Atomistry » Calcium » PDB 4gzt-4h82 » 4h76
Atomistry »
  Calcium »
    PDB 4gzt-4h82 »
      4h76 »

Calcium in PDB 4h76: Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor, PDB code: 4h76 was solved by E.A.Stura, L.Vera, E.Cassar-Lajeunesse, E.Nuti, V.Dive, A.Rossello, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.76 / 1.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.920, 62.890, 37.700, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.8

Other elements in 4h76:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor also contains other interesting chemical elements:

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 Broad Spectrum Hydroxamate Inhibitor (pdb code 4h76). 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 Broad Spectrum Hydroxamate Inhibitor, PDB code: 4h76:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4h76

Go back to Calcium Binding Sites List in 4h76
Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor


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 Broad Spectrum Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:11.4
occ:1.00
O A:HOH408 2.3 14.9 1.0
O A:GLY190 2.3 12.5 1.0
O A:GLY192 2.3 10.4 1.0
O A:ASP158 2.4 9.5 1.0
O A:HOH412 2.4 14.8 1.0
OD1 A:ASP194 2.4 10.4 1.0
CG A:ASP194 3.4 9.6 1.0
C A:GLY192 3.5 10.3 1.0
C A:GLY190 3.5 13.2 1.0
C A:ASP158 3.5 9.4 1.0
OD2 A:ASP194 3.8 11.1 1.0
C A:ILE191 4.0 12.7 1.0
O A:HOH502 4.0 25.3 1.0
N A:GLY192 4.1 11.8 1.0
O A:ILE191 4.2 10.2 1.0
O A:ALA157 4.2 13.3 1.0
N A:ASP194 4.2 9.7 1.0
CA A:ILE191 4.3 11.7 0.9
CA A:ASP158 4.4 7.4 1.0
CA A:GLY192 4.4 14.3 1.0
CA A:ILE191 4.4 11.9 0.1
O A:GLY188 4.4 15.3 1.0
N A:ILE191 4.4 12.2 1.0
N A:GLY193 4.5 10.7 1.0
N A:ILE159 4.5 9.9 1.0
CA A:GLY190 4.5 15.3 1.0
N A:GLY190 4.5 17.2 1.0
CA A:GLY193 4.6 11.2 1.0
CA A:ILE159 4.6 8.2 1.0
N A:LEU160 4.6 9.0 1.0
CB A:ASP194 4.6 8.6 1.0
C A:GLY193 4.6 10.5 1.0
CA A:ASP194 4.8 7.2 1.0
C A:SER189 4.8 13.8 1.0
O A:HOH531 4.9 20.9 1.0
CH2 A:TRP109 4.9 12.8 1.0

Calcium binding site 2 out of 3 in 4h76

Go back to Calcium Binding Sites List in 4h76
Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor


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 Broad Spectrum Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:14.9
occ:1.00
O A:GLU199 2.3 12.8 1.0
O A:HOH468 2.4 19.3 1.0
OD2 A:ASP124 2.4 15.4 1.0
O A:GLU201 2.4 13.3 1.0
OE2 A:GLU199 2.4 15.2 1.0
O A:HOH421 2.4 19.9 1.0
OD1 A:ASP124 2.7 16.4 1.0
CG A:ASP124 2.9 18.4 1.0
C A:GLU199 3.4 11.4 1.0
CD A:GLU199 3.5 14.2 1.0
C A:GLU201 3.6 12.7 1.0
CG A:GLU199 3.9 14.3 1.0
OG1 A:THR122 4.1 16.1 1.0
CA A:GLU199 4.1 13.1 1.0
CA A:PHE202 4.2 15.4 1.0
N A:PHE202 4.4 14.0 1.0
CD1 A:TRP203 4.4 10.0 1.0
CB A:ASP124 4.4 16.1 1.0
N A:GLU201 4.4 12.0 1.0
O A:HOH519 4.5 30.5 1.0
N A:ASP200 4.5 11.9 1.0
C A:ASP200 4.5 14.8 1.0
OE1 A:GLU199 4.6 15.2 1.0
CB A:GLU199 4.6 10.6 1.0
O A:HOH474 4.6 23.9 1.0
CA A:ASP200 4.7 12.3 1.0
CA A:GLU201 4.7 13.6 1.0
O A:HOH482 4.7 26.4 1.0
O A:HOH488 4.8 21.6 1.0
O A:HOH407 4.8 25.1 1.0
N A:TRP203 4.8 12.3 1.0
CD1 A:PHE202 4.8 20.5 1.0
NE1 A:TRP203 4.9 13.2 1.0

Calcium binding site 3 out of 3 in 4h76

Go back to Calcium Binding Sites List in 4h76
Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor


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 Broad Spectrum Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:11.2
occ:1.00
O A:GLY176 2.3 14.1 1.0
O A:ILE180 2.3 10.3 1.0
OD2 A:ASP198 2.3 12.6 1.0
O A:GLY178 2.3 14.2 1.0
OD1 A:ASP175 2.4 13.0 1.0
OE2 A:GLU201 2.4 20.1 1.0
C A:ILE180 3.5 9.2 1.0
CG A:ASP198 3.5 13.3 1.0
C A:GLY176 3.5 17.5 1.0
C A:GLY178 3.5 18.1 1.0
CG A:ASP175 3.5 12.2 1.0
CD A:GLU201 3.6 19.6 1.0
N A:ILE180 3.9 11.0 1.0
N A:GLY178 3.9 16.2 1.0
OD2 A:ASP175 4.1 12.7 1.0
N A:GLY176 4.1 11.8 1.0
CB A:ASP198 4.2 7.7 1.0
CA A:ILE180 4.2 8.6 1.0
C A:GLY179 4.2 11.8 1.0
C A:ASP175 4.3 11.9 1.0
C A:LYS177 4.3 15.4 1.0
CG A:GLU201 4.3 13.6 1.0
CA A:GLY178 4.3 18.6 1.0
N A:ASP175 4.3 13.1 1.0
CA A:GLY176 4.4 16.0 1.0
OD1 A:ASP198 4.4 9.3 1.0
N A:LYS177 4.4 16.8 1.0
N A:GLY179 4.5 12.9 1.0
CA A:LYS177 4.5 18.3 1.0
N A:LEU181 4.5 8.8 1.0
OE1 A:GLU201 4.6 19.6 1.0
CA A:GLY179 4.6 12.1 1.0
CA A:ASP175 4.6 11.0 1.0
CB A:ILE180 4.6 11.5 1.0
O A:ASP175 4.7 14.3 1.0
O A:GLY179 4.7 15.3 1.0
CB A:ASP175 4.7 11.0 1.0
CA A:LEU181 4.8 9.3 1.0
O A:LYS177 5.0 24.2 1.0

Reference:

C.Antoni, L.Vera, L.Devel, M.P.Catalani, B.Czarny, E.Cassar-Lajeunesse, E.Nuti, A.Rossello, V.Dive, E.A.Stura. Crystallization of Bi-Functional Ligand Protein Complexes. J.Struct.Biol. V. 182 246 2013.
ISSN: ISSN 1047-8477
PubMed: 23567804
DOI: 10.1016/J.JSB.2013.03.015
Page generated: Sun Jul 14 07:40:24 2024

Last articles

Ca in 3I6N
Ca in 3I77
Ca in 3I5E
Ca in 3I5I
Ca in 3I5H
Ca in 3I5G
Ca in 3I57
Ca in 3I08
Ca in 3I46
Ca in 3I4P
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy