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Chlorine 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:

Magnesium (Mg) 7 atoms
Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5lhv

Go back to Chlorine Binding Sites List in 5lhv
Chlorine binding site 1 out of 6 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 Chlorine with other atoms in the Cl 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:Cl306

b:38.3
occ:1.00
 O F:HOH524 2.6 18.3 1.0
N A:PHE133 3.0 15.9 1.0
O A:HOH600 3.1 49.3 1.0
O F:HOH658 3.3 47.9 1.0
CB A:PHE133 3.6 16.6 1.0
CG2 F:THR110 3.8 15.6 1.0
CA A:ASP132 3.9 14.2 1.0
CA A:PHE133 3.9 17.1 1.0
OG1 F:THR110 3.9 14.7 1.0
C A:ASP132 3.9 16.3 1.0
O F:MET152 4.0 16.4 1.0
OD1 A:ASP132 4.0 21.0 1.0
O A:HOH621 4.1 31.3 1.0
O A:PRO131 4.3 14.6 1.0
CA F:GLY153 4.3 13.9 1.0
C F:MET152 4.3 14.6 1.0
CB F:THR110 4.3 13.6 1.0
CB F:MET152 4.4 17.2 1.0
CG A:ASP132 4.5 19.0 1.0
N F:GLY153 4.5 13.9 1.0
O F:HOH528 4.6 21.7 0.7
O A:HOH534 4.7 15.3 1.0
CB A:ASP132 4.7 16.4 1.0
N A:ASP132 4.9 13.0 1.0
CG A:PHE133 4.9 17.1 1.0

Chlorine binding site 2 out of 6 in 5lhv

Go back to Chlorine Binding Sites List in 5lhv
Chlorine binding site 2 out of 6 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 Chlorine with other atoms in the Cl 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:Cl306

b:31.6
occ:1.00
 O B:HOH507 2.8 16.0 1.0
N B:PHE133 3.0 13.4 1.0
O B:HOH601 3.3 55.3 1.0
CB B:PHE133 3.5 14.1 1.0
CA B:ASP132 3.7 13.5 1.0
OD1 B:ASP132 3.8 17.1 1.0
CA B:PHE133 3.8 14.2 1.0
C B:ASP132 3.8 13.2 1.0
CG2 C:THR110 3.9 14.4 1.0
O C:MET152 4.1 15.9 1.0
O B:HOH645 4.1 31.3 1.0
OG1 C:THR110 4.2 12.7 1.0
O B:PRO131 4.2 12.4 1.0
CB C:MET152 4.3 16.2 1.0
CG B:ASP132 4.3 16.2 1.0
C C:MET152 4.4 12.7 1.0
CB C:THR110 4.4 12.9 1.0
CB B:ASP132 4.5 13.9 1.0
CA C:GLY153 4.6 12.5 1.0
N C:GLY153 4.7 12.8 1.0
O B:HOH559 4.8 14.3 1.0
N B:ASP132 4.8 12.9 1.0
O C:HOH542 4.8 26.0 0.9
CG B:PHE133 4.9 14.5 1.0
C B:PRO131 4.9 12.4 1.0
OD2 B:ASP132 5.0 17.5 1.0
C B:PHE133 5.0 15.0 1.0
N B:ASP134 5.0 15.4 1.0

Chlorine binding site 3 out of 6 in 5lhv

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Chlorine binding site 3 out of 6 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 Chlorine with other atoms in the Cl 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:Cl305

b:31.9
occ:1.00
 O C:HOH519 2.6 20.3 1.0
N C:PHE133 3.1 12.0 1.0
O C:HOH529 3.3 49.0 1.0
CB C:PHE133 3.5 14.9 1.0
CG2 B:THR110 3.7 16.0 1.0
OG1 B:THR110 3.8 15.6 1.0
CA C:ASP132 3.9 12.2 1.0
CA C:PHE133 4.0 13.4 1.0
C C:ASP132 4.0 12.3 1.0
O B:MET152 4.0 15.5 1.0
O C:HOH631 4.1 29.4 1.0
OD1 C:ASP132 4.1 16.6 1.0
CB B:THR110 4.2 14.0 1.0
CA B:GLY153 4.2 13.1 1.0
O C:PRO131 4.2 12.2 1.0
C B:MET152 4.3 14.8 1.0
CB B:MET152 4.4 16.2 1.0
N B:GLY153 4.4 13.9 1.0
O B:HOH514 4.5 26.3 0.8
CG C:ASP132 4.6 14.3 1.0
MG C:MG304 4.7 29.0 0.7
O C:HOH551 4.7 16.0 1.0
CB C:ASP132 4.8 12.6 1.0
CG C:PHE133 4.8 16.0 1.0
O C:HOH555 4.9 29.6 1.0
N C:ASP132 4.9 11.1 1.0

