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Zinc in PDB 4jij: Crystal Structure of An Inactive Mutant of Mmp-9 Catalytic Domain in Complex with A Fluorogenic Synthetic Peptidic Substrate

Enzymatic activity of Crystal Structure of An Inactive Mutant of Mmp-9 Catalytic Domain in Complex with A Fluorogenic Synthetic Peptidic Substrate

All present enzymatic activity of Crystal Structure of An Inactive Mutant of Mmp-9 Catalytic Domain in Complex with A Fluorogenic Synthetic Peptidic Substrate:
3.4.24.35;

Protein crystallography data

The structure of Crystal Structure of An Inactive Mutant of Mmp-9 Catalytic Domain in Complex with A Fluorogenic Synthetic Peptidic Substrate, PDB code: 4jij was solved by E.A.Stura, L.Vera, E.Cassar-Lajeunesse, I.Tranchant, M.Amoura, V.Dive, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.57 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 34.200, 57.400, 172.030, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19.5

Other elements in 4jij:

The structure of Crystal Structure of An Inactive Mutant of Mmp-9 Catalytic Domain in Complex with A Fluorogenic Synthetic Peptidic Substrate also contains other interesting chemical elements:

Strontium (Sr) 4 atoms
Iodine (I) 2 atoms
Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of An Inactive Mutant of Mmp-9 Catalytic Domain in Complex with A Fluorogenic Synthetic Peptidic Substrate (pdb code 4jij). 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 An Inactive Mutant of Mmp-9 Catalytic Domain in Complex with A Fluorogenic Synthetic Peptidic Substrate, PDB code: 4jij:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4jij

Go back to Zinc Binding Sites List in 4jij
Zinc binding site 1 out of 4 in the Crystal Structure of An Inactive Mutant of Mmp-9 Catalytic Domain in Complex with A Fluorogenic Synthetic Peptidic Substrate


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 An Inactive Mutant of Mmp-9 Catalytic Domain in Complex with A Fluorogenic Synthetic Peptidic Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:11.4
occ:1.00
 N3 A:AZI301 2.0 14.5 1.0
NE2 A:HIS236 2.0 10.8 1.0
NE2 A:HIS226 2.0 8.6 1.0
NE2 A:HIS230 2.0 10.1 1.0
CD2 A:HIS236 2.9 10.0 1.0
CD2 A:HIS230 3.0 9.7 1.0
CD2 A:HIS226 3.0 7.7 1.0
N2 A:AZI301 3.0 15.3 1.0
CE1 A:HIS236 3.0 15.0 1.0
CE1 A:HIS226 3.0 9.5 1.0
CE1 A:HIS230 3.0 11.1 1.0
O P:GLY4 3.3 20.6 1.0
C P:GLY4 3.7 16.4 1.0
CG A:HIS236 4.0 13.3 1.0
ND1 A:HIS236 4.0 14.0 1.0
N1 A:AZI301 4.1 13.4 1.0
ND1 A:HIS226 4.1 10.5 1.0
CG A:HIS226 4.1 9.5 1.0
ND1 A:HIS230 4.1 11.9 1.0
CG A:HIS230 4.1 10.1 1.0
N P:PHI5 4.2 11.5 1.0
CA P:PHI5 4.2 11.9 1.0
CB P:PHI5 4.3 11.9 1.0
CB P:LEU3 4.4 11.6 1.0
N P:GLY4 4.4 12.8 1.0
C P:LEU3 4.4 9.3 1.0
CD1 P:PHI5 4.4 12.7 1.0
O P:LEU3 4.5 10.6 1.0
CA P:GLY4 4.5 14.4 1.0
CG P:PHI5 4.6 12.1 1.0
CE A:MET244 4.7 9.8 1.0

Zinc binding site 2 out of 4 in 4jij

Go back to Zinc Binding Sites List in 4jij
Zinc binding site 2 out of 4 in the Crystal Structure of An Inactive Mutant of Mmp-9 Catalytic Domain in Complex with A Fluorogenic Synthetic Peptidic Substrate


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 An Inactive Mutant of Mmp-9 Catalytic Domain in Complex with A Fluorogenic Synthetic Peptidic Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:10.1
occ:1.00
 OD1 A:ASP177 1.9 11.4 1.0
ND1 A:HIS203 2.0 8.5 1.0
NE2 A:HIS175 2.0 10.9 1.0
NE2 A:HIS190 2.0 9.8 1.0
CG A:ASP177 2.9 11.9 1.0
CE1 A:HIS203 2.9 10.1 1.0
CE1 A:HIS190 2.9 9.3 1.0
CD2 A:HIS175 2.9 11.1 1.0
CE1 A:HIS175 3.1 10.9 1.0
CG A:HIS203 3.1 9.6 1.0
CD2 A:HIS190 3.1 8.5 1.0
OD2 A:ASP177 3.2 12.6 1.0
CB A:HIS203 3.5 8.7 1.0
NE2 A:HIS203 4.1 10.3 1.0
ND1 A:HIS190 4.1 9.1 1.0
CG A:HIS175 4.1 11.6 1.0
ND1 A:HIS175 4.1 12.5 1.0
CD2 A:HIS203 4.2 10.4 1.0
CG A:HIS190 4.2 8.8 1.0
CB A:ASP177 4.2 13.3 1.0
O A:TYR179 4.3 10.9 1.0
CE1 A:PHE192 4.4 12.2 1.0
O A:HOH484 4.5 17.6 1.0
CZ A:PHE181 4.6 9.2 1.0
CZ A:PHE192 4.6 10.3 1.0
CE2 A:PHE181 4.7 10.7 1.0
CA A:HIS203 4.9 6.4 1.0
O A:HOH414 5.0 12.7 1.0

