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Zinc 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:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor, PDB code: 3dpf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3dpf

Go back to Zinc Binding Sites List in 3dpf
Zinc 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 Zinc with other atoms in the Zn 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:Zn998

b:9.8
occ:1.00
 OD2 A:ASP149 2.1 7.4 1.0
NE2 A:HIS162 2.2 14.6 1.0
NE2 A:HIS147 2.2 13.5 1.0
O A:HOH1154 2.4 58.6 1.0
CD2 A:HIS175 2.4 9.5 1.0
CD2 A:HIS147 2.9 10.7 1.0
CG A:ASP149 3.0 13.0 1.0
CE1 A:HIS162 3.0 13.8 1.0
OD1 A:ASP149 3.3 12.6 1.0
CG A:HIS175 3.3 12.4 1.0
CD2 A:HIS162 3.3 14.3 1.0
CE1 A:HIS147 3.4 10.5 1.0
NE2 A:HIS175 3.5 13.8 1.0
CB A:HIS175 3.6 9.8 1.0
O A:HOH1055 3.8 59.2 1.0
O A:SER151 4.1 13.8 1.0
CG A:HIS147 4.2 10.9 1.0
ND1 A:HIS162 4.2 13.7 1.0
CB A:ASP149 4.3 16.7 1.0
ND1 A:HIS147 4.4 10.8 1.0
CG A:HIS162 4.4 13.0 1.0
CE1 A:PHE164 4.4 21.1 1.0
ND1 A:HIS175 4.5 14.9 1.0
CE1 A:HIS175 4.6 13.1 1.0
CZ A:PHE153 4.7 11.4 1.0
CZ A:PHE164 4.7 22.5 1.0
CE2 A:PHE153 4.7 11.8 1.0
O A:HOH1008 4.9 14.5 1.0
O A:HOH1038 4.9 18.1 1.0
CB A:SER151 5.0 18.2 1.0

Zinc binding site 2 out of 4 in 3dpf

Go back to Zinc Binding Sites List in 3dpf
Zinc 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 Zinc with other atoms in the Zn 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:Zn999

b:12.2
occ:1.00
 NE2 A:HIS201 2.2 13.1 1.0
NE2 A:HIS207 2.2 19.3 1.0
NE2 A:HIS197 2.3 13.2 1.0
O A:HOH1100 2.7 27.9 0.5
CD2 A:HIS207 3.0 18.4 1.0
CD2 A:HIS201 3.1 9.3 1.0
CD2 A:HIS197 3.1 12.9 1.0
O A:HOH1101 3.1 28.4 0.5
CE1 A:HIS201 3.2 13.9 1.0
CE1 A:HIS197 3.3 11.6 1.0
CE1 A:HIS207 3.3 17.9 1.0
O A:HOH1162 3.8 39.9 1.0
O A:HOH1202 4.2 50.8 1.0
CG A:HIS207 4.2 18.7 1.0
CG A:HIS201 4.3 9.2 1.0
ND1 A:HIS201 4.3 10.9 1.0
CG A:HIS197 4.3 10.2 1.0
O A:HOH1185 4.3 42.2 1.0
ND1 A:HIS207 4.3 18.5 1.0
ND1 A:HIS197 4.4 11.4 1.0
CAP A:AXB1 4.6 16.9 1.0
CE A:MET215 4.6 9.3 1.0
O A:HOH1022 4.9 13.1 1.0
OE2 A:GLU198 4.9 11.8 1.0
O A:HOH1099 4.9 26.1 0.5

Zinc binding site 3 out of 4 in 3dpf

Go back to Zinc Binding Sites List in 3dpf
Zinc 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 Zinc with other atoms in the Zn 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:Zn998

b:9.2
occ:1.00
 OD2 B:ASP149 2.1 9.8 1.0
NE2 B:HIS147 2.2 11.7 1.0
NE2 B:HIS162 2.3 14.3 1.0
CD2 B:HIS175 2.5 15.3 1.0
CD2 B:HIS147 2.9 10.4 1.0
CG B:ASP149 3.0 15.4 1.0
CE1 B:HIS162 3.1 14.2 1.0
OD1 B:ASP149 3.3 15.2 1.0
CD2 B:HIS162 3.3 14.2 1.0
CG B:HIS175 3.3 15.3 1.0
CE1 B:HIS147 3.4 13.6 1.0
CB B:HIS175 3.6 12.3 1.0
NE2 B:HIS175 3.6 17.7 1.0
O B:SER151 4.1 19.5 1.0
CG B:HIS147 4.1 12.0 1.0
ND1 B:HIS162 4.3 14.7 1.0
CE1 B:PHE164 4.3 17.2 1.0
CB B:ASP149 4.4 18.4 1.0
ND1 B:HIS147 4.4 12.3 1.0
CZ B:PHE164 4.4 19.6 1.0
CG B:HIS162 4.4 14.2 1.0
ND1 B:HIS175 4.5 16.7 1.0
CE1 B:HIS175 4.7 16.6 1.0
CZ B:PHE153 4.7 17.4 1.0
CE2 B:PHE153 4.8 17.5 1.0
CD2 B:TYR143 5.0 15.8 1.0

Zinc binding site 4 out of 4 in 3dpf

Go back to Zinc Binding Sites List in 3dpf
Zinc 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 Zinc with other atoms in the Zn 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:Zn999

b:10.2
occ:1.00
 NE2 B:HIS201 2.2 15.7 1.0
NE2 B:HIS207 2.2 21.0 1.0
NE2 B:HIS197 2.3 12.5 1.0
O B:HOH1097 2.8 19.6 1.0
CD2 B:HIS207 3.0 17.5 1.0
CD2 B:HIS197 3.1 11.4 1.0
CD2 B:HIS201 3.1 13.2 1.0
CE1 B:HIS201 3.2 15.9 1.0
CE1 B:HIS207 3.2 21.7 1.0
CE1 B:HIS197 3.3 9.5 1.0
O B:HOH1164 4.1 40.0 1.0
CG B:HIS207 4.2 18.5 1.0
ND1 B:HIS201 4.3 15.8 1.0
CG B:HIS201 4.3 13.3 1.0
ND1 B:HIS207 4.3 21.3 1.0
CG B:HIS197 4.3 9.5 1.0
ND1 B:HIS197 4.4 8.3 1.0
CAP B:AXB2 4.7 22.6 1.0
CE B:MET215 4.7 10.9 1.0
OE2 B:GLU198 4.9 13.4 1.0
O B:HOH1016 4.9 13.7 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: Thu Oct 24 12:17:32 2024

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