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Chlorine in PDB 4r2x: Unique Conformation of Uridine and Asymmetry of the Hexameric Molecule Revealed in the High-Resolution Structures of Shewanella Oneidensis Uridine Phosphorylase in the Free Form and in Complex with Uridine

Enzymatic activity of Unique Conformation of Uridine and Asymmetry of the Hexameric Molecule Revealed in the High-Resolution Structures of Shewanella Oneidensis Uridine Phosphorylase in the Free Form and in Complex with Uridine

All present enzymatic activity of Unique Conformation of Uridine and Asymmetry of the Hexameric Molecule Revealed in the High-Resolution Structures of Shewanella Oneidensis Uridine Phosphorylase in the Free Form and in Complex with Uridine:
2.4.2.3;

Protein crystallography data

The structure of Unique Conformation of Uridine and Asymmetry of the Hexameric Molecule Revealed in the High-Resolution Structures of Shewanella Oneidensis Uridine Phosphorylase in the Free Form and in Complex with Uridine, PDB code: 4r2x was solved by T.N.Safonova, N.N.Mordkovich, V.A.Manuvera, V.P.Veiko, V.O.Popov, K.M.Polyakov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.66 / 0.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.540, 95.930, 91.610, 90.00, 120.00, 90.00
R / Rfree (%) 14.9 / 16.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Unique Conformation of Uridine and Asymmetry of the Hexameric Molecule Revealed in the High-Resolution Structures of Shewanella Oneidensis Uridine Phosphorylase in the Free Form and in Complex with Uridine (pdb code 4r2x). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Unique Conformation of Uridine and Asymmetry of the Hexameric Molecule Revealed in the High-Resolution Structures of Shewanella Oneidensis Uridine Phosphorylase in the Free Form and in Complex with Uridine, PDB code: 4r2x:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4r2x

Go back to Chlorine Binding Sites List in 4r2x
Chlorine binding site 1 out of 4 in the Unique Conformation of Uridine and Asymmetry of the Hexameric Molecule Revealed in the High-Resolution Structures of Shewanella Oneidensis Uridine Phosphorylase in the Free Form and in Complex with Uridine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Unique Conformation of Uridine and Asymmetry of the Hexameric Molecule Revealed in the High-Resolution Structures of Shewanella Oneidensis Uridine Phosphorylase in the Free Form and in Complex with Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:7.9
occ:1.00
 HH22 C:ARG165 2.2 4.9 1.0
HA3 C:GLY93 2.9 5.7 1.0
O C:HOH434 3.1 6.5 1.0
O C:HOH485 3.1 8.0 1.0
HH12 C:ARG165 3.1 4.9 1.0
NH2 C:ARG165 3.1 6.9 1.0
H C:GLY93 3.1 4.0 1.0
O C:HOH436 3.3 9.2 1.0
N C:GLY93 3.4 5.5 1.0
HE1 C:PHE159 3.4 8.6 1.0
CA C:GLY93 3.5 5.4 1.0
OE1 C:GLN163 3.6 5.7 1.0
HH21 C:ARG165 3.6 4.9 1.0
HG12 C:VAL218 3.7 5.7 1.0
NH1 C:ARG165 3.8 5.8 1.0
HG11 C:VAL218 3.8 5.7 1.0
CZ C:ARG165 3.9 5.5 1.0
HA2 C:GLY93 3.9 5.7 1.0
CE1 C:PHE159 4.0 6.6 1.0
HB2 C:TYR192 4.1 3.8 1.0
CG1 C:VAL218 4.1 6.8 1.0
C C:THR92 4.2 6.0 1.0
HD3 C:ARG220 4.3 4.9 1.0
HG13 C:VAL218 4.3 5.7 1.0
HA C:THR92 4.3 4.0 1.0
HZ C:PHE159 4.3 8.6 1.0
CZ C:PHE159 4.4 6.8 1.0
O1 C:GOL303 4.5 7.7 1.0
O C:TYR192 4.5 5.0 1.0
HH11 C:ARG165 4.5 4.9 1.0
H11 C:GOL303 4.6 5.9 1.0
HE21 C:GLN163 4.7 3.7 1.0
HD12 C:ILE217 4.7 10.6 1.0
CD C:GLN163 4.7 5.4 1.0
CD1 C:PHE159 4.7 5.3 1.0
HH11 C:ARG220 4.8 4.9 1.0
C C:GLY93 4.8 5.3 1.0
HG13 C:ILE217 4.8 9.6 1.0
HD1 C:PHE159 4.8 8.6 1.0
CA C:THR92 4.8 5.3 1.0
HB3 C:TYR192 4.9 3.8 1.0
O C:THR92 4.9 6.3 1.0
CB C:TYR192 4.9 5.0 1.0

