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Chlorine in PDB 5miw: X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.

Enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.

All present enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.:
2.4.2.3;

Protein crystallography data

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A., PDB code: 5miw was solved by I.I.Prokofev, A.A.Lashkov, V.V.Balaev, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.03 / 1.28
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.513, 71.948, 89.332, 69.22, 72.20, 85.60
R / Rfree (%) 13.2 / 16.9

Other elements in 5miw:

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A. also contains other interesting chemical elements:

Sodium (Na) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A. (pdb code 5miw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A., PDB code: 5miw:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5miw

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Chlorine binding site 1 out of 8 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.


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 Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:12.1
occ:0.72
 O A:HOH676 3.1 26.6 1.0
N A:GLY25 3.1 9.8 1.0
O B:HOH599 3.2 17.9 1.0
N A:ASP26 3.4 10.5 1.0
NH2 A:ARG29 3.4 19.3 1.0
CD A:ARG29 3.7 19.0 1.0
CA A:GLY25 3.7 8.9 1.0
CA A:GLY92 4.0 12.8 1.0
C A:GLY25 4.1 10.2 1.0
O A:VAL91 4.1 11.3 1.0
CB A:ASP26 4.1 12.9 1.0
CB A:PRO24 4.1 9.7 1.0
C A:PRO24 4.2 9.2 1.0
NH2 B:ARG47 4.2 16.5 1.0
CZ A:ARG29 4.3 19.3 1.0
CA A:PRO24 4.4 8.9 1.0
CA A:ASP26 4.4 11.5 1.0
NE A:ARG29 4.5 19.4 1.0
N A:THR93 4.6 13.2 1.0
NH1 B:ARG47 4.7 14.1 1.0
O A:HOH655 4.7 47.7 1.0
C A:GLY92 4.7 13.4 1.0
CZ B:ARG47 4.8 15.7 1.0
C A:VAL91 4.8 10.2 1.0
CB A:ARG29 4.8 17.5 1.0
N A:GLY92 4.8 11.9 1.0
CG A:ARG29 4.9 18.3 1.0

Chlorine binding site 2 out of 8 in 5miw

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Chlorine binding site 2 out of 8 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.


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 Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:46.3
occ:1.00
 N B:GLY25 3.2 13.2 1.0
O A:HOH608 3.2 21.7 1.0
N B:ASP26 3.5 15.3 1.0
O B:HOH499 3.7 36.3 0.7
O B:HOH499 3.7 18.9 0.3
CA B:GLY25 3.8 13.1 1.0
NH2 A:ARG47 3.9 22.5 1.0
CA B:GLY92 4.0 13.0 1.0
O B:VAL91 4.0 11.4 1.0
C B:GLY25 4.1 13.9 1.0
CB B:ASP26 4.2 19.5 1.0
C B:PRO24 4.3 11.2 1.0
CG B:ARG29 4.3 22.3 0.3
CB B:PRO24 4.3 9.3 1.0
NH1 A:ARG47 4.4 18.6 1.0
CA B:PRO24 4.5 10.0 1.0
CG B:ARG29 4.5 26.7 0.7
CA B:ASP26 4.5 17.2 1.0
OE2 B:GLU237 4.5 31.1 0.5
CZ A:ARG47 4.5 20.3 1.0
CD B:ARG29 4.7 29.8 0.7
N B:THR93 4.7 11.2 1.0
C B:GLY92 4.8 12.3 1.0
C B:VAL91 4.8 10.3 1.0
N B:GLY92 4.9 11.2 1.0
O B:HOH412 5.0 19.2 1.0

Chlorine binding site 3 out of 8 in 5miw

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Chlorine binding site 3 out of 8 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.


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 Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:18.4
occ:0.67
 O C:HOH446 2.3 32.0 1.0
O C:HOH597 2.9 27.3 1.0
NE C:ARG29 2.9 14.9 0.2
NH2 C:ARG29 3.1 16.1 0.2
N C:GLY25 3.2 10.7 1.0
O D:HOH586 3.3 17.4 0.6
N C:ASP26 3.4 12.1 1.0
CZ C:ARG29 3.5 15.6 0.2
CD C:ARG29 3.5 13.2 0.3
NH1 C:ARG29 3.6 15.3 0.3
O D:HOH586 3.7 22.2 0.4
CA C:GLY25 3.8 11.3 1.0
CB C:ASP26 3.8 15.1 1.0
CB C:PRO24 4.0 10.1 1.0
CD C:ARG29 4.1 15.5 0.2
C C:GLY25 4.1 11.9 1.0
C C:PRO24 4.2 10.2 1.0
O C:VAL91 4.2 14.9 1.0
CA C:ASP26 4.2 13.7 1.0
NH2 D:ARG47 4.2 19.8 1.0
CA C:PRO24 4.3 9.6 1.0
CA C:GLY92 4.3 9.2 0.3
O C:HOH645 4.3 16.3 0.4
CG C:ARG29 4.4 18.4 0.4
CA C:GLY92 4.4 18.8 0.7
NE C:ARG29 4.4 14.0 0.3
CZ C:ARG29 4.4 14.4 0.3
CB C:ARG29 4.6 14.9 0.3
CB C:ARG29 4.6 15.9 0.2
CG C:ARG29 4.6 15.7 0.2
CG C:ARG29 4.7 14.0 0.3
NH1 D:ARG47 4.7 17.6 1.0
NH1 C:ARG29 4.8 15.2 0.2
CZ D:ARG47 4.8 18.3 1.0
CB C:ARG29 4.8 17.8 0.4
N C:THR93 4.9 18.3 0.7
O C:ASP26 5.0 13.6 1.0

