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

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

All present enzymatic activity of Crystal Structure of An Inactive Mutant of Mmp-9 Catalytic Domain in Complex with A Fluorogenic Synthetic Peptidic Substrate with A Fluorine Atom.:
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 with A Fluorine Atom., PDB code: 4jqg 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) 40.52 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 34.140, 57.480, 171.420, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.2

Other elements in 4jqg:

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

Fluorine (F) 2 atoms
Strontium (Sr) 3 atoms
Calcium (Ca) 3 atoms
Sodium (Na) 3 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 with A Fluorine Atom. (pdb code 4jqg). 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 with A Fluorine Atom., PDB code: 4jqg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4jqg

Go back to Zinc Binding Sites List in 4jqg
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 with A Fluorine Atom.


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 with A Fluorine Atom. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:14.8
occ:1.00
 NE2 A:HIS236 2.0 15.2 1.0
NE2 A:HIS226 2.0 11.3 1.0
N3 P:AZI600 2.0 18.3 1.0
NE2 A:HIS230 2.1 17.3 1.0
CD2 A:HIS236 2.9 14.4 1.0
CD2 A:HIS226 2.9 12.7 1.0
CE1 A:HIS226 3.0 11.8 1.0
N2 P:AZI600 3.0 13.6 1.0
CD2 A:HIS230 3.0 12.7 1.0
CE1 A:HIS236 3.0 21.4 1.0
CE1 A:HIS230 3.2 15.7 1.0
O P:GLY4 3.4 17.2 1.0
C P:GLY4 3.8 15.6 1.0
CG A:HIS236 4.0 18.2 1.0
ND1 A:HIS236 4.1 15.7 1.0
N1 P:AZI600 4.1 13.1 1.0
ND1 A:HIS226 4.1 13.6 1.0
CG A:HIS226 4.1 16.9 1.0
CG A:HIS230 4.2 11.8 1.0
N P:PFF5 4.2 13.4 1.0
CA P:PFF5 4.2 15.1 1.0
ND1 A:HIS230 4.2 16.1 1.0
CB P:PFF5 4.3 14.3 1.0
CB P:LEU3 4.3 13.8 1.0
CD2 P:PFF5 4.3 11.9 1.0
N P:GLY4 4.4 16.0 1.0
C P:LEU3 4.4 15.7 1.0
O P:LEU3 4.5 14.5 1.0
CA P:GLY4 4.6 13.2 1.0
CG P:PFF5 4.6 20.1 1.0
CE A:MET244 4.7 15.0 1.0

Zinc binding site 2 out of 4 in 4jqg

Go back to Zinc Binding Sites List in 4jqg
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 with A Fluorine Atom.


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 with A Fluorine Atom. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:12.3
occ:1.00
 OD1 A:ASP177 1.9 12.3 1.0
NE2 A:HIS190 2.0 12.0 1.0
ND1 A:HIS203 2.0 10.0 1.0
NE2 A:HIS175 2.0 14.0 1.0
CD2 A:HIS175 2.9 15.9 1.0
CG A:ASP177 2.9 12.5 1.0
CE1 A:HIS190 2.9 11.3 1.0
CE1 A:HIS203 3.0 12.2 1.0
CD2 A:HIS190 3.1 12.5 1.0
CG A:HIS203 3.1 12.3 1.0
CE1 A:HIS175 3.1 18.1 1.0
OD2 A:ASP177 3.3 12.9 1.0
CB A:HIS203 3.4 11.1 1.0
ND1 A:HIS190 4.1 11.8 1.0
CG A:HIS175 4.1 16.0 1.0
NE2 A:HIS203 4.1 10.6 1.0
CG A:HIS190 4.2 12.8 1.0
ND1 A:HIS175 4.2 17.1 1.0
CD2 A:HIS203 4.2 11.2 1.0
CB A:ASP177 4.2 14.3 1.0
O A:TYR179 4.3 13.8 1.0
CE1 A:PHE192 4.4 12.4 1.0
CZ A:PHE192 4.5 12.7 1.0
O A:HOH475 4.6 19.3 1.0
CZ A:PHE181 4.7 11.2 1.0
CE2 A:PHE181 4.8 15.4 1.0
O A:HOH412 4.9 16.5 1.0
CA A:HIS203 4.9 7.8 1.0

Zinc binding site 3 out of 4 in 4jqg

Go back to Zinc Binding Sites List in 4jqg
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 with A Fluorine Atom.