Chlorine binding site 2 out of 4 in 4r2x

Go back to Chlorine Binding Sites List in 4r2x
Chlorine binding site 2 out of 4 in the Unique Conformation of Uridine and Asymmetry of the Hexameric Molecule Revealed in the High-Resolution Structures of Shewanella Oneidensis Uridine Phosphorylase in the Free Form and in Complex with Uridine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Unique Conformation of Uridine and Asymmetry of the Hexameric Molecule Revealed in the High-Resolution Structures of Shewanella Oneidensis Uridine Phosphorylase in the Free Form and in Complex with Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl302

b:7.7
occ:1.00
 HH22 D:ARG165 2.2 4.7 1.0
HA3 D:GLY93 2.8 6.0 1.0
O D:HOH460 3.1 8.9 1.0
O D:HOH403 3.1 6.1 1.0
NH2 D:ARG165 3.1 6.2 1.0
H D:GLY93 3.1 4.5 1.0
HH12 D:ARG165 3.1 4.7 1.0
O D:HOH452 3.3 9.2 1.0
HE1 D:PHE159 3.4 3.9 1.0
N D:GLY93 3.4 6.0 1.0
CA D:GLY93 3.5 5.8 1.0
HH21 D:ARG165 3.6 4.7 1.0
OE1 D:GLN163 3.6 5.2 1.0
HG12 D:VAL218 3.7 5.9 1.0
NH1 D:ARG165 3.8 5.4 1.0
HG11 D:VAL218 3.8 5.9 1.0
CZ D:ARG165 3.9 5.5 1.0
CE1 D:PHE159 3.9 6.5 1.0
HA2 D:GLY93 3.9 6.0 1.0
HB2 D:TYR192 4.1 3.9 1.0
CG1 D:VAL218 4.1 7.2 1.0
C D:THR92 4.2 6.0 1.0
HZ D:PHE159 4.2 3.9 1.0
HD3 D:ARG220 4.2 5.0 1.0
HA D:THR92 4.3 4.5 1.0
HG13 D:VAL218 4.3 5.9 1.0
CZ D:PHE159 4.4 6.7 1.0
O1 D:GOL303 4.5 7.6 1.0
O D:TYR192 4.5 5.6 1.0
HD12 D:ILE217 4.5 11.7 1.0
HH11 D:ARG165 4.6 4.7 1.0
H11 D:GOL303 4.6 6.1 1.0
HE21 D:GLN163 4.7 3.8 1.0
CD1 D:PHE159 4.7 5.0 1.0
CD D:GLN163 4.7 4.8 1.0
HH11 D:ARG220 4.7 5.0 1.0
C D:GLY93 4.8 5.9 1.0
HG13 D:ILE217 4.8 9.2 1.0
HD1 D:PHE159 4.8 3.9 1.0
CA D:THR92 4.9 5.6 1.0
O D:THR92 4.9 6.5 1.0
HB3 D:TYR192 4.9 3.9 1.0
CB D:TYR192 4.9 5.1 1.0

Chlorine binding site 3 out of 4 in 4r2x

Go back to Chlorine Binding Sites List in 4r2x
Chlorine binding site 3 out of 4 in the Unique Conformation of Uridine and Asymmetry of the Hexameric Molecule Revealed in the High-Resolution Structures of Shewanella Oneidensis Uridine Phosphorylase in the Free Form and in Complex with Uridine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Unique Conformation of Uridine and Asymmetry of the Hexameric Molecule Revealed in the High-Resolution Structures of Shewanella Oneidensis Uridine Phosphorylase in the Free Form and in Complex with Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl302

