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

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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

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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

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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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