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Chlorine in PDB 4lzw: X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution

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

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

Protein crystallography data

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution, PDB code: 4lzw was solved by I.I.Prokofev, A.A.Lashkov, 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) 19.89 / 1.29
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.740, 95.850, 91.830, 90.00, 119.96, 90.00
R / Rfree (%) 17.8 / 21

Other elements in 4lzw:

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine 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 Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution (pdb code 4lzw). 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 Thymidine at 1.29 A Resolution, PDB code: 4lzw:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4lzw

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Chlorine binding site 1 out of 8 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine 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 Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:31.3
occ:1.00
 O A:HOH493 2.9 25.7 1.0
O B:HOH697 3.1 30.8 1.0
N A:GLY25 3.2 8.2 1.0
N A:ASP26 3.3 10.8 1.0
O A:HOH549 3.3 27.9 1.0
CG A:ARG29 3.7 19.2 1.0
CB A:ASP26 3.8 14.7 1.0
O A:HOH476 3.8 13.3 0.4
CB A:PRO24 3.9 7.5 1.0
CA A:GLY25 3.9 9.5 1.0
C A:PRO24 4.1 7.1 1.0
C A:GLY25 4.1 10.2 1.0
O A:VAL91 4.1 9.1 1.0
CA A:GLY92 4.1 8.7 0.6
CA A:PRO24 4.2 6.7 1.0
CA A:ASP26 4.2 12.7 1.0
NH2 B:ARG47 4.2 14.4 0.8
O A:HOH496 4.2 20.4 1.0
CA A:GLY92 4.3 8.9 0.4
CB A:ARG29 4.4 17.0 1.0
CD A:ARG29 4.6 20.8 1.0
NH1 B:ARG47 4.7 11.9 0.8
O A:ASP26 4.8 13.1 1.0
NH2 B:ARG47 4.8 13.0 0.2
CZ B:ARG47 4.8 13.1 0.8
NE A:ARG29 4.9 22.3 1.0
C A:VAL91 4.9 8.1 1.0
N A:GLY92 5.0 8.3 0.6

Chlorine binding site 2 out of 8 in 4lzw

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Chlorine binding site 2 out of 8 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine 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 Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:11.2
occ:1.00
 N A:ASN221 3.2 5.6 1.0
O A:HOH528 3.2 23.5 1.0
CG1 A:ILE220 3.8 9.5 1.0
CA A:ILE220 3.8 6.9 1.0
O A:ASN221 3.9 6.0 1.0
CG2 A:VAL103 3.9 13.9 1.0
CB A:GLN224 3.9 8.8 1.0
C A:ILE220 4.0 5.8 1.0
CE A:LYS225 4.0 16.5 1.0
CA A:ASN221 4.1 6.3 1.0
CB A:ASN221 4.2 7.4 1.0
CG A:GLN224 4.3 10.8 1.0
CB A:ILE220 4.3 7.5 1.0
CG A:LYS225 4.4 11.1 1.0
C A:ASN221 4.4 5.7 1.0
CD A:LYS225 4.5 13.8 1.0
O A:HOH520 4.7 23.1 1.0
CD1 A:ILE220 4.9 10.1 1.0
O A:ILE219 4.9 10.7 1.0
O A:HOH564 4.9 27.9 1.0
NZ A:LYS225 4.9 18.3 1.0
N A:ILE220 5.0 6.7 1.0

Chlorine binding site 3 out of 8 in 4lzw

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Chlorine binding site 3 out of 8 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine 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 Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl304

b:13.8
occ:1.00
 O B:HOH459 3.0 14.1 1.0
N B:GLY25 3.2 5.6 1.0
O B:HOH455 3.2 13.0 1.0
NH1 B:ARG29 3.4 7.9 0.6
N B:ASP26 3.5 7.0 1.0
CD B:ARG29 3.5 8.3 0.6
CA B:GLY92 3.8 12.2 0.3
CA B:GLY25 3.8 6.7 1.0
CB B:PRO24 3.9 5.8 1.0
CA B:GLY92 4.0 10.9 0.7
CB B:ASP26 4.0 9.4 1.0
O B:VAL91 4.0 9.3 1.0
CD B:ARG29 4.1 11.7 0.4
C B:PRO24 4.1 5.5 1.0
CA B:PRO24 4.2 6.2 1.0
C B:GLY25 4.2 7.7 1.0
CZ B:ARG29 4.3 7.8 0.6
NE B:ARG29 4.3 7.7 0.6
CA B:ASP26 4.4 7.9 1.0
O A:HOH516 4.5 20.1 1.0
NE B:ARG29 4.5 10.9 0.4
CB B:ARG29 4.5 8.1 0.6
O A:HOH543 4.6 12.6 0.6
C B:GLY92 4.6 13.1 0.3
CG B:ARG29 4.6 8.7 0.6
CB B:ARG29 4.6 9.8 0.4
N B:GLY92 4.7 11.2 0.3
N B:THR93 4.7 12.7 1.0
C B:VAL91 4.7 9.4 1.0
N B:GLY92 4.8 10.5 0.7
CG B:ARG29 4.8 11.1 0.4
C B:GLY92 4.9 11.2 0.7