Chlorine binding site 4 out of 8 in 5miw

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Chlorine binding site 4 out of 8 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.


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 Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:20.2
occ:0.72
 O B:HOH534 2.8 10.7 1.0
N C:PHE133 2.9 8.1 1.0
O C:HOH511 3.2 37.8 1.0
CB C:PHE133 3.4 10.9 1.0
O B:MET152 3.7 10.6 0.1
CA C:ASP132 3.8 8.9 1.0
CA C:PHE133 3.8 8.7 1.0
CG2 B:THR110 3.8 10.2 1.0
C C:ASP132 3.8 8.8 1.0
OD1 C:ASP132 3.9 11.1 0.9
O C:HOH436 4.0 35.3 1.0
O C:HOH655 4.1 25.8 1.0
OG1 B:THR110 4.1 9.5 1.0
O C:PRO131 4.2 7.6 1.0
O B:MET152 4.2 9.8 0.9
C B:MET152 4.3 10.7 0.1
CG C:ASP132 4.3 10.5 1.0
O C:HOH619 4.3 52.1 1.0
CB B:THR110 4.4 8.9 1.0
CB B:MET152 4.4 10.4 0.9
C B:MET152 4.4 9.8 0.9
CA B:GLY153 4.5 7.2 1.0
CB C:ASP132 4.6 10.1 1.0
O B:HOH689 4.6 36.9 1.0
N B:GLY153 4.7 9.5 1.0
O B:HOH515 4.7 20.3 1.0
CB B:MET152 4.7 13.7 0.1
CG C:PHE133 4.8 11.1 1.0
O C:HOH574 4.8 11.8 1.0
N C:ASP132 4.8 7.8 1.0
C C:PHE133 4.9 9.3 1.0
C C:PRO131 4.9 7.2 1.0
N C:ASP134 5.0 9.7 1.0
OD2 C:ASP132 5.0 10.3 1.0

Chlorine binding site 5 out of 8 in 5miw

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Chlorine binding site 5 out of 8 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.


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 Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:20.3
occ:0.65
 O D:HOH575 2.7 48.4 1.0
O D:HOH501 2.8 12.1 1.0
N D:PHE133 2.9 10.2 1.0
CB D:PHE133 3.5 12.7 1.0
CA D:ASP132 3.7 9.4 1.0
CA D:PHE133 3.8 10.6 1.0
C D:ASP132 3.8 10.3 1.0
CG2 E:THR110 3.8 9.8 1.0
OD1 D:ASP132 3.9 12.2 0.9
O D:HOH431 3.9 37.0 1.0
O E:MET152 4.1 11.3 1.0
O D:HOH655 4.1 24.8 1.0
OG1 E:THR110 4.2 8.9 1.0
O D:PRO131 4.2 8.8 1.0
CG D:ASP132 4.3 11.4 1.0
CB E:MET152 4.3 12.2 1.0
CB E:THR110 4.4 8.3 1.0
C E:MET152 4.4 9.5 1.0
CA E:GLY153 4.5 9.5 1.0
CB D:ASP132 4.5 10.5 1.0
N E:GLY153 4.6 9.3 1.0
O E:HOH442 4.6 23.7 1.0
O D:HOH568 4.7 11.8 1.0
N D:ASP132 4.8 8.2 1.0
CG D:PHE133 4.8 13.4 1.0
C D:PHE133 4.9 10.9 1.0
OD2 D:ASP132 4.9 11.9 0.9
C D:PRO131 4.9 7.7 1.0
N D:ASP134 4.9 11.8 1.0
O D:ASP132 5.0 11.2 1.0

Chlorine binding site 6 out of 8 in 5miw

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Chlorine binding site 6 out of 8 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.


