Calcium 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
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium 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 Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4jij

Go back to Calcium Binding Sites List in 4jij
Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca304

b:10.9
occ:1.00
 O A:GLY183 2.2 13.3 1.0
OE2 A:GLU208 2.2 15.0 1.0
O A:ASP185 2.3 15.3 1.0
OD2 A:ASP205 2.3 10.7 1.0
O A:LEU187 2.3 11.9 1.0
OD1 A:ASP182 2.4 12.0 1.0
CG A:ASP205 3.4 10.4 1.0
C A:LEU187 3.4 13.4 1.0
C A:ASP185 3.4 13.9 1.0
C A:GLY183 3.5 17.6 1.0
CD A:GLU208 3.5 14.3 1.0
CG A:ASP182 3.5 16.3 1.0
N A:LEU187 3.8 11.7 1.0
N A:ASP185 3.9 17.4 1.0
N A:GLY183 4.0 12.2 1.0
CB A:ASP205 4.0 8.8 1.0
OD2 A:ASP182 4.0 17.4 1.0
C A:LYS184 4.1 17.0 1.0
CA A:LEU187 4.1 11.1 1.0
CA A:ASP185 4.2 16.9 1.0
C A:GLY186 4.2 13.1 1.0
OE1 A:GLU208 4.3 18.2 1.0
N A:ASP182 4.3 11.4 1.0
OD1 A:ASP205 4.3 10.7 1.0
C A:ASP182 4.3 15.4 1.0
CA A:GLY183 4.3 17.4 1.0
CG A:GLU208 4.4 14.6 1.0
N A:LYS184 4.4 17.1 1.0
O A:LYS184 4.5 17.4 1.0
N A:GLY186 4.5 13.3 1.0
CA A:LYS184 4.5 18.5 1.0
N A:LEU188 4.5 9.8 1.0
O A:HOH557 4.5 30.6 1.0
CB A:LEU187 4.6 11.2 1.0
CA A:GLY186 4.6 12.9 1.0
CA A:ASP182 4.6 13.5 1.0
CB A:ASP182 4.7 15.1 1.0
CA A:LEU188 4.7 8.6 1.0
O A:GLY186 4.8 13.1 1.0
O A:ASP182 4.8 15.9 1.0

Calcium binding site 2 out of 2 in 4jij

Go back to Calcium Binding Sites List in 4jij
Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca 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
B:Ca303

b:13.4
occ:1.00
 OE2 B:GLU208 2.1 19.4 1.0
O B:GLY183 2.3 17.4 1.0
O B:LEU187 2.3 15.8 1.0
OD2 B:ASP205 2.3 14.2 1.0
O B:ASP185 2.3 18.7 1.0
OD1 B:ASP182 2.4 17.5 1.0
CD B:GLU208 3.4 18.2 1.0
C B:LEU187 3.4 14.5 1.0
CG B:ASP205 3.4 17.4 1.0
C B:GLY183 3.5 21.3 1.0
C B:ASP185 3.5 20.3 1.0
CG B:ASP182 3.6 21.4 1.0
N B:LEU187 3.8 16.5 1.0
N B:ASP185 3.9 20.2 1.0
N B:GLY183 4.0 17.4 1.0
C B:LYS184 4.1 20.7 1.0
CB B:ASP205 4.1 13.9 1.0
OE1 B:GLU208 4.1 21.2 1.0
CA B:LEU187 4.1 14.5 1.0
OD2 B:ASP182 4.1 21.3 1.0
CA B:ASP185 4.2 17.7 1.0
C B:GLY186 4.3 18.5 1.0
C B:ASP182 4.3 22.1 1.0
N B:ASP182 4.3 16.7 1.0
CA B:GLY183 4.3 17.2 1.0
OD1 B:ASP205 4.4 15.8 1.0
CG B:GLU208 4.4 17.1 1.0
N B:LEU188 4.4 12.6 1.0
N B:LYS184 4.4 18.0 1.0
O B:LYS184 4.4 20.9 1.0
CA B:LYS184 4.5 21.8 1.0
N B:GLY186 4.5 17.6 1.0
CB B:LEU187 4.6 16.3 1.0
CA B:LEU188 4.6 10.3 1.0
CA B:GLY186 4.7 17.4 1.0
CA B:ASP182 4.7 22.3 1.0
O B:ASP182 4.7 22.4 1.0
CB B:ASP182 4.8 23.1 1.0
O B:GLY186 4.9 17.8 1.0
O B:HOH555 4.9 32.0 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: Sat Dec 12 04:53:15 2020

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