Atomistry » Calcium » PDB 2ovx-2p9k » 2oxw
Atomistry »
  Calcium »
    PDB 2ovx-2p9k »
      2oxw »

Calcium in PDB 2oxw: Human Mmp-12 Complexed with the Peptide Iag

Enzymatic activity of Human Mmp-12 Complexed with the Peptide Iag

All present enzymatic activity of Human Mmp-12 Complexed with the Peptide Iag:
3.4.24.65;

Protein crystallography data

The structure of Human Mmp-12 Complexed with the Peptide Iag, PDB code: 2oxw was solved by V.Calderone, I.Bertini, M.Fragai, C.Luchinat, M.Maletta, K.J.Yeo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.96 / 1.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.888, 60.358, 54.521, 90.00, 115.73, 90.00
R / Rfree (%) 19.7 / 22.3

Other elements in 2oxw:

The structure of Human Mmp-12 Complexed with the Peptide Iag also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Mmp-12 Complexed with the Peptide Iag (pdb code 2oxw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Human Mmp-12 Complexed with the Peptide Iag, PDB code: 2oxw:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2oxw

Go back to Calcium Binding Sites List in 2oxw
Calcium binding site 1 out of 3 in the Human Mmp-12 Complexed with the Peptide Iag


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Mmp-12 Complexed with the Peptide Iag within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca266

b:15.7
occ:1.00
O A:HOH321 2.3 23.6 1.0
O A:ASP158 2.3 13.6 1.0
O A:GLY190 2.3 18.2 1.0
O A:GLY192 2.4 14.5 1.0
OD2 A:ASP194 2.5 15.0 1.0
O A:HOH281 2.5 16.2 1.0
C A:ASP158 3.4 12.6 1.0
CG A:ASP194 3.5 13.9 1.0
C A:GLY190 3.6 18.5 1.0
C A:GLY192 3.6 14.3 1.0
OD1 A:ASP194 3.9 15.5 1.0
C A:ILE191 4.0 17.2 1.0
O A:ALA157 4.0 15.5 1.0
N A:GLY192 4.1 16.2 1.0
O A:ILE191 4.2 16.7 1.0
CA A:ASP158 4.2 12.9 1.0
N A:ASP194 4.3 12.3 1.0
CA A:ILE191 4.3 18.4 1.0
N A:ILE159 4.4 12.1 1.0
N A:ILE191 4.4 18.3 1.0
CA A:GLY192 4.4 15.4 1.0
O A:GLY188 4.5 17.6 1.0
N A:GLY193 4.5 13.5 1.0
CA A:GLY190 4.5 18.8 1.0
N A:GLY190 4.6 18.8 1.0
CA A:ILE159 4.6 12.1 1.0
CA A:GLY193 4.6 13.1 1.0
O A:HOH392 4.7 29.8 1.0
N A:LEU160 4.7 12.2 1.0
C A:GLY193 4.7 12.8 1.0
CB A:ASP194 4.7 12.8 1.0
O A:HOH304 4.7 17.4 1.0
O A:HOH399 4.7 28.7 1.0
CA A:ASP194 4.9 12.6 1.0
C A:SER189 4.9 18.9 1.0
C A:ALA157 4.9 14.5 1.0

Calcium binding site 2 out of 3 in 2oxw

Go back to Calcium Binding Sites List in 2oxw
Calcium binding site 2 out of 3 in the Human Mmp-12 Complexed with the Peptide Iag


