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Sodium 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
Calcium (Ca) 3 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 3 in 4jqg

Go back to Sodium Binding Sites List in 4jqg
Sodium 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 Sodium with other atoms in the Na 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
B:Na309

b:21.6
occ:1.00
O B:HOH464 2.3 32.5 1.0
O B:HOH593 3.0 24.2 1.0
O B:HOH402 3.0 16.9 1.0
O A:HOH432 3.0 15.9 1.0
CD B:PRO255 3.4 17.5 1.0
CD A:PRO255 3.6 20.2 1.0
CD2 A:LEU147 3.7 17.4 1.0
CA B:PRO254 3.9 17.8 1.0
CB A:PRO254 4.0 18.8 1.0
O A:HOH433 4.0 12.6 1.0
CD2 B:LEU147 4.0 21.5 1.0
CA A:PRO254 4.1 16.8 1.0
CB B:PRO254 4.1 17.7 1.0
N B:PRO255 4.3 20.0 1.0
N A:PRO255 4.5 18.0 1.0
C B:PRO254 4.6 14.5 1.0
CG B:PRO255 4.6 21.6 1.0
C A:PRO254 4.8 18.2 1.0
CG A:PRO255 4.8 18.6 1.0
CG B:PRO254 4.9 21.5 1.0
CG A:PRO254 5.0 22.6 1.0
N B:PRO254 5.0 19.0 1.0

Sodium binding site 2 out of 3 in 4jqg

Go back to Sodium Binding Sites List in 4jqg
Sodium 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 Sodium with other atoms in the Na 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:Na310

b:35.4
occ:1.00
O B:HOH584 2.3 28.8 1.0
O B:HOH510 2.6 30.1 1.0
O B:HOH435 2.7 27.5 1.0
O B:HOH433 2.8 23.2 1.0
O B:HOH434 2.9 24.1 1.0
O B:ALA242 3.8 17.4 1.0
CA B:LEU243 3.9 17.9 1.0
NE B:ARG249 4.0 26.5 0.5
O B:HOH558 4.1 30.3 1.0
CG B:ARG249 4.1 26.9 0.5
CD1 B:LEU243 4.3 14.9 1.0
O B:ARG249 4.3 26.4 0.6
O B:ARG249 4.3 27.0 0.5
C B:ALA242 4.4 16.2 1.0
NH1 B:ARG249 4.4 25.7 0.5
F Q:PFF5 4.4 20.2 1.0
CZ B:ARG249 4.4 29.2 0.5
N B:LEU243 4.5 13.8 1.0
O B:LEU243 4.5 14.5 1.0
O B:GLU241 4.5 27.8 1.0
C B:LEU243 4.6 11.8 1.0
CD B:ARG249 4.7 30.4 0.5
CG2 B:THR251 4.7 35.4 1.0
CB B:LEU243 4.8 14.8 1.0

Sodium binding site 3 out of 3 in 4jqg

Go back to Sodium Binding Sites List in 4jqg
Sodium 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 Sodium with other atoms in the Na 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:Na311

b:30.1
occ:1.00
N B:HIS117 3.1 16.5 1.0
ND1 B:HIS118 3.3 22.7 1.0
O B:HOH427 3.4 35.7 1.0
O B:HOH419 3.7 22.1 1.0
CB B:HIS117 3.8 21.9 1.0
CE1 B:HIS118 3.8 17.7 1.0
CA B:HIS117 3.8 16.8 1.0
CE3 B:TRP116 3.9 14.8 1.0
CA B:TRP116 4.0 10.1 1.0
C B:TRP116 4.0 17.1 1.0
N B:HIS118 4.2 16.9 1.0
C B:HIS117 4.2 17.1 1.0
CD2 B:HIS117 4.3 19.0 1.0
CG B:HIS117 4.4 17.4 1.0
CG B:HIS118 4.6 18.8 1.0
O B:LYS115 4.6 12.6 1.0
CB B:TRP116 4.6 13.1 1.0
CZ3 B:TRP116 4.7 12.2 1.0
O B:HOH408 4.8 29.6 1.0
CD2 B:TRP116 4.9 9.8 1.0
O B:HIS117 4.9 18.3 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: Mon Oct 7 16:20:55 2024

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