Chlorine in PDB 8ruf: Crystal Structure of Rhizobium Etli L-Asparaginase Reav D187A Mutant

Protein crystallography data

The structure of Crystal Structure of Rhizobium Etli L-Asparaginase Reav D187A Mutant, PDB code: 8ruf was solved by K.Pokrywka, M.Grzechowiak, J.Sliwiak, P.Worsztynowicz, J.I.Loch, M.Ruszkowski, M.Gilski, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.57 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.715, 91.26, 114.197, 90, 96.95, 90
R / Rfree (%) 15.8 / 18.4

Other elements in 8ruf:

The structure of Crystal Structure of Rhizobium Etli L-Asparaginase Reav D187A Mutant also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav D187A Mutant (pdb code 8ruf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav D187A Mutant, PDB code: 8ruf:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8ruf

Go back to Chlorine Binding Sites List in 8ruf
Chlorine binding site 1 out of 4 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav D187A Mutant


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 Rhizobium Etli L-Asparaginase Reav D187A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:36.0
occ:1.00
 O A:HOH798 2.8 41.8 1.0
OG1 A:THR341 3.0 23.1 1.0
NH1 A:ARG12 3.2 17.7 1.0
CB A:ASN335 3.6 20.9 1.0
CA B:GLY188 3.6 17.9 1.0
CA A:ASN335 3.7 24.3 1.0
NH2 A:ARG12 3.7 19.9 1.0
CG2 A:THR341 3.9 22.2 1.0
CB A:THR341 3.9 19.0 1.0
CZ A:ARG12 3.9 19.9 1.0
N B:GLY188 3.9 18.8 1.0
N A:ASN335 4.1 22.2 1.0
O A:HOH616 4.1 26.5 1.0
O A:VAL334 4.3 26.2 1.0
C A:VAL334 4.3 25.2 1.0
O A:HOH805 4.4 43.5 1.0
C B:ALA187 4.5 17.8 1.0
O B:ALA187 4.6 19.6 1.0
O B:HOH799 4.7 39.6 1.0
C B:GLY188 4.9 18.1 1.0
N A:VAL334 5.0 24.0 1.0

Chlorine binding site 2 out of 4 in 8ruf

Go back to Chlorine Binding Sites List in 8ruf
Chlorine binding site 2 out of 4 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav D187A Mutant


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 Rhizobium Etli L-Asparaginase Reav D187A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:39.2
occ:1.00
 OG1 B:THR341 3.2 23.4 1.0
NH1 B:ARG12 3.2 21.4 1.0
CB B:ASN335 3.6 20.6 1.0
O B:HOH819 3.6 38.1 1.0
CA B:ASN335 3.7 22.9 1.0
CA A:GLY188 3.7 21.8 1.0
NH2 B:ARG12 3.7 22.6 1.0
CG2 B:THR341 3.9 25.0 1.0
CZ B:ARG12 3.9 19.2 1.0
N A:GLY188 4.0 18.7 1.0
CB B:THR341 4.0 21.6 1.0
N B:ASN335 4.1 21.7 1.0
O B:VAL334 4.2 24.0 1.0
C B:VAL334 4.2 21.8 1.0
C A:ALA187 4.5 17.7 1.0
O A:HOH765 4.5 46.6 1.0
O A:ALA187 4.6 19.4 1.0
O B:HOH735 4.8 23.2 1.0
N B:VAL334 4.9 23.3 1.0
C A:GLY188 5.0 22.4 1.0
CG B:ASN335 5.0 24.7 1.0

Chlorine binding site 3 out of 4 in 8ruf

Go back to Chlorine Binding Sites List in 8ruf
Chlorine binding site 3 out of 4 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav D187A Mutant


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 Rhizobium Etli L-Asparaginase Reav D187A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:35.0
occ:1.00
 O C:HOH819 2.9 36.2 1.0
OG1 C:THR341 3.0 21.8 1.0
NH1 C:ARG12 3.2 21.6 1.0
O C:HOH822 3.4 35.9 1.0
CB C:ASN335 3.5 19.8 1.0
CA D:GLY188 3.5 17.6 1.0
CA C:ASN335 3.6 20.7 1.0
NH2 C:ARG12 3.7 22.6 1.0
N D:GLY188 3.9 19.1 1.0
CZ C:ARG12 3.9 22.3 1.0
CB C:THR341 4.0 20.2 1.0
N C:ASN335 4.0 21.6 1.0
CG2 C:THR341 4.0 20.7 1.0
O C:HOH650 4.0 23.5 1.0
C C:VAL334 4.2 25.0 1.0
O C:HOH776 4.2 43.5 1.0
O C:VAL334 4.2 27.8 1.0
C D:ALA187 4.4 19.4 1.0
O C:HOH838 4.4 48.0 1.0
O D:ALA187 4.4 20.4 1.0
O D:HOH814 4.5 40.4 1.0
C D:GLY188 4.8 19.6 1.0
CG C:ASN335 4.9 21.1 1.0
N C:VAL334 5.0 22.1 1.0

Chlorine binding site 4 out of 4 in 8ruf

Go back to Chlorine Binding Sites List in 8ruf
Chlorine binding site 4 out of 4 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reav D187A Mutant


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 Rhizobium Etli L-Asparaginase Reav D187A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl414

b:34.4
occ:1.00
 OG1 D:THR341 3.1 22.7 1.0
NH1 D:ARG12 3.3 18.1 1.0
O D:HOH830 3.4 42.4 1.0
CB D:ASN335 3.5 19.6 1.0
CA C:GLY188 3.6 16.9 1.0
CA D:ASN335 3.7 23.2 1.0
NH2 D:ARG12 3.8 20.6 1.0
CG2 D:THR341 3.9 25.1 1.0
N C:GLY188 4.0 18.1 1.0
CZ D:ARG12 4.0 18.1 1.0
N D:ASN335 4.0 21.2 1.0
CB D:THR341 4.0 21.1 1.0
C D:VAL334 4.3 23.5 1.0
O D:VAL334 4.3 25.1 1.0
O D:HOH864 4.4 39.9 1.0
C C:ALA187 4.5 18.5 1.0
O C:ALA187 4.6 20.7 1.0
O D:HOH761 4.7 25.6 1.0
O C:HOH738 4.7 42.8 1.0
C C:GLY188 4.9 22.9 1.0
O D:HOH813 4.9 41.7 1.0
CG D:ASN335 4.9 24.9 1.0

Reference:

K.Pokrywka, M.Grzechowiak, J.Sliwiak, P.Worsztynowicz, J.I.Loch, M.Ruszkowski, M.Gilski, M.Jaskolski. Probing the Active Site of Class 3 L-Asparaginase By Mutagenesis. I. Tinkering with the Zinc Coordination Site of Reav Front Chem 2024.
ISSN: ESSN 2296-2646
DOI: 10.3389/FCHEM.2024.1381032
Page generated: Tue Jul 30 12:19:30 2024

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