Sodium in PDB 4lxi: Crystal Structure of the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda

Enzymatic activity of Crystal Structure of the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda

All present enzymatic activity of Crystal Structure of the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda:
3.7.1.8;

Protein crystallography data

The structure of Crystal Structure of the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda, PDB code: 4lxi was solved by S.Bhowmik, J.T.Bolin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	57.26 / 2.17
*Space group*	P 6₅ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	66.155, 66.155, 342.180, 90.00, 90.00, 120.00
*R / R_free (%)*	20.4 / 25.8

Other elements in 4lxi:

The structure of Crystal Structure of the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda (pdb code 4lxi). 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 Crystal Structure of the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda, PDB code: 4lxi:

Sodium binding site 1 out of 1 in 4lxi

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Sodium Binding Sites List in 4lxi

Sodium binding site 1 out of 1 in the Crystal Structure of the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda

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 S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na302 b:61.2 occ:1.00	O	A:HOH470	2.0	52.3	1.0
	O	A:ALA164	2.3	51.3	1.0
	O	A:HOH468	2.4	52.5	1.0
	O	A:THR167	2.5	42.9	1.0
	O	A:HOH469	2.6	48.7	1.0
	C	A:ALA164	3.5	51.3	1.0
	C	A:THR167	3.7	43.5	1.0
	O	A:HIS168	4.3	50.2	1.0
	CA	A:ALA164	4.4	50.4	1.0
	N	A:ALA165	4.4	51.6	1.0
	CA	A:HIS168	4.4	48.0	1.0
	O	A:HOH457	4.4	53.3	1.0
	CA	A:ALA165	4.5	50.9	1.0
	N	A:HIS168	4.5	47.0	1.0
	C	A:HIS168	4.6	48.7	1.0
	O	A:ALA165	4.6	52.3	1.0
	N	A:THR167	4.6	43.2	1.0
	C	A:ALA165	4.7	50.5	1.0
	CA	A:THR167	4.7	42.7	1.0
	CB	A:ALA164	4.7	47.9	1.0
	OG1	A:THR167	4.8	42.6	1.0

Reference:

A.C.Ruzzini, S.Bhowmik, S.Ghosh, K.C.Yam, J.T.Bolin, L.D.Eltis. A Substrate-Assisted Mechanism of Nucleophile Activation in A Ser-His-Asp Containing C-C Bond Hydrolase. Biochemistry V. 52 7428 2013.
ISSN: ISSN 0006-2960
PubMed: 24067021
DOI: 10.1021/BI401156A

Page generated: Mon Oct 7 16:52:25 2024

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