10.4 1.0
N A:GLY179 4.5 12.6 1.0
CA A:ASP175 4.6 10.5 1.0
CA A:GLY179 4.6 11.8 1.0
CB A:ASP175 4.7 10.8 1.0
CA A:LEU181 4.7 11.1 1.0
O A:ASP175 4.7 13.2 1.0
O A:HOH500 4.8 38.2 1.0
O A:GLY179 4.8 12.0 1.0
O A:LYS177 4.9 16.7 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: Sun Jul 14 17:24:49 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy