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Chlorine in PDB 5vr0: Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus

Enzymatic activity of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus

All present enzymatic activity of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus:
5.3.1.5;

Protein crystallography data

The structure of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus, PDB code: 5vr0 was solved by D.Borek, Z.Otwinowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.90 / 1.70
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.854, 98.061, 102.279, 90.00, 90.00, 90.00
R / Rfree (%) 11.9 / 14.2

Other elements in 5vr0:

The structure of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Calcium (Ca) 3 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus (pdb code 5vr0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus, PDB code: 5vr0:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 5vr0

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Chlorine binding site 1 out of 12 in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl881

b:32.2
occ:0.60
 NZ A:LYS240 2.8 11.0 1.0
O A:HOH512 3.0 23.6 0.5
CE A:LYS240 3.3 10.9 1.0
CB A:PRO209 3.4 12.5 1.0
OE2 A:GLU204 3.5 17.7 0.9
C A:PRO209 3.7 11.6 1.0
O A:PRO209 3.8 10.3 1.0
N A:GLU210 4.0 12.0 1.0
O A:HOH849 4.1 11.7 0.5
OE1 A:GLU204 4.2 19.0 0.9
CD A:GLU204 4.2 16.2 0.9
CA A:PRO209 4.2 11.8 1.0
CA A:GLU210 4.3 13.1 1.0
O A:HOH478 4.4 20.2 0.7
CG A:PRO209 4.5 14.1 1.0
CD A:LYS240 4.7 10.3 1.0
O A:HOH849 4.9 21.1 0.5

Chlorine binding site 2 out of 12 in 5vr0

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Chlorine binding site 2 out of 12 in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl882

b:8.8
occ:0.64
 NE2 A:GLN234 3.1 5.9 1.0
CG A:GLN234 3.6 5.6 1.0
CB A:ALA238 3.8 8.1 1.0
CE3 A:TRP237 3.8 7.2 1.0
CD A:GLN234 3.8 5.7 1.0
CZ3 A:TRP237 3.9 7.5 1.0
CD1 A:LEU200 4.0 6.0 1.0
O A:GLN234 4.2 5.6 1.0
CA A:ALA238 4.8 8.1 1.0
CB A:LEU200 4.8 5.9 1.0
CG A:LEU200 5.0 5.9 1.0

Chlorine binding site 3 out of 12 in 5vr0

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Chlorine binding site 3 out of 12 in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl883

b:12.2
occ:0.73
 O A:HOH479 2.7 16.7 0.9
O A:HOH834 2.8 27.7 1.0
O A:HOH866 2.9 39.6 1.0
N A:LEU241 3.2 7.5 1.0
C A:GLY239 3.5 8.2 1.0
N A:LYS240 3.5 8.0 1.0
CA A:GLY239 3.6 8.3 1.0
CB A:LEU241 3.8 7.3 1.0
CD2 A:LEU236 3.9 6.7 1.0
CA A:LEU241 3.9 7.4 1.0
O A:LEU241 4.0 7.8 1.0
O A:GLY239 4.0 8.2 1.0
CA A:LEU236 4.1 6.3 1.0
C A:LYS240 4.2 7.8 1.0
C A:LEU241 4.2 7.5 1.0
O A:LEU236 4.3 6.9 1.0
CA A:LYS240 4.4 8.2 1.0
O A:ALA235 4.4 6.0 1.0
N A:GLY239 4.5 8.3 1.0
O A:HOH699 4.5 37.3 0.8
O A:HOH591 4.7 26.9 0.9
C A:LEU236 4.7 6.6 1.0
O A:HOH680 4.7 24.0 0.8
CG A:LEU236 4.8 6.5 1.0
CB A:LEU236 4.9 6.4 1.0
N A:LEU236 4.9 6.0 1.0
O A:HOH636 5.0 31.9 0.8
C A:ALA235 5.0 5.9 1.0

Chlorine binding site 4 out of 12 in 5vr0

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Chlorine binding site 4 out of 12 in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl884

b:14.4
occ:0.71
 O A:HOH783 2.5 15.7 1.0
N A:ASP295 3.0 8.3 1.0
OE1 A:GLU294 3.0 7.3 1.0
OD1 A:ASP295 3.1 11.8 0.9
CA A:GLU294 3.3 7.0 1.0
CG A:ASP295 3.5 11.1 0.9
CD A:GLU294 3.6 6.9 1.0
CB A:GLU294 3.7 6.8 1.0
C A:GLU294 3.7 7.5 1.0
CA A:GLY298 3.8 8.7 1.0
N A:GLY298 3.9 9.7 1.0
OD2 A:ASP295 4.0 13.4 0.9
CA A:ASP295 4.0 9.2 0.9
O A:HOH426 4.1 8.0 1.0
OE2 A:GLU294 4.1 6.8 1.0
CB A:ASP295 4.2 10.0 0.9
CG A:GLU294 4.2 6.7 1.0
O A:ASP295 4.3 8.9 0.9
O A:THR293 4.4 6.8 1.0
O A:HOH801 4.5 15.1 1.0
C A:ASP295 4.5 9.5 0.9
N A:GLU294 4.6 6.8 1.0
O A:GLU294 4.9 7.2 1.0
C A:THR293 4.9 6.9 1.0

Chlorine binding site 5 out of 12 in 5vr0

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Chlorine binding site 5 out of 12 in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl885

b:21.5
occ:0.50
 NE A:ARG23 2.6 18.9 0.5
O A:HOH854 2.9 42.7 1.0
N A:ALA29 3.1 12.3 1.0
CG A:ARG23 3.2 16.2 0.5
CZ A:ARG23 3.2 19.0 0.5
CD A:ARG23 3.2 17.5 0.5
NH2 A:ARG23 3.4 19.9 0.5
CB A:ASP28 3.6 16.3 1.0
CA A:ASP28 3.7 14.6 1.0
CB A:ALA29 3.7 11.8 1.0
C A:ASP28 3.9 12.9 1.0
CG A:ASP28 3.9 17.6 1.0
CA A:ALA29 4.0 11.7 1.0
OD1 A:ASP28 4.0 20.4 1.0
CD A:ARG23 4.1 14.2 0.5
CB A:ARG23 4.3 13.9 0.5
NH1 A:ARG23 4.3 19.4 0.5
CG A:ARG23 4.4 13.1 0.5
OD2 A:ASP28 4.7 18.2 1.0
CB A:ARG23 4.9 12.0 0.5

Chlorine binding site 6 out of 12 in 5vr0

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Chlorine binding site 6 out of 12 in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl886

b:73.1
occ:1.00
 CA A:CA895 2.6 40.5 0.7
NH1 A:ARG109 3.6 12.6 1.0
O A:HOH553 3.9 20.6 1.0
CZ A:ARG109 4.5 12.1 1.0
NH2 A:ARG109 4.6 12.9 1.0
O A:HOH453 4.6 17.1 1.0

Chlorine binding site 7 out of 12 in 5vr0

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Chlorine binding site 7 out of 12 in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl887

b:52.5
occ:1.00
 O A:HOH835 2.5 21.7 1.0
O A:ASP9 2.8 13.2 1.0
CE1 A:TYR310 3.6 7.3 1.0
NE A:ARG284 3.6 14.3 1.0
CD A:ARG284 3.6 12.8 1.0
CG A:ARG284 3.7 11.2 1.0
C A:ASP9 3.8 13.0 1.0
CE1 A:PHE11 4.0 7.8 1.0
CD1 A:TYR310 4.0 7.1 1.0
CZ A:PHE11 4.0 7.4 1.0
CA A:ASP9 4.1 14.0 1.0
CZ A:TYR310 4.1 7.3 1.0
CB A:ASP9 4.1 13.5 1.0
CZ A:ARG284 4.2 16.8 1.0
OE2 A:GLU276 4.3 12.1 1.0
OH A:TYR310 4.4 7.8 1.0
CB A:ARG284 4.4 9.6 1.0
CD1 A:PHE11 4.7 7.7 1.0
OD1 A:ASP9 4.7 15.6 1.0
O A:HOH880 4.7 38.6 1.0
CE2 A:PHE11 4.7 7.0 1.0
NH2 A:ARG284 4.7 17.5 1.0
CG A:ASP9 4.8 14.3 1.0
NH1 A:ARG284 4.9 16.5 1.0
CG A:TYR310 4.9 6.8 1.0
NZ A:LYS314 4.9 14.2 1.0
CE2 A:TYR310 5.0 7.1 1.0

Chlorine binding site 8 out of 12 in 5vr0

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Chlorine binding site 8 out of 12 in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl888

b:70.7
occ:1.00
 O A:HOH797 2.8 17.2 1.0
CD A:ARG32 3.7 18.4 0.8
CG A:ARG32 3.9 16.3 0.8
NE A:ARG32 4.1 19.3 0.8
CB A:ARG32 4.3 15.3 1.0
CE2 A:PHE296 4.4 12.4 0.5
O A:HOH529 4.8 17.5 1.0
CD2 A:PHE296 4.9 12.4 0.5

Chlorine binding site 9 out of 12 in 5vr0

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Chlorine binding site 9 out of 12 in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl889

b:31.2
occ:1.00
 O A:GLU294 2.9 7.2 1.0
O A:THR30 3.0 9.9 1.0
C A:GLU294 3.5 7.5 1.0
CB A:THR30 3.7 9.3 1.0
OG1 A:THR30 3.7 8.8 1.0
O A:HOH518 3.8 14.2 0.9
C A:THR30 3.9 9.7 1.0
CG A:ARG31 3.9 8.4 1.0
CA A:ASP295 3.9 9.2 0.9
N A:ASP295 3.9 8.3 1.0
O A:ARG292 4.0 7.3 1.0
CA A:THR30 4.4 9.7 1.0
CB A:ASP295 4.4 10.0 0.9
O A:THR293 4.5 6.8 1.0
N A:GLU294 4.6 6.8 1.0
C A:THR293 4.6 6.9 1.0
CA A:GLU294 4.6 7.0 1.0
O A:HOH529 4.7 17.5 1.0
CD A:ARG31 4.7 8.0 1.0
N A:ARG31 4.8 9.4 1.0
CG2 A:THR30 4.9 9.5 1.0

Chlorine binding site 10 out of 12 in 5vr0

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Chlorine binding site 10 out of 12 in the Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl890

b:44.1
occ:1.00
 O A:HOH863 2.6 23.2 1.0
O A:HOH766 3.0 20.3 1.0
O A:HOH853 3.1 32.5 1.0
CD1 A:TRP270 3.4 5.5 1.0
CB A:ARG266 3.6 6.4 0.4
CB A:ARG266 3.8 6.5 0.6
NE1 A:TRP270 3.8 5.6 1.0
C A:ARG266 3.8 5.9 1.0
N A:ALA267 3.8 5.7 0.5
N A:ALA267 3.8 5.7 0.5
O A:HOH434 3.9 6.6 1.0
O A:ARG266 4.0 5.8 1.0
O A:HOH791 4.1 16.1 1.0
CA A:ALA267 4.2 5.6 0.5
CA A:ALA267 4.2 5.6 0.5
CA A:ARG266 4.4 6.2 1.0
CG A:TRP270 4.6 5.5 1.0
CB A:ALA267 4.7 5.6 0.5
CB A:ALA267 4.7 5.6 0.5
CG A:ARG266 4.8 6.7 0.4
OD1 A:ASP264 4.8 6.7 1.0
NE A:ARG266 4.9 7.0 0.6
CD A:ARG266 4.9 6.8 0.4

Reference:

D.Borek, R.Bromberg, J.Hattne, Z.Otwinowski. Real-Space Analysis of Radiation-Induced Specific Changes with Independent Component Analysis. J Synchrotron Radiat V. 25 451 2018.
ISSN: ESSN 1600-5775
PubMed: 29488925
DOI: 10.1107/S1600577517018148
Page generated: Fri Jul 26 19:00:22 2024

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