Atomistry » Zinc » PDB 4je8-4jsa » 4jij
Atomistry »
  Zinc »
    PDB 4je8-4jsa »
      4jij »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy