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Magnesium in PDB 5lhv: X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution

Enzymatic activity of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution

All present enzymatic activity of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution:
2.4.2.3;

Protein crystallography data

The structure of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution, PDB code: 5lhv was solved by I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, V.V.Balaev, C.Betzel, A.M.Mikhailov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.57 / 1.29
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.223, 71.648, 88.878, 69.70, 72.70, 86.24
R / Rfree (%) 14.5 / 17.8

Other elements in 5lhv:

The structure of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution (pdb code 5lhv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution, PDB code: 5lhv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5lhv

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Magnesium binding site 1 out of 7 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 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 Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:36.9
occ:0.72
 O C:HOH658 1.9 38.9 1.0
O A:HOH518 1.9 37.7 1.0
O A:HOH412 2.2 37.7 1.0
O A:HOH646 2.4 36.9 0.7
O C:HOH465 2.4 35.9 1.0
O A:HOH609 3.7 42.5 1.0
O C:HOH615 3.8 51.5 1.0
OE1 A:GLN180 4.0 19.0 1.0
O A:HOH443 4.0 42.1 1.0
CD A:ARG177 4.2 11.7 0.0
O C:HOH540 4.3 20.3 1.0
O C:HOH454 4.3 25.4 1.0
NE A:ARG177 4.4 16.1 1.0
NH1 A:ARG177 4.5 11.9 0.0
O4 A:SO4302 4.5 16.3 0.7
O C:GLN180 4.6 13.1 1.0
CG A:ARG177 4.7 14.1 1.0
O C:HOH456 4.7 39.9 0.9
NE A:ARG177 4.7 11.7 0.0
O A:HOH407 4.7 68.8 1.0
CD A:ARG177 4.8 14.2 1.0
CZ A:ARG177 4.8 17.2 1.0
CZ A:ARG177 4.9 11.9 0.0
O1 A:SO4302 4.9 19.6 0.7
CD A:GLN180 5.0 16.2 1.0

Magnesium binding site 2 out of 7 in 5lhv

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Magnesium binding site 2 out of 7 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 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 Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:37.9
occ:0.69
 O B:HOH542 1.9 38.2 1.0
O B:HOH419 2.1 38.6 1.0
O F:HOH660 2.2 38.4 1.0
O F:HOH558 2.3 36.3 1.0
O B:HOH648 2.4 39.8 1.0
O F:HOH643 2.6 38.5 1.0
OE1 B:GLN180 3.9 19.8 1.0
O F:HOH626 4.1 46.1 1.0
O B:HOH505 4.1 44.6 1.0
O B:HOH568 4.1 29.1 1.0
NE B:ARG177 4.2 16.5 1.0
O F:HOH543 4.3 21.0 1.0
O F:HOH510 4.4 25.1 1.0
O2 B:SO4302 4.4 17.3 0.7
CG B:ARG177 4.5 13.6 1.0
CD B:ARG177 4.5 15.0 1.0
O F:GLN180 4.6 16.3 1.0
CZ B:ARG177 4.7 17.7 1.0
O3 B:SO4302 4.8 20.5 0.7
O F:HOH428 4.9 41.1 1.0
CD B:GLN180 4.9 16.9 1.0

Magnesium binding site 3 out of 7 in 5lhv

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Magnesium binding site 3 out of 7 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg304

b:29.0
occ:0.70
 O C:HOH555 2.0 29.6 1.0
O C:HOH631 2.1 29.4 1.0
O C:HOH546 2.1 29.5 1.0
O C:HOH584 2.2 27.6 1.0
O C:HOH643 2.6 32.2 1.0
O B:HOH514 4.1 26.3 0.8
O C:HOH470 4.1 14.3 1.0
O B:HOH548 4.2 18.0 1.0
O C:HOH628 4.2 55.7 1.0
O C:ALA206 4.3 15.2 1.0
OD1 C:ASP132 4.4 16.6 1.0
O C:HOH525 4.4 17.8 1.0
CA C:ALA206 4.4 12.0 1.0
O C:LEU210 4.5 15.2 1.0
O C:HOH519 4.6 20.3 1.0
CL C:CL305 4.7 31.9 1.0
O C:HOH531 4.8 17.4 0.5
C C:ALA206 4.8 11.9 1.0
O B:HOH485 4.9 30.3 1.0
CB C:ALA206 4.9 12.3 1.0

