Sodium in PDB 3mmd: Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose

Enzymatic activity of Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose

All present enzymatic activity of Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose:
3.2.1.8;

Protein crystallography data

The structure of Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose, PDB code: 3mmd was solved by V.Solomon, G.Zolotnitsky, H.Feinberg, O.Tabachnikov, Y.Shoham, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	39.84 / 1.70
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	123.241, 61.856, 89.066, 90.00, 119.20, 90.00
*R / R_free (%)*	21.4 / 23.6

Other elements in 3mmd:

The structure of Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose (pdb code 3mmd). 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 the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose, PDB code: 3mmd:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3mmd

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Sodium Binding Sites List in 3mmd

Sodium binding site 1 out of 3 in the Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose

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 the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na410 b:13.4 occ:1.00	O	A:HOH556	2.2	25.1	1.0
	OD1	A:ASP297	2.3	24.0	1.0
	O	A:ALA374	2.3	18.9	1.0
	O	A:LYS379	2.4	28.0	1.0
	O	A:HOH520	2.5	22.8	1.0
	O	A:HOH584	2.5	26.5	1.0
	OD1	A:ASP377	2.5	26.5	1.0
	CG	A:ASP297	3.5	23.8	1.0
	C	A:ALA374	3.5	18.7	1.0
	CG	A:ASP377	3.5	25.4	1.0
	C	A:LYS379	3.5	29.4	1.0
	OD2	A:ASP377	3.7	27.0	1.0
	CE	A:LYS301	3.9	19.1	0.4
	CB	A:ASP297	4.2	21.0	1.0
	OXT	A:LYS379	4.3	30.8	1.0
	N	A:LYS379	4.3	28.8	1.0
	CA	A:ALA374	4.3	17.1	1.0
	OD2	A:ASP297	4.4	25.8	1.0
	O	A:HOH688	4.4	32.0	1.0
	CA	A:ASP297	4.4	20.4	1.0
	CA	A:ILE375	4.4	18.1	1.0
	N	A:ILE375	4.4	18.3	1.0
	O	A:HOH598	4.4	29.9	1.0
	CA	A:LYS379	4.5	28.5	1.0
	O	A:ASP297	4.5	21.4	1.0
	O	A:ASP377	4.6	24.2	1.0
	CG	A:LYS301	4.6	17.9	0.4
	NZ	A:LYS301	4.8	18.7	0.4
	C	A:ASP377	4.9	25.2	1.0
	CD	A:LYS301	4.9	19.1	0.4
	CB	A:ASP377	4.9	25.1	1.0
	C	A:ASP297	4.9	19.8	1.0
	CB	A:ALA374	5.0	17.9	1.0

Sodium binding site 2 out of 3 in 3mmd

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Sodium Binding Sites List in 3mmd

Sodium binding site 2 out of 3 in the Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose

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 the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na411 b:17.3 occ:1.00	CL	A:CL420	2.1	45.2	1.0
	O	A:HOH579	2.1	27.1	1.0
	NE2	A:HIS322	2.1	23.9	1.0
	OE1	A:GLU58	2.2	19.0	1.0
	OE2	A:GLU58	2.5	18.1	1.0
	CE1	A:HIS322	2.5	24.9	1.0
	CD	A:GLU58	2.6	19.0	1.0
	CD2	A:HIS322	3.4	22.8	1.0
	O3B	A:XYP451	3.8	23.7	1.0
	ND1	A:HIS322	3.8	23.9	1.0
	OE2	A:GLU35	3.8	19.1	1.0
	CG	A:GLU58	4.0	16.1	1.0
	O	A:HOH680	4.0	26.6	1.0
	CG	A:GLU35	4.1	14.9	1.0
	O	A:HOH521	4.2	18.9	1.0
	CG	A:HIS322	4.2	22.1	1.0
	O	A:HOH749	4.3	41.8	1.0
	CD	A:GLU35	4.4	17.5	1.0
	ND2	A:ASN59	4.4	18.0	1.0
	CB	A:GLU58	4.8	16.4	1.0
	O4B	A:XYP451	4.8	27.7	1.0
	O	A:HOH551	4.9	21.4	1.0
	C3B	A:XYP451	5.0	27.9	1.0

Sodium binding site 3 out of 3 in 3mmd

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Sodium Binding Sites List in 3mmd

Sodium binding site 3 out of 3 in the Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose

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 the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na412 b:20.2 occ:1.00	OD2	A:ASP282	2.1	23.4	1.0
	O	A:HOH685	2.1	31.0	1.0
	OD1	A:ASP282	2.6	23.0	1.0
	CG	A:ASP282	2.7	21.0	1.0
	O	A:HOH557	3.6	25.6	1.0
	O	A:HOH806	3.8	29.2	1.0
	O	A:HOH790	4.1	44.1	1.0
	CB	A:ASP282	4.1	20.9	1.0
	O	A:HOH581	4.2	40.9	1.0
	N	A:ASP282	4.6	20.7	1.0
	CD2	A:TYR281	4.6	22.6	1.0
	CA	A:ASP282	4.7	21.4	1.0
	CB	A:TYR281	4.8	21.1	1.0

Reference:

V.Solomon, G.Zolotnitsky, H.Feinberg, O.Tabachnikov, Y.Shoham, G.Shoham. Structural-Based Rational Mutagenesis of Xylanases From G.Stearothermophilus To Be Published.

Page generated: Sun Aug 17 16:13:50 2025

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