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Chlorine 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:

Magnesium (Mg) 2 atoms
Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 9 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 4g8j

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Chlorine binding site 1 out of 9 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 Chlorine with other atoms in the Cl 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:Cl302

b:16.4
occ:1.00
 O A:HOH488 3.0 26.9 1.0
O A:HOH592 3.1 23.9 1.0
N A:ASN221 3.2 12.2 1.0
CG1 A:ILE220 3.7 16.9 1.0
CA A:ILE220 3.8 14.3 1.0
CG2 A:VAL103 3.8 14.6 1.0
O A:ASN221 3.9 10.8 1.0
CE A:LYS225 3.9 24.0 1.0
C A:ILE220 4.0 15.3 1.0
CB A:GLN224 4.0 13.5 1.0
CA A:ASN221 4.1 14.1 1.0
CB A:ASN221 4.2 15.3 1.0
CG A:LYS225 4.3 13.7 1.0
CB A:ILE220 4.4 11.8 1.0
C A:ASN221 4.4 15.3 1.0
CG A:GLN224 4.5 14.9 1.0
CD A:LYS225 4.6 19.5 1.0
O A:ILE219 4.9 15.2 1.0
O A:HOH439 4.9 24.8 1.0
NZ A:LYS225 4.9 29.1 1.0
CD1 A:ILE220 5.0 18.3 1.0
N A:ILE220 5.0 16.1 1.0

Chlorine binding site 2 out of 9 in 4g8j

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Chlorine binding site 2 out of 9 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 Chlorine with other atoms in the Cl 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
A:Cl303

b:37.6
occ:1.00
 NH1 A:ARG29 3.1 27.4 0.5
O A:HOH532 3.1 24.2 1.0
N A:GLY25 3.2 15.8 1.0
CZ A:ARG29 3.3 22.9 0.5
NE A:ARG29 3.3 25.1 0.5
N A:ASP26 3.5 17.4 1.0
CB A:PRO24 3.9 14.7 1.0
CA A:GLY25 3.9 13.8 1.0
O A:VAL91 4.0 15.1 1.0
CA A:GLY92 4.1 16.0 1.0
CB A:ASP26 4.1 18.6 1.0
NH2 A:ARG29 4.1 18.2 0.5
C A:PRO24 4.1 11.8 1.0
CA A:PRO24 4.1 13.5 1.0
C A:GLY25 4.2 16.8 1.0
CG A:ARG29 4.3 25.0 0.5
CD A:ARG29 4.3 25.1 0.5
CA A:ASP26 4.4 18.3 1.0
NH2 B:ARG47 4.5 22.0 1.0
NH1 B:ARG47 4.7 14.4 1.0
CB A:ARG29 4.7 24.2 0.5
C A:VAL91 4.8 15.1 1.0
CB A:ARG29 4.8 24.3 0.5
N A:GLY92 4.9 17.3 1.0
N A:THR93 4.9 16.5 1.0
C A:GLY92 4.9 23.2 1.0
O A:ASP26 5.0 22.1 1.0

Chlorine binding site 3 out of 9 in 4g8j

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Chlorine binding site 3 out of 9 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 Chlorine with other atoms in the Cl binding site number 3 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
B:Cl302

b:24.7
occ:1.00
 N B:GLY25 3.1 14.2 1.0
O A:HOH461 3.1 21.8 1.0
N B:ASP26 3.3 14.8 1.0
O B:HOH588 3.3 20.8 1.0
NH1 B:ARG29 3.5 29.5 1.0
CD B:ARG29 3.6 25.9 1.0
CA B:GLY25 3.8 18.1 1.0
CB B:PRO24 3.9 12.0 1.0
CA B:GLY92 3.9 25.7 1.0
O A:HOH596 4.0 35.3 1.0
CB B:ASP26 4.0 16.9 1.0
C B:PRO24 4.0 10.3 1.0
O B:VAL91 4.1 14.7 1.0
C B:GLY25 4.1 13.8 1.0
CA B:PRO24 4.1 13.1 1.0
CA B:ASP26 4.3 14.2 1.0
CZ B:ARG29 4.5 21.6 1.0
O A:HOH564 4.5 24.0 1.0
NE B:ARG29 4.5 31.9 1.0
CB B:ARG29 4.6 18.2 1.0
CG B:ARG29 4.7 25.8 1.0
N B:THR93 4.7 28.3 1.0
C B:VAL91 4.8 16.6 1.0
N B:GLY92 4.8 19.9 1.0
NH2 A:ARG47 4.8 32.9 1.0
C B:GLY92 4.9 30.8 1.0
O B:ASP26 4.9 13.5 1.0