Magnesium binding site 4 out of 7 in 5lhv

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Magnesium binding site 4 out of 7 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg304

b:38.2
occ:0.64
 O B:HOH513 1.9 38.0 1.0
O D:HOH402 2.1 39.4 1.0
O B:HOH655 2.2 39.2 1.0
O B:HOH553 2.3 37.0 1.0
O B:HOH632 2.7 38.6 1.0
O B:HOH631 3.9 44.9 1.0
OE1 D:GLN180 3.9 20.9 1.0
O B:HOH545 4.1 21.2 1.0
O D:HOH432 4.2 46.2 1.0
O D:HOH513 4.2 33.1 1.0
NE D:ARG177 4.3 16.0 1.0
O B:HOH443 4.4 20.1 0.8
O B:GLN180 4.5 15.2 1.0
O4 B:SO4302 4.5 18.3 0.7
CG D:ARG177 4.5 15.2 1.0
CD D:ARG177 4.6 15.9 1.0
O B:HOH505 4.7 44.6 1.0
CZ D:ARG177 4.7 17.6 1.0
CD D:GLN180 4.9 19.1 1.0
O3 B:SO4302 4.9 20.5 0.7

Magnesium binding site 5 out of 7 in 5lhv

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Magnesium binding site 5 out of 7 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg304

b:38.7
occ:0.59
 O A:HOH639 1.9 39.9 1.0
O A:HOH468 2.0 38.9 1.0
O E:HOH412 2.1 39.7 1.0
O A:HOH483 2.4 36.8 1.0
O A:HOH635 2.4 39.8 1.0
O E:HOH633 3.5 45.1 1.0
O A:HOH607 3.7 49.8 1.0
OE1 E:GLN180 4.1 18.9 1.0
O E:HOH467 4.2 44.7 1.0
O A:HOH548 4.2 21.5 1.0
NE E:ARG177 4.3 16.9 1.0
O A:HOH459 4.3 27.1 1.0
O A:GLN180 4.5 13.6 1.0
O2 A:SO4302 4.5 15.8 0.7
CD E:ARG177 4.6 15.1 1.0
CG E:ARG177 4.6 12.8 1.0
CZ E:ARG177 4.7 18.4 1.0
O A:HOH443 4.8 42.1 1.0
O1 A:SO4302 4.9 19.6 0.7
CA A:GLY181 4.9 13.4 1.0
O A:HOH637 4.9 48.0 1.0

Magnesium binding site 6 out of 7 in 5lhv

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Magnesium binding site 6 out of 7 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg308

b:37.1
occ:0.49
 O E:HOH599 2.0 38.3 1.0
O E:HOH598 2.1 36.4 1.0
O E:HOH572 2.2 37.0 0.9
O E:HOH654 2.4 37.8 1.0
O D:HOH606 3.3 47.2 1.0
O D:HOH477 4.1 35.5 1.0
O E:ALA206 4.2 17.6 1.0
O D:HOH502 4.3 24.9 1.0
O E:HOH522 4.3 22.8 1.0
O E:HOH469 4.3 18.4 1.0
CA E:ALA206 4.4 14.2 1.0
O E:LEU210 4.5 18.0 1.0
OD1 E:ASP132 4.6 24.4 1.0
O D:HOH478 4.8 20.9 0.6
C E:ALA206 4.8 15.2 1.0
O D:HOH501 4.8 22.1 1.0
CL E:CL305 4.8 47.4 1.0
O D:HOH465 4.9 34.7 1.0
O E:CYS205 5.0 14.6 1.0
CB E:ALA206 5.0 15.5 1.0

Magnesium binding site 7 out of 7 in 5lhv

Go back to Magnesium Binding Sites List in 5lhv
Magnesium binding site 7 out of 7 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg304

b:43.5
occ:1.00
 O F:HOH425 1.9 43.6 1.0
O B:HOH469 2.0 43.4 1.0
O D:HOH612 2.1 44.1 1.0
O D:HOH492 2.1 42.3 1.0
O D:HOH570 3.5 27.9 0.5
O B:HOH404 4.0 63.5 1.0
O F:HOH428 4.1 41.1 1.0
OE1 F:GLN180 4.2 20.7 1.0
O D:HOH496 4.3 21.2 0.8
O D:HOH467 4.3 26.1 1.0
NE F:ARG177 4.3 15.6 1.0
O D:GLN180 4.4 16.8 1.0
O D:HOH570 4.5 19.2 0.5
O D:HOH432 4.5 46.2 1.0
O1 B:SO4302 4.6 18.3 0.7
O D:HOH611 4.7 53.1 1.0
CD F:ARG177 4.7 15.1 1.0
CG F:ARG177 4.7 14.2 1.0
CZ F:ARG177 4.7 16.6 1.0
O3 B:SO4302 4.7 20.5 0.7
CA D:GLY181 4.9 15.2 1.0
NH2 F:ARG177 5.0 18.5 1.0

Reference:

I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, V.V.Balaev, C.Betzel, A.M.Mikhailov. X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine and Sulfate Ion at 1.29 A Resolution To Be Published.
Page generated: Tue Aug 12 14:02:56 2025

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