Sodium in PDB 4wud: N-Terminal 43 kDa Fragment of the E. Coli Dna Gyrase B Subunit Grown From No Salt Condition

Enzymatic activity of N-Terminal 43 kDa Fragment of the E. Coli Dna Gyrase B Subunit Grown From No Salt Condition

All present enzymatic activity of N-Terminal 43 kDa Fragment of the E. Coli Dna Gyrase B Subunit Grown From No Salt Condition:
5.99.1.3;

Protein crystallography data

The structure of N-Terminal 43 kDa Fragment of the E. Coli Dna Gyrase B Subunit Grown From No Salt Condition, PDB code: 4wud was solved by S.J.Hearnshaw, T.T.Chung, C.E.M.Stevenson, A.Maxwell, D.M.Lawson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	27.54 / 1.95
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	87.800, 141.480, 80.300, 90.00, 90.00, 90.00
*R / R_free (%)*	18.5 / 21.9

Other elements in 4wud:

The structure of N-Terminal 43 kDa Fragment of the E. Coli Dna Gyrase B Subunit Grown From No Salt Condition also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the N-Terminal 43 kDa Fragment of the E. Coli Dna Gyrase B Subunit Grown From No Salt Condition (pdb code 4wud). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the N-Terminal 43 kDa Fragment of the E. Coli Dna Gyrase B Subunit Grown From No Salt Condition, PDB code: 4wud:

Sodium binding site 1 out of 1 in 4wud

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Sodium Binding Sites List in 4wud

Sodium binding site 1 out of 1 in the N-Terminal 43 kDa Fragment of the E. Coli Dna Gyrase B Subunit Grown From No Salt Condition

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of N-Terminal 43 kDa Fragment of the E. Coli Dna Gyrase B Subunit Grown From No Salt Condition within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na403 b:44.3 occ:1.00	O	A:HOH569	2.3	40.1	1.0
	O	A:HOH527	2.4	40.0	1.0
	O	A:HOH609	2.4	48.4	1.0
	O	A:HOH528	2.5	47.9	1.0
	O	A:LYS103	2.6	36.8	1.0
	O	A:ASP105	2.7	41.4	1.0
	C	A:LYS103	3.4	35.5	1.0
	C	A:ASP105	3.5	43.1	1.0
	N	A:ASP105	3.9	41.2	1.0
	CA	A:LYS103	3.9	33.9	1.0
	O	A:PRO328	4.1	42.1	1.0
	CA	A:ASP105	4.2	44.5	1.0
	C	A:PHE104	4.2	39.5	1.0
	N	A:PHE104	4.3	35.0	1.0
	N	A:ASP106	4.3	45.1	1.0
	CB	A:LYS103	4.3	33.1	1.0
	O	A:TYR109	4.4	42.8	1.0
	O	A:HOH523	4.4	39.9	1.0
	O	A:HOH560	4.4	38.2	1.0
	O	A:HOH597	4.5	44.6	1.0
	CA	A:ASP106	4.5	47.7	1.0
	OG	A:SER112	4.5	33.7	1.0
	CA	A:PHE104	4.5	36.7	1.0
	O	A:HOH551	4.6	36.1	1.0
	OD1	A:ASP329	4.6	49.4	1.0
	O	A:PHE104	4.9	42.0	1.0
	CB	A:ASP106	4.9	51.1	1.0

Reference:

S.J.Hearnshaw, T.T.Chung, C.E.M.Stevenson, A.Maxwell, D.M.Lawson. The Role of Monovalent Cations in the Atpase Reaction of Dna Gyrase Acta Crystallogr.,Sect.D V. 71 996 2015.
ISSN: ESSN 1399-0047
DOI: 10.1107/S1399004715002916

Page generated: Sun Aug 17 22:09:04 2025

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