b:9.6
occ:1.00
 HH22 F:ARG165 2.2 5.2 1.0
HA3 F:GLY93 2.9 8.1 1.0
NH2 F:ARG165 3.1 7.5 1.0
O F:HOH452 3.1 11.2 1.0
O F:HOH413 3.1 7.4 1.0
HH12 F:ARG165 3.1 5.2 1.0
H F:GLY93 3.1 5.5 1.0
HE1 F:PHE159 3.3 4.7 1.0
N F:GLY93 3.4 6.7 1.0
O F:HOH433 3.4 10.8 1.0
CA F:GLY93 3.5 6.8 1.0
HH21 F:ARG165 3.6 5.2 1.0
OE1 F:GLN163 3.6 6.4 1.0
HG12 F:VAL218 3.6 8.2 1.0
NH1 F:ARG165 3.8 6.4 1.0
HG11 F:VAL218 3.8 8.2 1.0
CE1 F:PHE159 3.9 8.2 1.0
CZ F:ARG165 3.9 6.5 1.0
HA2 F:GLY93 3.9 8.1 1.0
CG1 F:VAL218 4.1 10.5 1.0
HB2 F:TYR192 4.2 3.9 1.0
HZ F:PHE159 4.2 4.7 1.0
C F:THR92 4.2 6.9 1.0
HG13 F:VAL218 4.3 8.2 1.0
HA F:THR92 4.3 5.5 1.0
CZ F:PHE159 4.3 7.7 1.0
HD3 F:ARG220 4.4 6.0 1.0
O1 F:GOL305 4.5 9.8 1.0
O F:TYR192 4.5 5.6 1.0
HH11 F:ARG165 4.6 5.2 1.0
HE21 F:GLN163 4.6 4.3 1.0
H11 F:GOL305 4.7 5.2 1.0
CD F:GLN163 4.7 5.4 1.0
CD1 F:PHE159 4.7 6.9 1.0
HD12 F:ILE217 4.7 11.1 1.0
C F:GLY93 4.8 6.6 1.0
HD1 F:PHE159 4.8 4.7 1.0
HH11 F:ARG220 4.8 6.0 1.0
CA F:THR92 4.9 6.6 1.0
O F:THR92 4.9 7.5 1.0
HG13 F:ILE217 4.9 10.5 1.0
HB3 F:TYR192 4.9 3.9 1.0
CB F:TYR192 5.0 5.1 1.0

Chlorine binding site 4 out of 4 in 4r2x

Go back to Chlorine Binding Sites List in 4r2x
Chlorine binding site 4 out of 4 in the Unique Conformation of Uridine and Asymmetry of the Hexameric Molecule Revealed in the High-Resolution Structures of Shewanella Oneidensis Uridine Phosphorylase in the Free Form and in Complex with Uridine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Unique Conformation of Uridine and Asymmetry of the Hexameric Molecule Revealed in the High-Resolution Structures of Shewanella Oneidensis Uridine Phosphorylase in the Free Form and in Complex with Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:10.2
occ:1.00
 HH22 A:ARG165 2.3 6.0 1.0
HA3 A:GLY93 2.9 7.0 1.0
O A:HOH456 3.1 12.1 1.0
HH12 A:ARG165 3.1 6.0 1.0
O A:HOH435 3.1 7.7 1.0
NH2 A:ARG165 3.1 8.6 1.0
H A:GLY93 3.2 5.3 1.0
O A:HOH419 3.4 11.9 1.0
HE1 A:PHE159 3.4 4.6 1.0
N A:GLY93 3.4 6.7 1.0
CA A:GLY93 3.6 6.9 1.0
OE1 A:GLN163 3.6 6.5 1.0
HG12 A:VAL218 3.6 7.0 1.0
HH21 A:ARG165 3.6 6.0 1.0
NH1 A:ARG165 3.8 7.4 1.0
HG11 A:VAL218 3.8 7.0 1.0
CZ A:ARG165 3.9 6.8 1.0
CE1 A:PHE159 3.9 8.5 1.0
HA2 A:GLY93 4.0 7.0 1.0
CG1 A:VAL218 4.1 9.4 1.0
HB2 A:TYR192 4.2 4.1 1.0
C A:THR92 4.2 7.2 1.0
HZ A:PHE159 4.2 4.6 1.0
HA A:THR92 4.3 5.3 1.0
HG13 A:VAL218 4.3 7.0 1.0
HD3 A:ARG220 4.4 6.5 1.0
CZ A:PHE159 4.4 9.0 1.0
O A:TYR192 4.5 5.3 1.0
O3 A:GOL303 4.5 9.8 1.0
HH11 A:ARG165 4.5 6.0 1.0
HE21 A:GLN163 4.6 4.5 1.0
CD A:GLN163 4.7 5.5 1.0
CD1 A:PHE159 4.7 7.5 1.0
C A:GLY93 4.8 6.7 1.0
CA A:THR92 4.8 6.3 1.0
HD1 A:PHE159 4.8 4.6 1.0
HH11 A:ARG220 4.8 6.5 1.0
O A:THR92 4.9 8.8 1.0
HB3 A:TYR192 4.9 4.1 1.0
HD12 A:ILE217 4.9 11.3 1.0
CB A:TYR192 5.0 5.3 1.0
HG13 A:ILE217 5.0 9.8 1.0

Reference:

T.N.Safonova, N.N.Mordkovich, V.A.Manuvera, V.P.Veiko, V.O.Popov, K.P.Polyakov. High-Syn Conformation of Uridine and Asymmetry of the Hexameric Molecule Revealed in the High-Resolution Structures of Shewanella Oneidensis Mr-1 Uridine Phosphorylase in the Free Form and in Complex with Uridine. Acta Crystallogr.,Sect.D V. 70 3310 2014.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004714024079
Page generated: Fri Jul 26 01:03:01 2024

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