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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 / Rfree (%) 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

Go back to 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

Go back to 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: Mon Aug 11 13:12:04 2025

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