Sodium in PDB 4uzu: Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution

Enzymatic activity of Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution

All present enzymatic activity of Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution:
3.2.1.1;

Protein crystallography data

The structure of Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution, PDB code: 4uzu was solved by W.A.Offen, C.Anderson, T.V.Borchert, K.S.Wilson, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	92.92 / 1.90
*Space group*	I 4₁ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	108.180, 108.180, 181.490, 90.00, 90.00, 90.00
*R / R_free (%)*	16.993 / 21.029

Other elements in 4uzu:

The structure of Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution (pdb code 4uzu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution, PDB code: 4uzu:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4uzu

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Sodium Binding Sites List in 4uzu

Sodium binding site 1 out of 3 in the Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na1491 b:13.1 occ:1.00	OD2	A:ASP201	2.3	14.2	1.0
	OD2	A:ASP162	2.3	13.1	1.0
	O	A:LEU202	2.4	12.4	1.0
	OD2	A:ASP195	2.4	11.6	1.0
	OD2	A:ASP184	2.5	14.3	1.0
	OD1	A:ASP195	2.9	11.7	1.0
	CG	A:ASP195	3.0	13.1	1.0
	CG	A:ASP184	3.3	14.2	1.0
	CG	A:ASP162	3.3	13.6	1.0
	CG	A:ASP201	3.4	13.1	1.0
	C	A:LEU202	3.4	13.0	1.0
	O	A:HOH2201	3.7	13.2	1.0
	CB	A:ASP162	3.7	13.3	1.0
	O	A:HOH2110	3.7	12.9	1.0
	OD1	A:ASP184	3.8	14.9	1.0
	OD1	A:ASP201	3.8	13.3	1.0
	CA	A:ASP203	3.9	12.3	1.0
	N	A:ASP203	4.1	12.2	1.0
	CB	A:ASP184	4.1	13.0	1.0
	CA	A:CA1484	4.2	12.6	1.0
	N	A:MET204	4.3	14.7	1.0
	N	A:ASP184	4.3	11.6	1.0
	OD1	A:ASP162	4.4	14.9	1.0
	CA	A:CA1483	4.4	12.8	1.0
	CB	A:ASP195	4.5	11.8	1.0
	N	A:LEU202	4.5	13.3	1.0
	O	A:ASP201	4.6	12.2	1.0
	C	A:ASP201	4.6	12.8	1.0
	CA	A:LEU202	4.6	12.8	1.0
	CB	A:ASP201	4.6	13.1	1.0
	C	A:ASP203	4.6	12.8	1.0
	CE3	A:TRP183	4.8	9.2	1.0
	N	A:ASP162	4.9	12.7	1.0
	CA	A:ASP184	4.9	12.3	1.0
	CA	A:ASP162	4.9	12.5	1.0
	CB	A:ASP203	4.9	11.5	1.0

Sodium binding site 2 out of 3 in 4uzu

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Sodium Binding Sites List in 4uzu

Sodium binding site 2 out of 3 in the Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na1492 b:23.8 occ:1.00	O	A:HOH2145	2.2	18.4	1.0
	O	A:HOH2144	2.3	20.5	1.0
	O	A:HOH2143	2.4	12.5	1.0
	OD2	A:ASP125	3.8	11.5	1.0
	OD1	A:ASP125	4.2	10.1	1.0
	CB	A:ASN127	4.2	8.2	1.0
	O	A:HOH2061	4.3	23.9	1.0
	CG	A:ASP125	4.5	10.5	1.0
	ND2	A:ASN127	4.5	7.7	1.0
	CG	A:ASN127	4.9	8.3	1.0

Sodium binding site 3 out of 3 in 4uzu

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Sodium Binding Sites List in 4uzu

Sodium binding site 3 out of 3 in the Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na1490 b:20.9 occ:1.00	O	A:HOH2242	2.3	29.0	1.0
	O	A:HOH2261	2.3	18.2	1.0
	OD1	A:ASP232	2.3	11.4	1.0
	O	A:HOH2241	2.5	21.8	1.0
	OE1	A:GLU262	2.5	14.8	1.0
	CD	A:GLU262	3.3	13.5	1.0
	CG	A:ASP232	3.3	11.8	1.0
	OE2	A:GLU262	3.5	14.4	1.0
	OD2	A:ASP232	3.8	12.0	1.0
	O	A:HOH2243	3.9	17.4	1.0
	O	A:HOH2247	3.9	18.9	1.0
	N	A:ALA233	3.9	11.6	1.0
	O	A:HOH2100	4.0	30.6	1.0
	OD2	A:ASP329	4.1	16.2	1.0
	NH2	A:ARG230	4.2	10.9	1.0
	CB	A:ALA233	4.3	11.1	1.0
	CA	A:ALA233	4.3	12.0	1.0
	O	A:HOH2318	4.4	18.9	1.0
	NH1	A:ARG230	4.5	10.6	1.0
	CB	A:ASP232	4.6	11.1	1.0
	CG	A:GLU262	4.7	13.1	1.0
	CA	A:ASP232	4.7	10.9	1.0
	C	A:ASP232	4.7	11.9	1.0
	CZ	A:ARG230	4.8	11.0	1.0

Reference:

W.A.Offen, A.Viksoe-Nielsen, T.V.Borchert, K.S.Wilson, G.J.Davies. Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution Acta Crystallogr.,Sect.F V. 71 66 2015.
ISSN: ISSN 1744-3091
PubMed: 25615972
DOI: 10.1107/S2053230X14026508

Page generated: Mon Oct 7 18:47:59 2024

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