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Calcium in PDB 3dpf: 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: 3dpf 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 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.300, 69.210, 81.230, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 27

Other elements in 3dpf:

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 3dpf). 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: 3dpf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3dpf

Go back to Calcium Binding Sites List in 3dpf
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:14.2
occ:1.00
 O A:GLY171 2.5 11.5 1.0
O A:GLY169 2.5 17.0 1.0
O A:ASP137 2.5 14.2 1.0
OD1 A:ASP173 2.6 14.8 1.0
O A:HOH1002 2.9 17.7 1.0
CG A:ASP173 3.4 14.2 1.0
C A:ASP137 3.6 16.1 1.0
C A:GLY171 3.6 14.7 1.0
C A:GLY169 3.7 18.4 1.0
OD2 A:ASP173 3.8 14.0 1.0
C A:ILE170 3.9 14.5 1.0
N A:GLY171 3.9 14.8 1.0
N A:ASP173 4.2 9.6 1.0
O A:ILE170 4.2 11.6 1.0
CA A:GLY171 4.3 12.7 1.0
O A:ALA136 4.3 18.6 1.0
O A:GLY167 4.3 20.6 1.0
CA A:ASP137 4.3 16.7 1.0
CA A:ILE170 4.4 15.6 1.0
ND2 A:ASN139 4.4 10.4 1.0
N A:ILE138 4.5 15.0 1.0
N A:ILE170 4.5 16.2 1.0
N A:GLY172 4.6 12.9 1.0
CB A:ASP173 4.6 11.7 1.0
CA A:ILE138 4.6 15.0 1.0
C A:GLY172 4.6 10.5 1.0
N A:GLY169 4.7 18.9 1.0
CA A:GLY172 4.7 10.4 1.0
CA A:ASP173 4.7 11.4 1.0
CA A:GLY169 4.8 18.9 1.0
N A:ASN139 4.8 12.2 1.0
CH2 A:TRP88 4.8 16.6 1.0
C A:GLN168 4.9 20.4 1.0

Calcium binding site 2 out of 4 in 3dpf

Go back to Calcium Binding Sites List in 3dpf
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:13.7
occ:1.00
 O A:ASN157 2.4 11.1 1.0
OD2 A:ASP177 2.5 5.3 1.0
O A:GLY155 2.5 17.6 1.0
O A:ILE159 2.5 13.7 1.0
OE2 A:GLU180 2.6 21.4 1.0
O A:HOH1205 2.8 58.2 1.0
CG A:ASP177 3.4 11.2 1.0
C A:ILE159 3.5 14.2 1.0
CD A:GLU180 3.6 21.4 1.0
OD2 A:ASP154 3.6 21.5 1.0
C A:ASN157 3.6 14.2 1.0
C A:GLY155 3.7 18.8 1.0
N A:ILE159 3.9 13.6 1.0
CB A:ASP177 3.9 9.5 1.0
CG A:ASP154 4.0 27.6 1.0
N A:GLY155 4.1 18.5 1.0
N A:ASP154 4.1 19.4 1.0
N A:ASN157 4.1 15.0 1.0
OD1 A:ASP154 4.2 33.1 1.0
C A:ASP154 4.2 19.7 1.0
CA A:ILE159 4.2 14.7 1.0
C A:PRO156 4.2 17.3 1.0
C A:GLY158 4.3 14.1 1.0
OE1 A:GLU180 4.3 19.8 1.0
CG A:GLU180 4.4 23.7 1.0
CA A:ASN157 4.4 14.3 1.0
OD1 A:ASP177 4.4 7.8 1.0
N A:LEU160 4.4 13.3 1.0
O A:PRO156 4.4 14.7 1.0
CA A:GLY155 4.5 18.8 1.0
CA A:ASP154 4.5 20.3 1.0
N A:GLY158 4.6 14.1 1.0
O A:ASP154 4.6 19.3 1.0
CA A:GLY158 4.6 14.2 1.0
CA A:LEU160 4.6 13.9 1.0
CB A:ILE159 4.6 15.0 1.0
N A:PRO156 4.7 19.2 1.0
CA A:PRO156 4.7 18.5 1.0
O A:GLY158 4.8 11.2 1.0
CB A:ASP154 4.9 22.9 1.0