Chlorine binding site 4 out of 8 in 4lzw

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Chlorine binding site 4 out of 8 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine 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 Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl303

b:4.9
occ:0.76
 O C:HOH480 3.0 16.8 1.0
N C:GLY25 3.1 5.8 1.0
O C:HOH608 3.3 22.0 1.0
NH2 C:ARG29 3.3 9.2 1.0
N C:ASP26 3.4 6.5 1.0
CD C:ARG29 3.5 7.6 1.0
CA C:GLY25 3.8 6.2 1.0
CA C:GLY92 3.9 9.9 1.0
CB C:ASP26 4.0 7.1 1.0
O C:VAL91 4.0 8.1 1.0
CB C:PRO24 4.0 4.6 1.0
C C:GLY25 4.1 6.4 1.0
C C:PRO24 4.1 5.5 1.0
CA C:PRO24 4.3 4.8 1.0
CZ C:ARG29 4.3 7.3 1.0
CA C:ASP26 4.3 6.4 1.0
N C:THR93 4.3 10.1 1.0
NE C:ARG29 4.3 7.5 1.0
OG1 C:THR93 4.4 9.7 0.4
O C:HOH545 4.6 15.3 0.7
NH2 D:ARG47 4.6 15.2 1.0
CB C:ARG29 4.6 6.6 1.0
C C:GLY92 4.6 12.1 1.0
CG C:ARG29 4.7 6.8 1.0
C C:VAL91 4.7 7.7 1.0
N C:GLY92 4.7 9.3 1.0
NH1 D:ARG47 4.9 14.9 1.0

Chlorine binding site 5 out of 8 in 4lzw

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Chlorine binding site 5 out of 8 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine 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 Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl303

b:9.6
occ:1.00
 O C:HOH590 3.0 18.1 1.0
O D:HOH466 3.0 15.2 1.0
N D:GLY25 3.2 5.8 1.0
O D:HOH593 3.3 17.7 0.4
NH1 D:ARG29 3.3 11.1 1.0
N D:ASP26 3.5 7.2 1.0
CD D:ARG29 3.5 9.3 1.0
CA D:GLY25 3.8 6.7 1.0
CA D:GLY92 3.9 9.2 1.0
CB D:PRO24 4.0 4.1 1.0
CB D:ASP26 4.0 7.8 1.0
O D:VAL91 4.0 8.0 1.0
C D:PRO24 4.1 4.9 1.0
C D:GLY25 4.2 7.1 1.0
O D:HOH445 4.2 4.6 0.4
CA D:PRO24 4.2 5.4 1.0
CZ D:ARG29 4.3 10.1 1.0
NE D:ARG29 4.3 9.4 1.0
O D:HOH562 4.4 17.2 0.6
CA D:ASP26 4.4 7.0 1.0
N D:THR93 4.5 9.7 1.0
CB D:ARG29 4.7 8.1 1.0
C D:GLY92 4.7 11.4 1.0
O D:HOH593 4.7 12.0 0.6
CG D:ARG29 4.7 9.2 1.0
C D:VAL91 4.8 6.7 1.0
N D:GLY92 4.8 7.6 1.0
NH2 C:ARG47 4.9 14.1 1.0

Chlorine binding site 6 out of 8 in 4lzw

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Chlorine binding site 6 out of 8 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine 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 Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl304