Zinc binding site 3 out of 4 in 4jij

Go back to Zinc Binding Sites List in 4jij
Zinc binding site 3 out of 4 in the Crystal Structure of An Inactive Mutant of Mmp-9 Catalytic Domain in Complex with A Fluorogenic Synthetic Peptidic Substrate


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 An Inactive Mutant of Mmp-9 Catalytic Domain in Complex with A Fluorogenic Synthetic Peptidic Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:12.6
occ:1.00
 NE2 B:HIS236 2.0 10.6 1.0
N1 Q:AZI101 2.0 15.7 1.0
NE2 B:HIS230 2.0 12.7 1.0
NE2 B:HIS226 2.0 10.4 1.0
CD2 B:HIS236 2.9 11.2 1.0
CD2 B:HIS226 2.9 10.6 1.0
CD2 B:HIS230 3.0 12.2 1.0
CE1 B:HIS236 3.0 14.3 1.0
N2 Q:AZI101 3.0 19.6 1.0
CE1 B:HIS230 3.1 10.4 1.0
CE1 B:HIS226 3.1 12.8 1.0
O Q:GLY4 3.4 19.5 1.0
C Q:GLY4 3.8 18.5 1.0
CG B:HIS236 4.0 15.0 1.0
ND1 B:HIS236 4.0 13.9 1.0
N3 Q:AZI101 4.1 18.5 1.0
CG B:HIS230 4.1 12.2 1.0
CG B:HIS226 4.1 9.5 1.0
ND1 B:HIS230 4.1 12.1 1.0
N Q:PHI5 4.2 15.0 1.0
ND1 B:HIS226 4.2 10.2 1.0
CA Q:PHI5 4.3 16.8 1.0
CB Q:PHI5 4.3 13.9 1.0
N Q:GLY4 4.4 14.1 1.0
CB Q:LEU3 4.4 13.7 1.0
C Q:LEU3 4.4 13.6 1.0
O Q:LEU3 4.5 16.9 1.0
CD1 Q:PHI5 4.5 13.4 1.0
CA Q:GLY4 4.5 14.8 1.0
CG Q:PHI5 4.7 14.1 1.0
CE B:MET244 4.7 10.5 1.0

Zinc binding site 4 out of 4 in 4jij

Go back to Zinc Binding Sites List in 4jij
Zinc binding site 4 out of 4 in the Crystal Structure of An Inactive Mutant of Mmp-9 Catalytic Domain in Complex with A Fluorogenic Synthetic Peptidic Substrate


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 An Inactive Mutant of Mmp-9 Catalytic Domain in Complex with A Fluorogenic Synthetic Peptidic Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:14.8
occ:1.00
 OD1 B:ASP177 2.0 16.0 1.0
ND1 B:HIS203 2.0 16.7 1.0
NE2 B:HIS190 2.1 14.0 1.0
NE2 B:HIS175 2.1 12.0 1.0
CG B:ASP177 2.9 18.4 1.0
CE1 B:HIS190 2.9 16.4 1.0
CD2 B:HIS175 3.0 15.2 1.0
CE1 B:HIS203 3.0 15.6 1.0
CG B:HIS203 3.1 16.1 1.0
CE1 B:HIS175 3.1 17.1 1.0
CD2 B:HIS190 3.1 13.6 1.0
OD2 B:ASP177 3.3 19.0 1.0
CB B:HIS203 3.4 12.1 1.0
NE2 B:HIS203 4.1 15.3 1.0
ND1 B:HIS190 4.1 12.9 1.0
CG B:HIS175 4.1 17.0 1.0
ND1 B:HIS175 4.1 18.3 1.0
CD2 B:HIS203 4.2 11.5 1.0
CG B:HIS190 4.2 12.9 1.0
CB B:ASP177 4.2 21.5 1.0
O B:TYR179 4.3 17.8 1.0
CE1 B:PHE192 4.4 12.0 1.0
CZ B:PHE192 4.5 14.6 1.0
CZ B:PHE181 4.5 12.4 1.0
CE2 B:PHE181 4.8 16.1 1.0
O B:HOH432 4.8 16.7 1.0
CA B:HIS203 5.0 13.1 1.0

Reference:

I.Tranchant, L.Vera, B.Czarny, M.Amoura, E.Cassar, F.Beau, E.A.Stura, V.Dive. Halogen Bonding Controls Selectivity of Fret Substrate Probes For Mmp-9. Chem.Biol. V. 21 408 2014.
ISSN: ISSN 1074-5521
PubMed: 24583051
DOI: 10.1016/J.CHEMBIOL.2014.01.008
Page generated: Sun Oct 27 01:17:56 2024

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