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 Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl302

b:20.6
occ:0.60
 O D:HOH471 2.4 26.9 1.0
O C:HOH632 2.8 27.3 1.0
N D:GLY25 3.2 10.9 1.0
N D:ASP26 3.3 12.1 1.0
O D:HOH512 3.4 22.8 0.7
O D:HOH572 3.6 45.8 1.0
CB D:ASP26 3.8 13.9 1.0
CB D:PRO24 3.8 11.9 1.0
CA D:GLY25 3.9 11.4 1.0
CG D:ARG29 4.0 21.8 0.8
C D:GLY25 4.1 12.1 1.0
C D:PRO24 4.1 10.0 1.0
CA D:PRO24 4.2 10.5 1.0
CA D:ASP26 4.2 13.1 1.0
O D:VAL91 4.3 16.2 1.0
CD D:ARG29 4.4 19.7 0.2
NH1 C:ARG47 4.4 22.2 1.0
CA D:GLY92 4.4 12.6 0.5
CB D:ARG29 4.4 16.6 0.2
CB D:ARG29 4.5 19.1 0.8
O D:HOH537 4.5 34.9 1.0
CA D:GLY92 4.6 18.9 0.5
CG D:ARG29 4.6 17.7 0.2
O D:HOH456 4.8 39.2 1.0
O D:ASP26 4.8 13.3 1.0
O D:HOH538 4.9 23.4 1.0
NH2 C:ARG47 4.9 19.9 1.0
NE D:ARG29 5.0 26.0 0.8
CZ C:ARG47 5.0 20.8 1.0

Chlorine binding site 7 out of 8 in 5miw

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Chlorine binding site 7 out of 8 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl301

b:37.7
occ:1.00
 O F:HOH614 2.8 22.7 1.0
N E:GLY25 3.2 11.5 1.0
NH1 E:ARG29 3.4 31.2 0.4
N E:ASP26 3.5 16.3 1.0
NH2 E:ARG29 3.5 32.9 0.6
NE E:ARG29 3.6 32.4 0.6
CA E:GLY25 3.6 13.1 1.0
CZ E:ARG29 3.6 31.0 0.4
NH2 E:ARG29 3.8 30.1 0.4
CA E:GLY92 3.9 11.8 1.0
CZ E:ARG29 4.0 32.6 0.6
NH1 F:ARG47 4.0 22.2 1.0
O E:VAL91 4.0 10.6 1.0
C E:GLY25 4.1 13.7 1.0
CB E:ASP26 4.2 20.9 1.0
NH2 F:ARG47 4.3 19.0 1.0
C E:PRO24 4.3 11.0 1.0
NE E:ARG29 4.3 29.8 0.4
CA E:ASP26 4.5 18.6 1.0
CZ F:ARG47 4.5 20.9 1.0
CB E:PRO24 4.5 10.2 1.0
N E:THR93 4.6 10.3 1.0
CA E:PRO24 4.6 10.1 1.0
C E:GLY92 4.7 11.9 1.0
CD E:ARG29 4.7 29.8 0.6
O E:HOH409 4.7 17.4 1.0
CG E:ARG29 4.8 26.1 0.6
C E:VAL91 4.8 10.2 1.0
N E:GLY92 4.8 10.2 1.0
CD E:ARG29 4.8 27.5 0.4
NH2 E:ARG90 5.0 14.6 1.0

Chlorine binding site 8 out of 8 in 5miw

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Chlorine binding site 8 out of 8 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl301

b:23.4
occ:0.67
 O F:HOH409 2.3 26.6 1.0
O F:HOH645 2.8 27.4 1.0
N F:GLY25 3.2 9.3 1.0
NH1 F:ARG29 3.3 15.4 0.4
N F:ASP26 3.3 10.8 1.0
CD F:ARG29 3.3 15.9 0.4
O F:HOH598 3.5 36.4 1.0
CB F:ASP26 3.8 12.4 1.0
CA F:GLY25 3.8 9.8 1.0
CB F:PRO24 3.9 8.6 1.0
O F:VAL91 4.1 10.7 0.5
C F:GLY25 4.1 10.7 1.0
CG F:ARG29 4.2 14.4 0.6
O E:HOH422 4.2 22.6 0.5
C F:PRO24 4.2 8.4 1.0
CZ F:ARG29 4.2 15.0 0.4
NE F:ARG29 4.2 16.6 0.4
NH2 E:ARG47 4.2 22.4 1.0
CA F:ASP26 4.2 12.0 1.0
CA F:PRO24 4.3 8.0 1.0
CA F:GLY92 4.3 9.9 0.5
O F:VAL91 4.3 13.3 0.5
CA F:GLY92 4.4 10.9 0.5
CB F:ARG29 4.4 14.2 0.4
CG F:ARG29 4.5 14.9 0.4
CB F:ARG29 4.5 13.8 0.6
NH1 E:ARG47 4.8 17.7 1.0
O F:HOH411 4.8 38.0 1.0
CZ E:ARG47 4.8 20.0 1.0
O F:ASP26 4.9 11.3 1.0
C F:VAL91 4.9 11.1 0.5

Reference:

I.I.Prokofev, A.A.Lashkov, V.V.Balaev, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov. X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uracil at 1.28 A. To Be Published.
Page generated: Sat Jul 12 05:30:25 2025

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