Magnesium in PDB 4g8j: X-Ray Structure of Uridine Phosphorylease From Vibrio Cholerae Complexed with Thymidine at 2.12 A Resolution

Enzymatic activity of X-Ray Structure of Uridine Phosphorylease From Vibrio Cholerae Complexed with Thymidine at 2.12 A Resolution

All present enzymatic activity of X-Ray Structure of Uridine Phosphorylease From Vibrio Cholerae Complexed with Thymidine at 2.12 A Resolution:
2.4.2.3;

Protein crystallography data

The structure of X-Ray Structure of Uridine Phosphorylease From Vibrio Cholerae Complexed with Thymidine at 2.12 A Resolution, PDB code: 4g8j was solved by A.A.Lashkov, A.G.Gabdoulkhakov, I.I.Prokofev, S.E.Sotnichenko, C.Betzel, A.M.Mikhailov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	11.99 / 2.12
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	91.796, 95.905, 91.890, 90.00, 119.96, 90.00
*R / R_free (%)*	14.9 / 19.7

Other elements in 4g8j:

The structure of X-Ray Structure of Uridine Phosphorylease From Vibrio Cholerae Complexed with Thymidine at 2.12 A Resolution also contains other interesting chemical elements:

Chlorine	(Cl)	9 atoms
Sodium	(Na)	3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of Uridine Phosphorylease From Vibrio Cholerae Complexed with Thymidine at 2.12 A Resolution (pdb code 4g8j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Structure of Uridine Phosphorylease From Vibrio Cholerae Complexed with Thymidine at 2.12 A Resolution, PDB code: 4g8j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4g8j

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Magnesium Binding Sites List in 4g8j

Magnesium binding site 1 out of 2 in the X-Ray Structure of Uridine Phosphorylease From Vibrio Cholerae Complexed with Thymidine at 2.12 A Resolution

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Uridine Phosphorylease From Vibrio Cholerae Complexed with Thymidine at 2.12 A Resolution within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg304 b:30.1 occ:1.00	O	A:HOH578	2.1	31.0	1.0
	O	A:HOH575	2.1	23.7	1.0
	O	A:HOH574	2.1	32.4	1.0
	O	A:HOH576	2.1	23.2	1.0
	O	A:HOH577	2.1	20.8	1.0
	O	A:HOH573	2.1	18.2	1.0
	O	A:PHE171	3.8	18.0	1.0
	O	A:HOH579	3.9	22.0	1.0
	O	A:THR170	4.2	13.7	1.0
	O	A:HOH494	4.3	24.5	1.0
	O	A:HOH468	4.7	24.4	1.0
	C	A:PHE171	4.8	12.7	1.0

Magnesium binding site 2 out of 2 in 4g8j

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Magnesium Binding Sites List in 4g8j

Magnesium binding site 2 out of 2 in the X-Ray Structure of Uridine Phosphorylease From Vibrio Cholerae Complexed with Thymidine at 2.12 A Resolution

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Uridine Phosphorylease From Vibrio Cholerae Complexed with Thymidine at 2.12 A Resolution within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
F:Mg305 b:30.4 occ:1.00	O	F:HOH556	2.1	19.3	1.0
	O	F:HOH560	2.1	27.6	1.0
	O	F:HOH559	2.1	25.5	1.0
	O	F:HOH557	2.1	27.9	1.0
	O	F:HOH558	2.1	24.1	1.0
	O	F:HOH561	2.1	24.9	1.0
	O	F:PHE171	3.7	17.7	1.0
	O	F:HOH563	4.2	21.1	1.0
	O	F:THR170	4.3	14.6	1.0
	O	F:HOH504	4.4	23.5	1.0
	O	F:HOH562	4.7	21.6	1.0
	C	F:PHE171	4.7	12.9	1.0

Reference:

A.A.Lashkov, A.G.Gabdoulkhakov, I.I.Prokofev, S.E.Sotnichenko, C.Betzel, A.M.Mikhailov. X-Ray Structure of Uridine Phosphorylease From Vibrio Cholerae Complexed with Thymidine To Be Published.

Page generated: Fri Aug 16 15:27:55 2024

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