Atomistry » Calcium » PDB 3dcq-3dsw » 3dng
Atomistry »
  Calcium »
    PDB 3dcq-3dsw »
      3dng »

Calcium in PDB 3dng: Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor

Enzymatic activity of Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor

All present enzymatic activity of Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor:
3.4.24.34;

Protein crystallography data

The structure of Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor, PDB code: 3dng was solved by G.Pochetti, R.Montanari, F.Mazza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.344, 69.384, 52.707, 90.00, 92.35, 90.00
R / Rfree (%) 22 / 28

Other elements in 3dng:

The structure of Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor (pdb code 3dng). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor, PDB code: 3dng:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3dng

Go back to Calcium Binding Sites List in 3dng
Calcium binding site 1 out of 4 in the Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating 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 Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca996

b:9.7
occ:1.00
 O A:ASP137 2.5 9.8 1.0
O A:GLY169 2.6 8.8 1.0
O A:GLY171 2.6 9.3 1.0
OD1 A:ASP173 2.6 7.8 1.0
CG A:ASP173 3.5 7.1 1.0
C A:ASP137 3.6 12.6 1.0
C A:GLY171 3.7 9.4 1.0
C A:GLY169 3.7 11.3 1.0
OD2 A:ASP173 3.9 7.6 1.0
N A:GLY171 4.1 10.6 1.0
C A:ILE170 4.1 11.0 1.0
ND2 A:ASN139 4.2 13.8 1.0
N A:ASP173 4.3 4.8 1.0
O A:ALA136 4.3 15.9 1.0
O A:ILE170 4.4 9.5 1.0
CA A:ASP137 4.4 13.9 1.0
CA A:ILE170 4.4 11.2 1.0
O A:GLY167 4.4 10.5 1.0
CA A:GLY171 4.5 10.0 1.0
N A:ILE170 4.5 11.6 1.0
N A:ILE138 4.5 9.9 1.0
N A:GLY169 4.6 13.4 1.0
CA A:ILE138 4.7 8.8 1.0
N A:GLY172 4.7 9.6 1.0
CA A:GLY169 4.7 13.8 1.0
CB A:ASP173 4.7 5.5 1.0
C A:GLY172 4.7 7.6 1.0
CA A:GLY172 4.7 7.7 1.0
N A:ASN139 4.8 10.2 1.0
C A:GLN168 4.8 13.3 1.0
O A:HOH1018 4.8 10.9 1.0
O A:HOH1160 4.9 36.0 1.0
CH2 A:TRP88 4.9 12.2 1.0
CA A:ASP173 4.9 5.6 1.0

Calcium binding site 2 out of 4 in 3dng

Go back to Calcium Binding Sites List in 3dng
Calcium binding site 2 out of 4 in the Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating 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 Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca997

b:10.9
occ:1.00
 O A:ILE159 2.4 9.5 1.0
O A:GLY155 2.4 12.1 1.0
O A:ASN157 2.4 11.0 1.0
OD1 A:ASP154 2.5 5.2 1.0
OD2 A:ASP177 2.6 7.4 1.0
OE2 A:GLU180 2.8 22.1 1.0
CD A:GLU180 3.5 19.2 1.0
C A:ILE159 3.5 9.4 1.0
CG A:ASP177 3.6 9.3 1.0
C A:ASN157 3.6 9.8 1.0
C A:GLY155 3.6 12.8 1.0
CG A:ASP154 3.8 9.9 1.0
N A:ILE159 3.8 11.8 1.0
N A:ASN157 4.0 11.3 1.0
N A:GLY155 4.1 10.2 1.0
CB A:ASP177 4.1 6.7 1.0
OE1 A:GLU180 4.1 17.6 1.0
CG A:GLU180 4.2 18.0 1.0
C A:PRO156 4.2 11.2 1.0
CA A:ILE159 4.2 10.4 1.0
C A:GLY158 4.2 11.3 1.0
N A:ASP154 4.3 10.3 1.0
C A:ASP154 4.3 10.7 1.0
CA A:ASN157 4.3 11.9 1.0
OD2 A:ASP154 4.4 11.1 1.0
CA A:GLY155 4.4 12.2 1.0
OD1 A:ASP177 4.5 7.2 1.0
CB A:ILE159 4.5 12.8 1.0
N A:PRO156 4.5 13.6 1.0
N A:LEU160 4.5 6.4 1.0
O A:PRO156 4.5 9.6 1.0
N A:GLY158 4.6 10.7 1.0
CA A:PRO156 4.6 12.6 1.0
CA A:GLY158 4.6 10.3 1.0
CA A:ASP154 4.6 11.5 1.0
O A:ASP154 4.7 9.5 1.0
CA A:LEU160 4.7 5.9 1.0
CB A:ASP154 4.8 10.1 1.0
O A:GLY158 4.8 11.8 1.0

