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 / R_free (%)*	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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0

	© Copyright 2008-2020 by atomistry.com
Home \| Site Map \| Copyright \| Contact us \| Privacy