Calcium binding site 3 out of 4 in 3dpf

Go back to Calcium Binding Sites List in 3dpf
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:18.7
occ:1.00
 O B:GLY169 2.5 19.8 1.0
O B:ASP137 2.6 18.8 1.0
O B:GLY171 2.6 12.2 1.0
OD1 B:ASP173 2.7 13.8 1.0
O B:HOH1098 2.9 29.0 1.0
CG B:ASP173 3.4 14.1 1.0
C B:GLY169 3.6 19.8 1.0
OD2 B:ASP173 3.6 12.4 1.0
C B:GLY171 3.7 14.1 1.0
C B:ASP137 3.7 20.2 1.0
C B:ILE170 3.9 15.6 1.0
O B:ILE170 3.9 14.2 1.0
N B:GLY171 4.1 16.3 1.0
N B:ASP173 4.2 8.1 1.0
O B:HOH1080 4.2 32.8 1.0
O B:GLY167 4.2 12.6 1.0
CA B:ILE170 4.3 17.4 1.0
O B:ALA136 4.4 22.2 1.0
ND2 B:ASN139 4.4 21.5 1.0
N B:ILE170 4.4 17.7 1.0
CA B:GLY171 4.4 14.4 1.0
CA B:ASP137 4.5 20.6 1.0
N B:GLY169 4.5 20.9 1.0
CA B:GLY169 4.6 19.8 1.0
CB B:ASP173 4.6 10.0 1.0
N B:GLY172 4.6 12.5 1.0
N B:ILE138 4.6 20.0 1.0
C B:GLY172 4.7 10.3 1.0
CA B:GLY172 4.7 10.2 1.0
CA B:ILE138 4.8 19.1 1.0
CH2 B:TRP88 4.8 13.1 1.0
CA B:ASP173 4.8 9.3 1.0
O B:HOH1034 4.8 19.2 1.0
C B:GLN168 4.9 20.7 1.0
N B:ASN139 4.9 17.9 1.0

Calcium binding site 4 out of 4 in 3dpf

Go back to Calcium Binding Sites List in 3dpf
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:16.2
occ:1.00
 O B:ASN157 2.5 18.0 1.0
O B:GLY155 2.5 17.9 1.0
O B:ILE159 2.5 17.0 1.0
OD2 B:ASP177 2.5 13.7 1.0
OE2 B:GLU180 2.7 25.9 1.0
OD1 B:ASP154 2.7 18.7 1.0
CG B:ASP177 3.3 15.4 1.0
O B:HOH1168 3.5 55.0 1.0
CD B:GLU180 3.5 22.0 1.0
C B:ILE159 3.6 16.5 1.0
C B:ASN157 3.6 18.9 1.0
C B:GLY155 3.7 19.2 1.0
CB B:ASP177 3.8 13.4 1.0
N B:ILE159 4.0 15.5 1.0
CG B:ASP154 4.0 19.9 1.0
N B:ASN157 4.1 19.3 1.0
N B:GLY155 4.1 19.4 1.0
OE1 B:GLU180 4.1 17.9 1.0
O B:HOH1200 4.1 29.3 1.0
C B:ASP154 4.2 19.1 1.0
N B:ASP154 4.2 18.4 1.0
CG B:GLU180 4.3 22.2 1.0
OD1 B:ASP177 4.3 13.3 1.0
C B:PRO156 4.3 19.9 1.0
CA B:ILE159 4.3 17.0 1.0
C B:GLY158 4.3 16.9 1.0
CA B:ASN157 4.4 19.2 1.0
CA B:GLY155 4.5 19.2 1.0
N B:LEU160 4.6 13.6 1.0
CA B:ASP154 4.6 18.8 1.0
N B:GLY158 4.6 17.9 1.0
O B:ASP154 4.6 18.9 1.0
O B:PRO156 4.6 18.7 1.0
CA B:GLY158 4.7 17.0 1.0
N B:PRO156 4.7 20.0 1.0
CB B:ILE159 4.7 20.1 1.0
CA B:PRO156 4.7 19.9 1.0
CA B:LEU160 4.7 13.2 1.0
OD2 B:ASP154 4.8 19.1 1.0
O B:GLY158 4.8 15.4 1.0
CB B:ASP154 4.9 17.5 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: Tue Jul 8 11:41:26 2025

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