Chlorine binding site 4 out of 9 in 4g8j

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Chlorine binding site 4 out of 9 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 Chlorine with other atoms in the Cl binding site number 4 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
C:Cl305

b:18.3
occ:1.00
 O D:HOH456 3.0 20.6 1.0
N C:GLY25 3.2 13.6 1.0
O C:HOH568 3.3 26.7 1.0
NH2 C:ARG29 3.4 15.8 1.0
N C:ASP26 3.4 14.3 1.0
CD C:ARG29 3.6 18.5 1.0
CA C:GLY25 3.8 14.5 1.0
CA C:GLY92 3.9 17.9 1.0
CB C:ASP26 4.0 16.6 1.0
O C:VAL91 4.1 16.9 1.0
C C:GLY25 4.1 14.0 1.0
CB C:PRO24 4.1 11.9 1.0
C C:PRO24 4.2 11.6 1.0
N C:THR93 4.3 16.4 1.0
CA C:PRO24 4.3 13.3 1.0
CA C:ASP26 4.3 16.2 1.0
CZ C:ARG29 4.4 20.1 1.0
NE C:ARG29 4.4 15.7 1.0
NH2 D:ARG47 4.5 18.3 1.0
C C:GLY92 4.6 20.0 1.0
O C:HOH563 4.7 26.1 1.0
CB C:ARG29 4.7 14.4 1.0
N C:GLY92 4.7 14.6 1.0
C C:VAL91 4.7 14.1 1.0
CG C:ARG29 4.8 13.8 1.0
NH1 D:ARG47 4.9 20.2 1.0
CG2 C:THR93 4.9 30.2 1.0

Chlorine binding site 5 out of 9 in 4g8j

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Chlorine binding site 5 out of 9 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 Chlorine with other atoms in the Cl binding site number 5 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
D:Cl302

b:17.1
occ:1.00
 O D:HOH511 3.0 22.3 1.0
O C:HOH538 3.1 22.4 1.0
N D:GLY25 3.2 13.3 1.0
NH1 D:ARG29 3.2 23.7 1.0
N D:ASP26 3.4 11.3 1.0
CD D:ARG29 3.6 20.2 1.0
CA D:GLY25 3.8 12.2 1.0
CA D:GLY92 3.9 19.7 1.0
O D:VAL91 4.0 13.7 1.0
CB D:PRO24 4.0 11.6 1.0
CB D:ASP26 4.1 14.2 1.0
C D:PRO24 4.1 12.4 1.0
C D:GLY25 4.1 13.6 1.0
O C:HOH495 4.2 20.0 1.0
CZ D:ARG29 4.2 20.5 1.0
CA D:PRO24 4.2 11.1 1.0
NE D:ARG29 4.3 19.7 1.0
CA D:ASP26 4.4 13.8 1.0
N D:THR93 4.5 20.5 1.0
C D:GLY92 4.7 24.2 1.0
CB D:ARG29 4.7 11.0 1.0
N D:GLY92 4.7 14.9 1.0
C D:VAL91 4.7 13.0 1.0
CG D:ARG29 4.7 20.6 1.0
NH2 C:ARG47 4.8 23.4 1.0
NH1 C:ARG47 4.9 19.9 1.0

Chlorine binding site 6 out of 9 in 4g8j

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Chlorine binding site 6 out of 9 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 Chlorine with other atoms in the Cl binding site number 6 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
E:Cl303

b:31.0
occ:1.00
 O E:HOH497 2.9 23.3 1.0
N E:GLY25 3.2 15.2 1.0
O E:HOH421 3.3 26.8 1.0
N E:ASP26 3.4 11.7 1.0
CB E:ASP26 3.9 18.9 1.0
CA E:GLY25 3.9 14.6 1.0
CB E:PRO24 3.9 14.0 1.0
CA E:GLY92 4.0 30.4 1.0
CG E:ARG29 4.1 33.5 1.0
O E:VAL91 4.2 17.0 1.0
C E:PRO24 4.2 13.1 1.0
C E:GLY25 4.2 15.5 1.0
CA E:PRO24 4.2 16.8 1.0
NH2 F:ARG47 4.3 32.6 1.0
CA E:ASP26 4.3 15.6 1.0
CB E:ARG29 4.6 23.8 1.0
O E:HOH549 4.7 17.1 1.0
NH1 F:ARG47 4.8 23.0 1.0
C E:VAL91 4.9 17.0 1.0
N E:GLY92 4.9 24.1 1.0
O E:ASP26 4.9 16.4 1.0
CZ F:ARG47 4.9 24.1 1.0
C E:GLY92 5.0 34.0 1.0