Chlorine binding site 4 out of 6 in 5lhv

Go back to Chlorine Binding Sites List in 5lhv
Chlorine binding site 4 out of 6 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 Chlorine with other atoms in the Cl 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:Cl305

b:39.7
occ:1.00
 O D:HOH500 2.8 20.1 1.0
N D:PHE133 3.2 20.0 1.0
O D:HOH554 3.3 48.7 1.0
CB D:PHE133 3.6 21.9 1.0
CG2 E:THR110 3.8 15.3 1.0
CA D:ASP132 3.9 18.4 1.0
OD1 D:ASP132 3.9 23.8 1.0
O E:MET152 4.0 17.3 1.0
CA D:PHE133 4.0 20.8 1.0
C D:ASP132 4.0 18.7 1.0
OG1 E:THR110 4.0 15.7 1.0
O D:HOH602 4.2 42.4 1.0
CA E:GLY153 4.3 15.3 1.0
O D:PRO131 4.3 16.0 1.0
C E:MET152 4.3 16.4 1.0
CB E:THR110 4.3 15.0 1.0
CB E:MET152 4.4 20.8 1.0
CG D:ASP132 4.4 22.6 1.0
O E:HOH524 4.5 24.2 0.7
N E:GLY153 4.5 15.0 1.0
O D:HOH543 4.6 46.1 1.0
CB D:ASP132 4.7 20.1 1.0
O D:HOH497 4.8 22.2 1.0
N D:ASP132 4.9 16.8 1.0
CG D:PHE133 5.0 22.6 1.0

Chlorine binding site 5 out of 6 in 5lhv

Go back to Chlorine Binding Sites List in 5lhv
Chlorine binding site 5 out of 6 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 Chlorine with other atoms in the Cl 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:Cl305

b:47.4
occ:1.00
 O D:HOH501 2.7 22.1 1.0
O E:HOH632 3.0 48.7 1.0
N E:PHE133 3.2 19.5 1.0
CB E:PHE133 3.7 21.6 1.0
OD1 E:ASP132 3.8 24.4 1.0
CA E:ASP132 3.9 18.1 1.0
CG2 D:THR110 3.9 19.2 1.0
O D:MET152 4.0 22.6 1.0
C E:ASP132 4.1 19.2 1.0
CA E:PHE133 4.1 21.5 1.0
OG1 D:THR110 4.1 19.1 1.0
O E:HOH654 4.1 37.8 1.0
C D:MET152 4.3 21.4 1.0
CB D:MET152 4.4 23.4 1.0
CG E:ASP132 4.4 22.4 1.0
O D:HOH477 4.4 35.5 1.0
CA D:GLY153 4.4 19.5 1.0
O E:PRO131 4.4 16.4 1.0
CB D:THR110 4.4 18.2 1.0
N D:GLY153 4.6 20.7 1.0
CB E:ASP132 4.7 19.7 1.0
O E:HOH599 4.8 38.3 1.0
MG E:MG308 4.8 37.1 0.5
N E:ASP132 5.0 16.3 1.0

Chlorine binding site 6 out of 6 in 5lhv

Go back to Chlorine Binding Sites List in 5lhv
Chlorine binding site 6 out of 6 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 Chlorine with other atoms in the Cl 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
F:Cl305

b:24.2
occ:0.62
 O A:HOH526 2.7 16.2 1.0
N F:PHE133 2.9 14.1 1.0
O F:HOH628 3.4 53.1 1.0
CB F:PHE133 3.5 15.6 1.0
CG2 A:THR110 3.7 14.8 1.0
CA F:ASP132 3.8 11.9 1.0
C F:ASP132 3.8 12.8 1.0
CA F:PHE133 3.8 14.8 1.0
OD1 F:ASP132 4.0 17.4 1.0
OG1 A:THR110 4.0 14.8 1.0
O A:MET152 4.1 18.4 1.0
O F:PRO131 4.2 13.2 1.0
CB A:MET152 4.2 18.8 1.0
CB A:THR110 4.3 14.5 1.0
O F:HOH407 4.3 32.3 1.0
C A:MET152 4.3 16.0 1.0
CG F:ASP132 4.4 16.8 1.0
CA A:GLY153 4.4 14.3 1.0
N A:GLY153 4.6 15.0 1.0
CB F:ASP132 4.6 14.2 1.0
O F:HOH561 4.6 14.8 1.0
N F:ASP132 4.8 11.0 1.0
O2 F:GOL307 4.9 36.5 0.8
CG F:PHE133 4.9 16.6 1.0
O A:HOH560 4.9 27.2 1.0
C F:PRO131 4.9 12.1 1.0
CA A:MET152 5.0 17.2 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: Fri Jul 26 11:38:45 2024

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