b:18.6
occ:0.81
 O E:HOH493 2.2 11.4 0.6
O F:HOH488 2.9 16.2 1.0
N E:GLY25 3.2 6.7 1.0
O E:HOH490 3.2 14.5 0.6
N E:ASP26 3.3 8.0 1.0
CD E:ARG29 3.5 12.5 0.6
NH1 E:ARG29 3.6 13.2 0.6
O E:HOH490 3.6 17.3 0.4
CB E:ASP26 3.9 10.5 1.0
CA E:GLY25 3.9 7.0 1.0
CB E:PRO24 3.9 7.7 1.0
NH2 F:ARG47 4.0 16.6 0.6
C E:GLY25 4.1 7.8 1.0
C E:PRO24 4.1 5.8 1.0
O E:VAL91 4.2 9.6 1.0
CA E:GLY92 4.2 11.1 0.5
NH1 F:ARG47 4.2 19.4 0.4
CA E:PRO24 4.2 6.6 1.0
CA E:ASP26 4.2 9.2 1.0
CG E:ARG29 4.2 16.0 0.4
CD E:ARG29 4.3 17.5 0.4
NE E:ARG29 4.4 11.8 0.6
CA E:GLY92 4.4 11.7 0.5
CB E:ARG29 4.4 13.8 0.4
CZ E:ARG29 4.4 12.8 0.6
CB E:ARG29 4.4 11.6 0.6
CG E:ARG29 4.6 12.5 0.6
CZ F:ARG47 4.7 15.5 0.6
NH1 F:ARG47 4.8 13.8 0.6
O E:HOH614 4.8 32.2 1.0
N E:THR93 4.9 12.9 0.5
NE E:ARG29 4.9 18.7 0.4
O E:ASP26 4.9 9.4 1.0
C E:VAL91 5.0 9.3 1.0

Chlorine binding site 7 out of 8 in 4lzw

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Chlorine binding site 7 out of 8 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine 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 7 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl303

b:28.4
occ:1.00
 O F:HOH686 2.9 30.6 1.0
O F:HOH585 3.0 31.1 1.0
N F:GLY25 3.2 7.9 1.0
O E:HOH717 3.3 28.3 1.0
N F:ASP26 3.4 10.5 1.0
CG F:ARG29 3.5 20.2 1.0
CB F:ASP26 3.8 12.8 1.0
CB F:PRO24 3.8 7.2 1.0
CA F:GLY25 4.0 8.8 1.0
O F:HOH526 4.1 23.8 1.0
C F:PRO24 4.2 7.4 1.0
O F:HOH480 4.2 15.1 0.5
O F:VAL91 4.2 9.7 1.0
CA F:PRO24 4.2 6.6 1.0
C F:GLY25 4.2 10.0 1.0
CA F:ASP26 4.2 11.1 1.0
NH2 E:ARG47 4.3 10.4 0.7
CB F:ARG29 4.3 16.0 1.0
CD F:ARG29 4.3 22.8 1.0
NH1 E:ARG47 4.4 14.4 0.3
CA F:GLY92 4.4 9.9 0.4
CA F:GLY92 4.4 10.3 0.6
NE F:ARG29 4.5 24.7 1.0
NH1 E:ARG47 4.8 8.0 0.7
OE1 F:GLU237 4.8 33.4 1.0
O F:ASP26 4.8 11.4 1.0
CZ E:ARG47 4.9 9.7 0.7
NH2 E:ARG47 5.0 14.3 0.3
CZ E:ARG47 5.0 14.3 0.3
C F:VAL91 5.0 8.6 1.0

Chlorine binding site 8 out of 8 in 4lzw

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Chlorine binding site 8 out of 8 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine 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 8 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl305

b:10.4
occ:0.89
 NZ F:LYS225 2.8 16.1 0.3
O F:HOH569 2.9 29.9 1.0
N F:ASN221 3.1 6.8 1.0
O F:HOH637 3.2 25.9 1.0
O F:HOH615 3.3 24.8 1.0
CA F:ILE220 3.8 6.8 1.0
CG1 F:ILE220 3.8 10.7 1.0
CG1 F:VAL103 3.9 13.5 0.2
O F:ASN221 3.9 7.8 1.0
CG2 F:VAL103 3.9 11.9 0.8
CB F:GLN224 4.0 9.3 1.0
C F:ILE220 4.0 6.5 1.0
CE F:LYS225 4.0 14.9 0.7
CA F:ASN221 4.1 6.7 1.0
CB F:ASN221 4.2 7.8 1.0
CE F:LYS225 4.2 15.0 0.3
CG F:LYS225 4.3 11.6 0.7
CB F:ILE220 4.4 8.7 1.0
CG F:GLN224 4.4 11.0 1.0
C F:ASN221 4.4 6.3 1.0
CG F:LYS225 4.5 11.9 0.3
CD F:LYS225 4.5 13.4 0.7
O F:HOH504 4.7 22.1 1.0
NZ F:LYS225 4.8 16.1 0.7
O F:ILE219 4.8 9.2 1.0
CD F:LYS225 4.9 13.5 0.3
O F:HOH654 4.9 30.9 1.0
N F:ILE220 4.9 7.2 1.0

Reference:

I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov. X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution To Be Published.
Page generated: Sun Jul 21 19:27:36 2024

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