Calcium binding site 3 out of 4 in 3dng

Go back to Calcium Binding Sites List in 3dng
Calcium binding site 3 out of 4 in the Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating 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 Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca996

b:8.8
occ:1.00
 O B:ASP137 2.5 7.6 1.0
O B:GLY169 2.5 12.3 1.0
O B:GLY171 2.6 9.1 1.0
OD1 B:ASP173 2.6 4.8 1.0
O B:HOH1051 2.8 23.2 1.0
CG B:ASP173 3.5 7.3 1.0
C B:ASP137 3.6 11.9 1.0
C B:GLY171 3.7 9.8 1.0
C B:GLY169 3.7 12.7 1.0
OD2 B:ASP173 3.9 11.9 1.0
C B:ILE170 4.0 13.5 1.0
ND2 B:ASN139 4.1 18.0 1.0
N B:GLY171 4.1 12.4 1.0
O B:ALA136 4.2 18.6 1.0
N B:ASP173 4.3 6.8 1.0
O B:ILE170 4.3 14.5 1.0
CA B:ASP137 4.4 13.9 1.0
CA B:ILE170 4.4 13.8 1.0
O B:GLY167 4.5 13.9 1.0
CA B:GLY171 4.5 11.3 1.0
N B:ILE170 4.5 11.5 1.0
N B:ILE138 4.6 10.7 1.0
CA B:ILE138 4.6 10.6 1.0
N B:GLY169 4.7 13.8 1.0
N B:GLY172 4.7 8.5 1.0
C B:GLY172 4.7 8.3 1.0
CA B:GLY169 4.7 13.9 1.0
CB B:ASP173 4.7 7.4 1.0
CA B:GLY172 4.7 8.6 1.0
N B:ASN139 4.7 10.1 1.0
CH2 B:TRP88 4.8 10.7 1.0
CA B:ASP173 4.9 6.8 1.0
C B:GLN168 5.0 16.1 1.0

Calcium binding site 4 out of 4 in 3dng

Go back to Calcium Binding Sites List in 3dng
Calcium binding site 4 out of 4 in the Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca997

b:14.3
occ:1.00
 O B:ILE159 2.4 8.5 1.0
O B:GLY155 2.5 14.9 1.0
O B:ASN157 2.5 15.6 1.0
OD2 B:ASP177 2.6 11.4 1.0
OD1 B:ASP154 2.6 13.2 1.0
OE2 B:GLU180 2.6 19.5 1.0
CG B:ASP177 3.4 9.0 1.0
CD B:GLU180 3.5 17.3 1.0
C B:ILE159 3.6 10.8 1.0
C B:GLY155 3.6 17.3 1.0
C B:ASN157 3.7 15.8 1.0
CG B:ASP154 3.7 15.2 1.0
N B:ILE159 3.9 12.2 1.0
CB B:ASP177 3.9 5.7 1.0
N B:GLY155 4.0 16.6 1.0
N B:ASN157 4.1 17.7 1.0
N B:ASP154 4.1 13.5 1.0
OE1 B:GLU180 4.1 15.9 1.0
C B:ASP154 4.2 16.5 1.0
C B:PRO156 4.2 18.8 1.0
CG B:GLU180 4.2 15.3 1.0
CA B:ILE159 4.2 12.4 1.0
OD1 B:ASP177 4.3 12.5 1.0
C B:GLY158 4.3 14.3 1.0
OD2 B:ASP154 4.4 14.4 1.0
CA B:ASN157 4.4 17.2 1.0
CA B:GLY155 4.5 17.4 1.0
O B:PRO156 4.5 19.7 1.0
CA B:ASP154 4.5 16.0 1.0
CB B:ILE159 4.6 15.4 1.0
N B:PRO156 4.6 18.6 1.0
N B:LEU160 4.6 8.5 1.0
O B:ASP154 4.6 19.2 1.0
CA B:PRO156 4.6 18.8 1.0
N B:GLY158 4.7 15.1 1.0
CA B:GLY158 4.7 13.3 1.0
CB B:ASP154 4.7 15.5 1.0
CA B:LEU160 4.8 7.5 1.0
O B:GLY158 5.0 13.5 1.0

Reference:

G.Pochetti, R.Montanari, C.Gege, C.Chevrier, A.G.Taveras, F.Mazza. Extra Binding Region Induced By Non-Zinc Chelating Inhibitors Into the S(1)' Subsite of Matrix Metalloproteinase 8 (Mmp-8) J.Med.Chem. V. 52 1040 2009.
ISSN: ISSN 0022-2623
PubMed: 19173605
DOI: 10.1021/JM801166J
Page generated: Sat Jul 13 09:03:40 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy