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

Strontium binding site 1 out of 3 in 4jqg

Go back to Strontium Binding Sites List in 4jqg
Strontium 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 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 with A Fluorine Atom. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr304

b:22.2
occ:1.00
 O A:ASP165 2.5 15.4 1.0
O A:GLY197 2.6 18.7 1.0
O A:GLN199 2.6 10.5 1.0
OD1 A:ASP201 2.6 13.5 1.0
O A:HOH581 2.6 25.7 1.0
O A:HOH562 2.7 16.4 1.0
O A:HOH414 3.0 22.9 1.0
CG A:ASP201 3.6 13.7 1.0
C A:ASP165 3.6 17.1 1.0
C A:GLY197 3.8 15.1 1.0
C A:GLN199 3.8 11.6 1.0
O A:ALA164 3.8 22.3 1.0
OD2 A:ASP201 3.9 12.0 1.0
C A:ILE198 4.2 14.9 1.0
O A:ILE198 4.3 13.5 1.0
CA A:ASP165 4.3 15.3 1.0
N A:GLN199 4.3 12.5 1.0
N A:ASP201 4.4 12.1 1.0
CA A:GLY200 4.5 12.9 1.0
N A:ILE166 4.5 13.8 1.0
N A:GLY200 4.6 13.3 1.0
CA A:ILE198 4.6 13.9 1.0
C A:GLY200 4.6 12.5 1.0
N A:GLY197 4.6 16.9 1.0
N A:ILE198 4.6 13.8 1.0
CA A:GLY197 4.7 12.9 1.0
O A:GLY195 4.7 13.9 1.0
N A:VAL167 4.7 13.6 1.0
CA A:GLN199 4.7 13.4 1.0
CA A:ILE166 4.7 11.3 1.0
C A:ALA164 4.8 16.3 1.0
CB A:ASP201 4.8 13.5 1.0
O A:HOH501 4.9 26.0 1.0
O A:HOH548 4.9 31.4 1.0
C A:PRO196 4.9 17.0 1.0
O A:HOH449 4.9 14.6 1.0
CA A:ASP201 5.0 12.5 1.0

Strontium binding site 2 out of 3 in 4jqg

Go back to Strontium Binding Sites List in 4jqg
Strontium 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 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 with A Fluorine Atom. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr304

b:27.0
occ:1.00
 O B:GLY197 2.5 16.4 1.0
O B:HOH448 2.5 11.4 1.0
OD1 B:ASP201 2.5 15.1 1.0
O B:ASP165 2.6 12.8 1.0
O B:GLN199 2.6 11.8 1.0
O B:HOH451 2.9 30.5 1.0
O B:ALA164 3.3 21.7 1.0
C B:ASP165 3.4 15.6 1.0
CG B:ASP201 3.5 20.4 1.0
C B:GLY197 3.7 22.7 1.0
C B:GLN199 3.8 15.6 1.0
OD2 B:ASP201 3.9 17.1 1.0
O B:HOH542 4.0 23.1 1.0
CA B:ASP165 4.1 15.3 1.0
C B:ILE198 4.3 12.5 1.0
N B:ASP201 4.3 16.1 1.0
O B:HOH452 4.3 36.0 1.0
C B:ALA164 4.4 22.1 1.0
N B:ILE166 4.4 14.3 1.0
N B:GLN199 4.4 15.5 1.0
N B:GLY197 4.4 22.1 1.0
O B:GLY195 4.4 16.4 1.0
N B:VAL167 4.4 14.9 1.0
O B:ILE198 4.5 15.7 1.0
CA B:GLY197 4.5 26.4 1.0
CA B:GLY200 4.5 12.0 1.0
CG2 B:VAL167 4.6 15.9 1.0
O B:HOH411 4.6 23.9 1.0
C B:GLY200 4.6 14.4 1.0
N B:GLY200 4.6 13.5 1.0
N B:ILE198 4.6 18.4 1.0
CA B:ILE166 4.7 12.3 1.0
CA B:ILE198 4.7 24.1 1.0
CA B:GLN199 4.7 13.7 1.0
N B:ASP165 4.7 16.0 1.0
CB B:ASP201 4.8 19.2 1.0
CA B:ASP201 4.9 13.6 1.0
C B:PRO196 4.9 15.9 1.0

Strontium binding site 3 out of 3 in 4jqg

Go back to Strontium Binding Sites List in 4jqg
Strontium 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 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 with A Fluorine Atom. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr305

b:28.9
occ:1.00
 O B:GLU208 2.4 24.5 1.0
O B:ASP206 2.6 28.9 1.0
O B:HOH420 2.6 30.1 1.0
OD2 B:ASP131 2.6 20.5 1.0
O1 B:PGO306 2.6 29.0 1.0
OD1 B:ASP206 2.7 22.1 1.0
OD1 B:ASP131 2.7 24.2 1.0
O2 B:PGO306 2.8 34.0 1.0
CG B:ASP131 3.0 24.2 1.0
C1 B:PGO306 3.1 34.5 1.0
C2 B:PGO306 3.5 32.4 1.0
C B:ASP206 3.5 28.0 1.0
C B:GLU208 3.6 24.5 1.0
CG B:ASP206 3.7 23.8 1.0
CA B:ASP206 4.2 21.5 1.0
OG B:SER129 4.3 18.2 1.0
N B:GLU208 4.3 19.0 1.0
CA B:LEU209 4.4 27.9 1.0
N B:LEU209 4.4 25.2 1.0
C B:ASP207 4.4 29.3 1.0
CD1 B:TRP210 4.4 19.3 1.0
O B:HOH588 4.4 22.2 0.5
N B:ASP207 4.4 21.6 1.0
OD2 B:ASP206 4.5 23.8 1.0
O B:HOH431 4.5 30.4 1.0
CB B:ASP206 4.5 18.5 1.0
CB B:ASP131 4.5 20.7 1.0
CA B:GLU208 4.6 22.3 1.0
CA B:ASP207 4.6 21.3 1.0
O B:HOH588 4.6 21.1 0.5
O B:HOH574 4.7 30.5 1.0
N B:TRP210 4.8 25.8 1.0
C3 B:PGO306 4.8 31.5 1.0
O B:ASP207 4.9 26.0 1.0
NE1 B:TRP210 5.0 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: Wed Dec 16 02:24:00 2020

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