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Strontium 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:

Iodine (I) 2 atoms
Calcium (Ca) 2 atoms
Zinc (Zn) 4 atoms

Strontium Binding Sites:

The binding sites of Strontium 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 Strontium atom.
In total 4 binding sites of Strontium 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 Strontium binding site number: 1; 2; 3; 4;

Strontium binding site 1 out of 4 in 4jij

Go back to Strontium Binding Sites List in 4jij
Strontium 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 Strontium with other atoms in the Sr 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:Sr305

b:14.3
occ:1.00
 O A:ASP165 2.5 13.3 1.0
O A:GLY197 2.5 14.3 1.0
O A:HOH455 2.5 13.1 1.0
O A:HOH565 2.5 21.0 1.0
O A:GLN199 2.5 9.9 1.0
OD1 A:ASP201 2.6 10.2 1.0
O A:HOH418 2.7 17.2 1.0
C A:ASP165 3.5 8.9 1.0
CG A:ASP201 3.6 14.2 1.0
C A:GLY197 3.7 14.1 1.0
O A:ALA164 3.7 19.4 1.0
C A:GLN199 3.7 8.4 1.0
OD2 A:ASP201 3.9 12.0 1.0
C A:ILE198 4.3 9.3 1.0
CA A:ASP165 4.3 11.2 1.0
N A:GLN199 4.4 8.8 1.0
O A:ILE198 4.4 11.0 1.0
O A:HOH513 4.4 29.2 1.0
N A:GLY197 4.5 13.2 1.0
CA A:GLY200 4.5 8.9 1.0
N A:ASP201 4.5 9.0 1.0
N A:ILE166 4.5 9.4 1.0
CA A:GLY197 4.6 14.5 1.0
N A:GLY200 4.6 8.4 1.0
O A:GLY195 4.6 13.5 1.0
N A:ILE198 4.6 11.1 1.0
C A:GLY200 4.6 10.9 1.0
CA A:ILE198 4.6 11.4 1.0
N A:VAL167 4.6 8.4 1.0
CA A:GLN199 4.7 9.8 1.0
CA A:ILE166 4.7 8.6 1.0
C A:ALA164 4.8 13.5 1.0
O A:HOH566 4.8 36.0 1.0
CB A:ASP201 4.8 9.5 1.0
C A:PRO196 4.9 15.1 1.0
CG2 A:VAL167 5.0 12.3 1.0

Strontium binding site 2 out of 4 in 4jij

Go back to Strontium Binding Sites List in 4jij
Strontium 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 Strontium with other atoms in the Sr 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:Sr306

b:20.3
occ:1.00
 O A:GLU208 2.4 12.7 1.0
O1 A:PGO307 2.5 16.9 1.0
O A:ASP206 2.5 12.1 1.0
O2 A:PGO307 2.6 22.5 1.0
OD2 A:ASP131 2.6 14.8 1.0
O A:HOH434 2.6 24.4 1.0
OD1 A:ASP206 2.7 20.6 1.0
OD1 A:ASP131 3.0 26.5 1.0
CG A:ASP131 3.1 18.4 1.0
C1 A:PGO307 3.4 25.2 1.0
C2 A:PGO307 3.5 26.9 1.0
C A:ASP206 3.6 13.3 1.0
C A:GLU208 3.6 11.9 1.0
CG A:ASP206 3.7 19.3 1.0
OG A:SER129 4.1 13.6 1.0
CA A:ASP206 4.2 11.7 1.0
N A:GLU208 4.3 11.7 1.0
N A:LEU209 4.4 12.2 1.0
CA A:LEU209 4.4 12.0 1.0
O A:HOH423 4.4 36.3 1.0
C A:ASP207 4.4 13.2 1.0
O A:HOH433 4.5 19.2 1.0
OD2 A:ASP206 4.5 20.2 1.0
CB A:ASP206 4.5 15.6 1.0
N A:ASP207 4.5 12.4 1.0
CA A:GLU208 4.6 11.5 1.0
CD1 A:TRP210 4.6 12.1 1.0
CB A:ASP131 4.6 15.0 1.0
CA A:ASP207 4.7 13.8 1.0
C3 A:PGO307 4.7 33.2 1.0
O A:HOH424 4.8 28.6 1.0
N A:TRP210 4.9 11.8 1.0
O A:ASP207 4.9 16.7 1.0