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 with A Fluorine Atom. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:15.2
occ:1.00
 N1 Q:AZI600 2.0 16.5 1.0
NE2 B:HIS236 2.0 17.1 1.0
NE2 B:HIS226 2.0 17.1 1.0
NE2 B:HIS230 2.1 13.6 1.0
CD2 B:HIS230 2.8 14.7 1.0
CD2 B:HIS236 2.9 13.5 1.0
CD2 B:HIS226 2.9 19.1 1.0
N2 Q:AZI600 3.0 27.1 1.0
CE1 B:HIS236 3.1 16.3 1.0
CE1 B:HIS226 3.1 14.3 1.0
CE1 B:HIS230 3.2 15.6 1.0
O Q:GLY4 3.4 20.6 1.0
C Q:GLY4 3.8 19.3 1.0
CG B:HIS236 4.0 19.5 1.0
ND1 B:HIS236 4.1 17.4 1.0
N3 Q:AZI600 4.1 21.5 1.0
CG B:HIS230 4.1 13.0 1.0
CG B:HIS226 4.1 13.8 1.0
ND1 B:HIS226 4.1 14.8 1.0
N Q:PFF5 4.2 18.3 1.0
ND1 B:HIS230 4.2 11.4 1.0
CA Q:PFF5 4.2 23.1 1.0
CB Q:PFF5 4.3 17.8 1.0
CD2 Q:PFF5 4.3 21.3 1.0
O Q:LEU3 4.4 19.9 1.0
CB Q:LEU3 4.4 20.8 1.0
C Q:LEU3 4.4 24.4 1.0
N Q:GLY4 4.4 18.8 1.0
CA Q:GLY4 4.6 18.1 1.0
CG Q:PFF5 4.6 18.8 1.0
CE B:MET244 4.6 16.0 1.0

Zinc binding site 4 out of 4 in 4jqg

Go back to Zinc Binding Sites List in 4jqg
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 with A Fluorine Atom.


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 with A Fluorine Atom. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:18.6
occ:1.00
 OD1 B:ASP177 1.9 24.2 1.0
NE2 B:HIS190 2.1 17.8 1.0
NE2 B:HIS175 2.1 18.9 1.0
ND1 B:HIS203 2.1 17.6 1.0
CD2 B:HIS175 2.9 21.8 1.0
CG B:ASP177 2.9 23.7 1.0
CE1 B:HIS190 2.9 19.4 1.0
CE1 B:HIS203 3.0 20.3 1.0
CG B:HIS203 3.1 17.3 1.0
CE1 B:HIS175 3.1 20.5 1.0
CD2 B:HIS190 3.1 18.0 1.0
OD2 B:ASP177 3.3 25.7 1.0
CB B:HIS203 3.5 14.7 1.0
CG B:HIS175 4.1 19.7 1.0
ND1 B:HIS190 4.1 20.1 1.0
NE2 B:HIS203 4.1 11.1 1.0
ND1 B:HIS175 4.2 19.6 1.0
O B:TYR179 4.2 21.8 1.0
CB B:ASP177 4.2 21.8 1.0
CD2 B:HIS203 4.2 14.4 1.0
CG B:HIS190 4.2 16.9 1.0
CE1 B:PHE192 4.4 16.0 1.0
CZ B:PHE181 4.5 15.5 1.0
CZ B:PHE192 4.5 18.0 1.0
CE2 B:PHE181 4.7 21.2 1.0
O B:HOH432 4.8 21.3 1.0
CA B:HIS203 4.9 17.6 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 01:23:41 2024

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