Chlorine binding site 7 out of 9 in 4g8j

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Chlorine binding site 7 out of 9 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 Chlorine with other atoms in the Cl binding site number 7 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:Cl302

b:16.5
occ:1.00
 NZ F:LYS225 2.7 35.8 1.0
N F:ASN221 3.1 12.3 1.0
CG1 F:ILE220 3.7 18.1 1.0
CA F:ILE220 3.8 14.4 1.0
CG2 F:VAL103 3.8 17.9 1.0
O F:ASN221 3.8 11.5 1.0
C F:ILE220 3.9 13.3 1.0
CE F:LYS225 4.0 26.5 1.0
CB F:GLN224 4.0 15.1 1.0
CA F:ASN221 4.0 12.8 1.0
CB F:ASN221 4.1 14.2 1.0
CB F:ILE220 4.3 14.6 1.0
CG F:LYS225 4.3 19.6 1.0
C F:ASN221 4.4 14.9 1.0
CG F:GLN224 4.4 18.5 1.0
CD F:LYS225 4.7 23.5 1.0
O F:HOH551 4.8 25.3 1.0
O F:ILE219 4.9 16.6 1.0
N F:ILE220 4.9 15.5 1.0
CD1 F:ILE220 4.9 17.8 1.0

Chlorine binding site 8 out of 9 in 4g8j

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Chlorine binding site 8 out of 9 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 Chlorine with other atoms in the Cl binding site number 8 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:Cl303

b:36.0
occ:1.00
 N F:GLY25 3.2 16.9 1.0
N F:ASP26 3.4 16.4 1.0
CB F:PRO24 3.8 15.1 1.0
O F:HOH470 3.9 35.4 1.0
CG F:ARG29 3.9 34.1 1.0
CA F:GLY25 3.9 15.1 1.0
CB F:ASP26 4.0 18.1 1.0
C F:PRO24 4.1 11.0 1.0
CA F:PRO24 4.1 15.9 1.0
O F:VAL91 4.1 16.2 1.0
C F:GLY25 4.2 14.0 1.0
CA F:GLY92 4.2 20.0 1.0
CA F:ASP26 4.3 17.9 1.0
CB F:ARG29 4.4 24.5 1.0
NH2 E:ARG47 4.6 18.7 1.0
NE F:ARG29 4.7 39.5 1.0
NH1 E:ARG47 4.8 19.2 1.0
O F:ASP26 4.8 18.8 1.0
C F:VAL91 4.8 16.4 1.0
CD F:ARG29 4.9 38.5 1.0
N F:GLY92 5.0 17.0 1.0

Chlorine binding site 9 out of 9 in 4g8j

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Chlorine binding site 9 out of 9 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 Chlorine with other atoms in the Cl binding site number 9 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:Cl304

b:33.7
occ:1.00
 O F:HOH491 2.6 28.9 1.0
N F:VAL175 3.0 11.8 1.0
NE2 F:GLN180 3.1 26.7 1.0
O F:VAL175 3.4 11.3 1.0
CA F:ARG174 3.7 14.5 1.0
CE1 F:TYR168 3.7 12.4 1.0
C F:ARG174 3.8 16.2 1.0
CG F:ARG174 3.8 25.2 1.0
CA F:VAL175 3.9 11.4 1.0
C F:VAL175 4.1 12.4 1.0
CD F:GLN180 4.1 18.4 1.0
CB F:VAL175 4.2 12.2 1.0
CB F:ARG174 4.2 14.3 1.0
CG F:GLN180 4.3 15.1 1.0
O F:GLY173 4.5 14.4 1.0
CD1 F:TYR168 4.5 11.4 1.0
OH F:TYR168 4.6 12.9 1.0
CZ F:TYR168 4.6 10.6 1.0
O D:HOH507 4.7 31.7 1.0
N F:ARG174 4.8 14.5 1.0
CD F:ARG174 4.9 23.4 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: Sat Dec 12 10:38:53 2020

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