Strontium binding site 3 out of 4 in 4jij

Go back to Strontium Binding Sites List in 4jij
Strontium 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 Strontium with other atoms in the Sr 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:Sr304

b:17.9
occ:1.00
 O B:GLY197 2.4 14.6 1.0
O B:ASP165 2.5 12.6 1.0
O B:HOH451 2.5 12.9 1.0
O B:HOH455 2.5 21.0 1.0
OD1 B:ASP201 2.5 12.2 1.0
O B:GLN199 2.6 12.4 1.0
O B:ALA164 3.2 16.2 1.0
C B:ASP165 3.4 14.2 1.0
CG B:ASP201 3.5 13.7 1.0
C B:GLY197 3.6 15.6 1.0
C B:GLN199 3.7 12.4 1.0
OD2 B:ASP201 3.9 12.9 1.0
CA B:ASP165 4.1 13.4 1.0
O B:HOH548 4.2 23.9 1.0
C B:ILE198 4.2 12.3 1.0
C B:ALA164 4.3 17.9 1.0
O B:ILE198 4.3 14.2 1.0
N B:ASP201 4.4 13.4 1.0
N B:ILE166 4.4 11.6 1.0
N B:GLN199 4.4 12.6 1.0
N B:GLY197 4.4 15.3 1.0
CA B:GLY200 4.5 11.9 1.0
O B:GLY195 4.5 13.5 1.0
CA B:GLY197 4.5 17.0 1.0
N B:VAL167 4.5 10.3 1.0
N B:GLY200 4.5 10.2 1.0
C B:GLY200 4.5 12.9 1.0
N B:ILE198 4.6 14.0 1.0
CG2 B:VAL167 4.7 15.3 1.0
CA B:ILE198 4.7 15.2 1.0
CA B:GLN199 4.7 11.4 1.0
CA B:ILE166 4.7 8.0 1.0
N B:ASP165 4.7 11.9 1.0
CB B:ASP201 4.8 9.6 1.0
O B:HOH411 4.9 19.6 1.0
C B:PRO196 4.9 15.9 1.0
CA B:ASP201 4.9 10.7 1.0

Strontium binding site 4 out of 4 in 4jij

Go back to Strontium Binding Sites List in 4jij
Strontium 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 Strontium with other atoms in the Sr 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:Sr305

b:17.5
occ:1.00
 O B:GLU208 2.5 18.8 1.0
O B:ASP206 2.5 20.1 1.0
OD2 B:ASP131 2.5 18.7 1.0
O B:HOH422 2.6 18.1 1.0
O1 B:PGO306 2.6 20.6 1.0
OD1 B:ASP206 2.6 16.4 1.0
O2 B:PGO306 2.6 19.6 1.0
OD1 B:ASP131 2.7 18.1 1.0
CG B:ASP131 3.0 16.5 1.0
C B:ASP206 3.5 17.7 1.0
CG B:ASP206 3.5 15.6 1.0
C1 B:PGO306 3.6 25.4 1.0
C2 B:PGO306 3.6 21.0 1.0
C B:GLU208 3.6 18.3 1.0
CA B:ASP206 4.1 15.8 1.0
OG B:SER129 4.2 15.7 1.0
O B:HOH541 4.3 28.2 1.0
OD2 B:ASP206 4.3 19.1 1.0
N B:GLU208 4.4 14.3 1.0
CB B:ASP206 4.4 14.8 1.0
N B:LEU209 4.4 16.0 1.0
CA B:LEU209 4.4 18.6 1.0
CB B:ASP131 4.5 15.4 1.0
CD1 B:TRP210 4.5 14.0 1.0
N B:ASP207 4.5 15.7 1.0
C B:ASP207 4.5 20.3 1.0
O B:HOH573 4.6 29.4 1.0
CA B:GLU208 4.6 16.6 1.0
C3 B:PGO306 4.7 25.4 1.0
CA B:ASP207 4.7 16.1 1.0
N B:TRP210 4.8 15.7 1.0
O B:HOH423 5.0 19.5 0.4

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: Fri Oct 11 05:35:08 2024

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