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Calcium 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
Zinc (Zn) 4 atoms
Sodium (Na) 3 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 with A Fluorine Atom. (pdb code 4jqg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 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 with A Fluorine Atom., PDB code: 4jqg:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4jqg

Go back to Calcium Binding Sites List in 4jqg
Calcium binding site 1 out of 3 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 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 with A Fluorine Atom. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:15.8
occ:1.00
 OE2 A:GLU208 2.2 14.9 1.0
O A:ASP185 2.3 18.0 1.0
O A:GLY183 2.3 20.0 1.0
OD2 A:ASP205 2.3 17.2 1.0
O A:LEU187 2.3 14.2 1.0
OD1 A:ASP182 2.4 14.1 1.0
CG A:ASP205 3.4 11.4 1.0
CD A:GLU208 3.4 16.1 1.0
C A:ASP185 3.4 17.7 1.0
C A:LEU187 3.5 17.6 1.0
C A:GLY183 3.5 18.8 1.0
CG A:ASP182 3.5 16.6 1.0
N A:ASP185 3.9 16.4 1.0
N A:LEU187 3.9 12.8 1.0
CB A:ASP205 3.9 8.9 1.0
N A:GLY183 4.0 18.6 1.0
C A:LYS184 4.1 17.3 1.0
OD2 A:ASP182 4.1 19.6 1.0
OE1 A:GLU208 4.2 15.0 1.0
CA A:ASP185 4.2 19.3 1.0
CA A:LEU187 4.2 14.4 1.0
C A:GLY186 4.3 13.1 1.0
N A:ASP182 4.3 16.5 1.0
CG A:GLU208 4.3 17.3 1.0
C A:ASP182 4.3 18.0 1.0
OD1 A:ASP205 4.3 17.6 1.0
CA A:GLY183 4.4 16.1 1.0
N A:LYS184 4.4 13.2 1.0
O A:LYS184 4.4 18.0 1.0
N A:GLY186 4.5 17.3 1.0
CA A:LYS184 4.5 20.1 1.0
O A:HOH541 4.5 29.9 1.0
N A:LEU188 4.5 14.0 1.0
CA A:GLY186 4.6 14.7 1.0
CA A:ASP182 4.7 18.3 1.0
CB A:LEU187 4.7 17.1 1.0
CA A:LEU188 4.7 12.0 1.0
CB A:ASP182 4.7 19.0 1.0
O A:GLY186 4.8 15.7 1.0
O A:ASP182 4.9 16.4 1.0
CD2 A:LEU188 5.0 18.1 1.0

Calcium binding site 2 out of 3 in 4jqg

Go back to Calcium Binding Sites List in 4jqg
Calcium binding site 2 out of 3 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 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 with A Fluorine Atom. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:31.8
occ:1.00
 O A:HOH577 2.1 22.0 1.0
O A:GLU208 2.3 15.5 1.0
O1 A:PGO312 2.4 23.5 1.0
OD2 A:ASP131 2.5 18.5 1.0
O A:ASP206 2.7 15.8 1.0
CG A:ASP131 3.4 20.6 1.0
C A:GLU208 3.4 19.2 1.0
C1 A:PGO312 3.5 30.4 1.0
OD1 A:ASP131 3.6 19.5 1.0
C2 A:PGO312 3.6 31.9 1.0
C A:ASP206 3.8 17.6 1.0
O A:HOH457 3.8 25.7 1.0
O A:HOH427 3.8 21.2 1.0
O A:HOH419 4.0 35.8 1.0
OG A:SER129 4.1 19.1 1.0
N A:GLU208 4.2 15.1 1.0
C A:ASP207 4.2 20.7 1.0
N A:LEU209 4.2 13.6 1.0
OD1 A:ASP206 4.2 20.4 1.0
CA A:LEU209 4.3 14.3 1.0
C3 A:PGO312 4.4 34.9 1.0
CA A:GLU208 4.4 12.4 1.0
O A:ASP207 4.5 20.2 1.0
CA A:ASP207 4.6 14.4 1.0
CD1 A:TRP210 4.6 10.2 1.0
N A:ASP207 4.6 18.7 1.0
CA A:ASP206 4.6 12.6 1.0
O2 A:PGO312 4.7 39.4 1.0
CB A:ASP131 4.7 13.8 1.0
N A:TRP210 4.7 13.6 1.0
CG A:ASP206 4.9 24.0 1.0

Calcium binding site 3 out of 3 in 4jqg

Go back to Calcium Binding Sites List in 4jqg
Calcium binding site 3 out of 3 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 Calcium with other atoms in the Ca 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:Ca303

b:19.8
occ:1.00
 OE2 B:GLU208 2.2 30.6 1.0
O B:LEU187 2.3 18.8 1.0
OD2 B:ASP205 2.3 18.1 1.0
O B:ASP185 2.3 22.2 1.0
O B:GLY183 2.3 26.1 1.0
OD1 B:ASP182 2.4 29.0 1.0
CG B:ASP205 3.4 21.0 1.0
C B:LEU187 3.4 19.8 1.0
C B:ASP185 3.4 24.7 1.0
CD B:GLU208 3.5 26.4 1.0
CG B:ASP182 3.5 22.9 1.0
C B:GLY183 3.6 28.4 1.0
N B:ASP185 3.8 25.2 1.0
N B:LEU187 3.9 22.4 1.0
CB B:ASP205 4.0 19.9 1.0
C B:LYS184 4.0 29.8 1.0
OD2 B:ASP182 4.1 25.1 1.0
CA B:LEU187 4.2 21.5 1.0
CA B:ASP185 4.2 24.2 1.0
N B:GLY183 4.2 21.9 1.0
N B:ASP182 4.2 23.9 1.0
C B:ASP182 4.3 28.0 1.0
C B:GLY186 4.3 23.2 1.0
CG B:GLU208 4.3 25.2 1.0
OE1 B:GLU208 4.3 24.0 1.0
OD1 B:ASP205 4.3 22.5 1.0
O B:LYS184 4.4 31.2 1.0
N B:LEU188 4.4 17.4 1.0
N B:LYS184 4.5 26.0 1.0
CA B:GLY183 4.5 22.1 1.0
N B:GLY186 4.5 18.9 1.0
CB B:LEU187 4.5 20.9 1.0
CA B:LYS184 4.5 28.4 1.0
CA B:LEU188 4.6 19.3 1.0
CA B:ASP182 4.6 27.9 1.0
O B:ASP182 4.6 22.8 1.0
CA B:GLY186 4.7 26.4 1.0
CB B:ASP182 4.7 22.9 1.0
O B:HOH550 4.8 35.3 1.0
O B:GLY186 4.8 22.5 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 Jul 14 08:35:35 2024

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