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Zinc 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:

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 3dng). 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: 3dng:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3dng

Go back to Zinc Binding Sites List in 3dng
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 2.0 8.7 1.0
NE2 A:HIS147 2.1 9.2 1.0
NE2 A:HIS162 2.2 6.5 1.0
CD2 A:HIS175 2.4 9.7 1.0
CD2 A:HIS147 2.9 5.9 1.0
CG A:ASP149 3.0 9.2 1.0
CE1 A:HIS162 3.0 5.4 1.0
CD2 A:HIS162 3.2 4.9 1.0
CE1 A:HIS147 3.3 9.7 1.0
OD1 A:ASP149 3.3 8.5 1.0
CG A:HIS175 3.3 10.2 1.0
NE2 A:HIS175 3.5 12.9 1.0
CB A:HIS175 3.6 7.1 1.0
O A:SER151 4.1 15.2 1.0
CG A:HIS147 4.1 7.9 1.0
ND1 A:HIS162 4.2 6.0 1.0
ND1 A:HIS147 4.3 7.2 1.0
CB A:ASP149 4.3 9.9 1.0
CG A:HIS162 4.3 5.9 1.0
CE1 A:PHE164 4.3 14.0 1.0
ND1 A:HIS175 4.5 11.4 1.0
CE1 A:HIS175 4.6 12.5 1.0
CE2 A:PHE153 4.7 8.8 1.0
CZ A:PHE153 4.7 10.1 1.0
CZ A:PHE164 4.8 16.4 1.0
O A:HOH1054 4.9 14.7 1.0
O A:HOH1142 4.9 70.6 0.0
O A:HOH1013 4.9 9.4 1.0
CB A:SER151 5.0 21.0 1.0

Zinc binding site 2 out of 4 in 3dng

Go back to Zinc Binding Sites List in 3dng
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:11.1
occ:1.00
 NE2 A:HIS207 2.2 11.0 1.0
NE2 A:HIS201 2.2 8.4 1.0
NE2 A:HIS197 2.3 6.8 1.0
O A:HOH1109 2.6 44.5 1.0
O A:HOH1001 2.6 15.1 1.0
CD2 A:HIS207 3.0 13.4 1.0
CD2 A:HIS197 3.1 7.6 1.0
CD2 A:HIS201 3.2 9.7 1.0
CE1 A:HIS201 3.2 11.8 1.0
CE1 A:HIS207 3.2 12.6 1.0
CE1 A:HIS197 3.3 8.0 1.0
CG A:HIS207 4.2 12.8 1.0
ND1 A:HIS207 4.2 13.6 1.0
CG A:HIS197 4.3 6.0 1.0
ND1 A:HIS201 4.3 8.8 1.0
CG A:HIS201 4.4 11.0 1.0
ND1 A:HIS197 4.4 3.9 1.0
OAC A:AXA1 4.5 22.0 1.0
N1 A:AXA1 4.5 18.3 1.0
O A:HOH1000 4.6 30.7 1.0
OE2 A:GLU198 4.6 15.9 1.0
CAV A:AXA1 4.7 20.5 1.0
O A:HOH1003 4.7 21.4 1.0
CE A:MET215 4.8 6.6 1.0
O A:HOH1002 4.8 12.0 1.0
O A:HOH1006 4.9 58.9 1.0

Zinc binding site 3 out of 4 in 3dng

Go back to Zinc Binding Sites List in 3dng
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:9.4
occ:1.00
 OD2 B:ASP149 2.1 10.2 1.0
NE2 B:HIS147 2.1 9.8 1.0
NE2 B:HIS162 2.2 10.0 1.0
O B:HOH1086 2.2 65.6 0.0
CD2 B:HIS175 2.5 5.7 1.0
CD2 B:HIS147 2.9 8.5 1.0
CE1 B:HIS162 3.0 8.7 1.0
CG B:ASP149 3.1 12.4 1.0
CD2 B:HIS162 3.3 7.5 1.0
CE1 B:HIS147 3.3 8.2 1.0
CG B:HIS175 3.3 6.1 1.0
OD1 B:ASP149 3.3 12.8 1.0
NE2 B:HIS175 3.6 6.8 1.0
CB B:HIS175 3.6 2.7 1.0
CG B:HIS147 4.1 9.1 1.0
O B:SER151 4.1 17.4 1.0
ND1 B:HIS162 4.2 8.1 1.0
ND1 B:HIS147 4.2 8.2 1.0
CG B:HIS162 4.3 6.8 1.0
CB B:ASP149 4.4 14.8 1.0
CE1 B:PHE164 4.4 18.0 1.0
ND1 B:HIS175 4.5 8.0 1.0
CE1 B:HIS175 4.7 8.2 1.0
CZ B:PHE153 4.7 9.6 1.0
CZ B:PHE164 4.7 18.1 1.0
O B:HOH1088 4.8 16.6 1.0
CE2 B:PHE153 4.8 6.8 1.0
O B:HOH1011 4.9 11.5 1.0

Zinc binding site 4 out of 4 in 3dng

Go back to Zinc Binding Sites List in 3dng
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:13.1
occ:1.00
 NE2 B:HIS207 2.1 10.8 1.0
NE2 B:HIS197 2.3 5.3 1.0
NE2 B:HIS201 2.3 7.5 1.0
O B:HOH1000 2.3 15.8 1.0
CD2 B:HIS207 3.1 13.5 1.0
CE1 B:HIS207 3.1 13.1 1.0
CD2 B:HIS197 3.1 7.2 1.0
CD2 B:HIS201 3.2 6.6 1.0
CE1 B:HIS197 3.3 4.1 1.0
CE1 B:HIS201 3.3 9.1 1.0
O B:HOH1146 3.5 57.9 1.0
ND1 B:HIS207 4.2 14.4 1.0
CG B:HIS207 4.2 13.7 1.0
CG B:HIS197 4.3 5.3 1.0
ND1 B:HIS197 4.3 6.0 1.0
CG B:HIS201 4.4 8.9 1.0
ND1 B:HIS201 4.4 5.1 1.0
N1 B:AXA2 4.6 23.5 1.0
OAC B:AXA2 4.6 28.4 1.0
O B:HOH1001 4.6 25.9 1.0
OE2 B:GLU198 4.6 14.0 1.0
O B:HOH1002 4.8 2.5 1.0
CAV B:AXA2 4.8 26.6 1.0
CE B:MET215 4.8 9.8 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 12:15:54 2024

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