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Mmp-12 Complexed with the Peptide Iag within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca267

b:11.6
occ:1.00
O A:GLU199 2.3 11.8 1.0
O A:HOH277 2.4 14.1 1.0
OE2 A:GLU199 2.4 12.5 1.0
OD2 A:ASP124 2.4 11.8 1.0
O A:GLU201 2.4 12.1 1.0
O A:HOH278 2.4 14.5 1.0
OD1 A:ASP124 2.6 11.8 1.0
CG A:ASP124 2.8 10.9 1.0
CD A:GLU199 3.5 12.4 1.0
C A:GLU199 3.5 11.6 1.0
C A:GLU201 3.6 11.6 1.0
CG A:GLU199 3.9 13.0 1.0
CA A:GLU199 4.1 11.6 1.0
OG1 A:THR122 4.1 11.6 1.0
CA A:PHE202 4.2 12.1 1.0
CB A:ASP124 4.4 11.5 1.0
N A:PHE202 4.4 12.1 1.0
CD1 A:TRP203 4.4 11.8 1.0
N A:GLU201 4.4 12.0 1.0
N A:ASP200 4.5 11.8 1.0
C A:ASP200 4.5 12.6 1.0
OE1 A:GLU199 4.6 13.3 1.0
CB A:GLU199 4.6 12.0 1.0
CA A:GLU201 4.7 12.0 1.0
CA A:ASP200 4.7 12.4 1.0
O A:HOH286 4.7 16.1 1.0
CD1 A:PHE202 4.8 13.7 1.0
NH2 A:ARG165 4.8 18.7 1.0
N A:TRP203 4.9 11.9 1.0
NE1 A:TRP203 4.9 11.6 1.0

Calcium binding site 3 out of 3 in 2oxw

Go back to Calcium Binding Sites List in 2oxw
Calcium binding site 3 out of 3 in the Human Mmp-12 Complexed with the Peptide Iag


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Mmp-12 Complexed with the Peptide Iag within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca268

b:16.9
occ:1.00
OE2 A:GLU201 2.3 18.7 1.0
OD1 A:ASP198 2.3 14.6 1.0
O A:GLY178 2.3 17.9 1.0
O A:GLY176 2.3 16.4 1.0
O A:ILE180 2.3 16.0 1.0
OD2 A:ASP175 2.4 16.7 1.0
CG A:ASP198 3.4 12.3 1.0
C A:ILE180 3.4 15.5 1.0
C A:GLY178 3.5 18.1 1.0
CD A:GLU201 3.5 16.6 1.0
C A:GLY176 3.5 17.2 1.0
CG A:ASP175 3.6 17.6 1.0
N A:GLY178 3.9 18.5 1.0
N A:ILE180 3.9 16.8 1.0
CB A:ASP198 4.0 11.7 1.0
N A:GLY176 4.1 17.2 1.0
OD1 A:ASP175 4.1 19.4 1.0
C A:LYS177 4.2 18.6 1.0
CA A:ILE180 4.2 16.3 1.0
OE1 A:GLU201 4.2 17.8 1.0
C A:GLY179 4.3 17.3 1.0
CA A:GLY178 4.3 18.3 1.0
C A:ASP175 4.3 17.4 1.0
N A:ASP175 4.3 17.3 1.0
OD2 A:ASP198 4.3 12.7 1.0
N A:LEU181 4.4 14.4 1.0
N A:LYS177 4.4 17.6 1.0
CA A:GLY176 4.4 17.2 1.0
CA A:LYS177 4.5 18.7 1.0
CG A:GLU201 4.5 13.4 1.0
N A:GLY179 4.5 18.0 1.0
CA A:LEU181 4.6 14.0 1.0
O A:HOH427 4.7 27.8 1.0
CA A:ASP175 4.7 17.3 1.0
CA A:GLY179 4.7 17.6 1.0
CB A:ASP175 4.7 17.9 1.0
O A:ASP175 4.7 17.8 1.0
CB A:ILE180 4.7 16.9 1.0
O A:LYS177 4.8 19.5 1.0
O A:GLY179 4.8 18.2 1.0

Reference:

I.Bertini, V.Calderone, M.Fragai, C.Luchinat, M.Maletta, K.J.Yeo. Snapshots of the Reaction Mechanism of Matrix Metalloproteinases. Angew.Chem.Int.Ed.Engl. V. 45 7952 2006.
ISSN: ISSN 1433-7851
PubMed: 17096442
DOI: 10.1002/ANIE.200603100
Page generated: Sat Dec 12 03:49:14 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