Chlorine in PDB 8ori: Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic)

Protein crystallography data

The structure of Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic), PDB code: 8ori was solved by J.Loch, P.Worsztynowicz, J.Sliwiak, B.Imiolczyk, M.Grzechowiak, M.Gilski, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.42 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.2, 89.881, 169.797, 90, 90, 90
R / Rfree (%) 13 / 17.7

Other elements in 8ori:

The structure of Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic) (pdb code 8ori). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic), PDB code: 8ori:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 8ori

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Chlorine binding site 1 out of 10 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic)


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 Reaiv (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:26.0
occ:1.00
 O A:HOH813 2.8 38.4 1.0
O A:HOH736 3.0 45.7 1.0
O A:HOH809 3.0 29.8 1.0
N A:GLU214 3.3 18.6 1.0
CD A:ARG172 3.3 53.0 1.0
CA A:LEU213 3.8 17.1 1.0
CD A:ARG217 3.9 17.6 1.0
NH1 A:ARG217 3.9 22.6 1.0
CB A:GLU214 3.9 27.4 1.0
CB A:ARG217 3.9 15.2 1.0
CG A:GLU214 4.0 35.8 1.0
C A:LEU213 4.1 18.1 1.0
CD2 A:LEU213 4.1 19.2 1.0
CG A:ARG172 4.2 42.3 1.0
CA A:GLU214 4.2 19.3 1.0
CB A:LEU213 4.3 17.2 1.0
CG A:ARG217 4.3 17.0 1.0
NH2 A:ARG172 4.3 68.3 1.0
NE A:ARG172 4.3 61.2 1.0
NE A:ARG217 4.5 18.5 1.0
CZ A:ARG217 4.5 19.4 1.0
O A:GLY212 4.6 27.4 1.0
CZ A:ARG172 4.7 66.0 1.0
CG A:LEU213 4.8 18.2 1.0
O A:GLU214 4.9 15.8 1.0
CB A:ARG172 5.0 29.7 1.0

Chlorine binding site 2 out of 10 in 8ori

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Chlorine binding site 2 out of 10 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic)


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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 Reaiv (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:28.6
occ:1.00
 O A:HOH811 3.0 31.0 1.0
O A:HOH751 3.0 25.6 1.0
N A:ARG284 3.1 11.9 1.0
N A:THR283 3.5 14.1 1.0
CG A:ARG284 3.5 12.7 1.0
CB A:ARG284 3.6 12.1 1.0
CB A:ALA282 3.9 16.0 1.0
CA A:ARG284 3.9 11.9 1.0
CD A:ARG284 4.0 12.4 1.0
C A:THR283 4.0 12.6 1.0
CA A:THR283 4.0 12.3 1.0
CB A:THR283 4.1 17.0 1.0
C A:ALA282 4.1 12.4 1.0
CA A:ALA282 4.2 12.2 1.0
O A:HOH778 4.4 51.3 1.0
OG1 A:THR283 4.7 23.6 1.0
NE A:ARG284 4.7 11.8 1.0
O A:ALA282 5.0 12.7 1.0

Chlorine binding site 3 out of 10 in 8ori

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Chlorine binding site 3 out of 10 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic)


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 Reaiv (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl704

b:14.0
occ:1.00
 O B:HOH1093 3.1 29.0 1.0
NH2 B:ARG198 3.3 15.5 1.0
N B:LEU32 3.3 12.5 1.0
CB B:LEU32 3.9 12.8 1.0
CA B:LYS31 4.1 14.0 1.0
CA B:LEU32 4.2 12.3 1.0
C B:LYS31 4.2 13.8 1.0
CG B:LYS31 4.3 21.1 1.0
CZ B:ARG198 4.4 15.5 1.0
O B:GLY30 4.6 17.5 1.0
NH1 B:ARG198 4.6 16.1 1.0
O B:LEU32 4.7 17.9 1.0
CB B:LYS31 4.8 15.9 1.0
C B:LEU32 4.9 12.1 1.0

Chlorine binding site 4 out of 10 in 8ori

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Chlorine binding site 4 out of 10 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic)


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 Reaiv (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl705

b:22.8
occ:1.00
 NH2 B:ARG172 2.8 50.5 1.0
CZ B:ARG172 3.1 52.0 1.0
O B:HOH1119 3.2 36.6 1.0
N B:GLU214 3.3 17.2 1.0
NE B:ARG172 3.3 47.5 1.0
NH1 B:ARG217 3.7 22.4 1.0
CD B:ARG217 3.7 17.2 1.0
CA B:LEU213 3.8 15.1 1.0
CG B:GLU214 3.8 32.0 1.0
CB B:GLU214 3.9 23.8 1.0
NH1 B:ARG172 4.0 56.1 1.0
C B:LEU213 4.0 16.1 1.0
CB B:ARG217 4.0 14.7 1.0
CD2 B:LEU213 4.1 18.2 1.0
CA B:GLU214 4.2 17.6 1.0
CB B:LEU213 4.2 14.8 1.0
CG B:ARG217 4.3 15.6 1.0
CZ B:ARG217 4.3 20.7 1.0
NE B:ARG217 4.3 16.5 1.0
CD B:ARG172 4.4 39.1 1.0
O B:GLY212 4.6 25.3 1.0
CB B:ARG172 4.7 25.0 1.0
CG B:LEU213 4.8 15.7 1.0
CG B:ARG172 4.8 33.4 1.0
O B:GLU214 5.0 16.9 1.0

Chlorine binding site 5 out of 10 in 8ori

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Chlorine binding site 5 out of 10 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic)


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 Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:23.3
occ:1.00
 O C:HOH840 3.0 34.1 1.0
NH1 C:ARG172 3.1 68.5 1.0
N C:GLU214 3.3 15.8 1.0
CG C:ARG172 3.6 41.1 1.0
CD C:ARG172 3.7 51.9 1.0
CD C:ARG217 3.8 17.1 1.0
CA C:LEU213 3.8 16.6 1.0
NH1 C:ARG217 3.8 21.5 1.0
CB C:GLU214 3.9 19.6 1.0
CG C:GLU214 3.9 26.9 1.0
CB C:ARG217 4.0 14.4 1.0
C C:LEU213 4.1 16.4 1.0
CD2 C:LEU213 4.1 18.5 1.0
CZ C:ARG172 4.2 66.3 1.0
CA C:GLU214 4.2 15.6 1.0
CG C:ARG217 4.2 15.2 1.0
CB C:LEU213 4.3 16.0 1.0
NE C:ARG172 4.4 59.8 1.0
NE C:ARG217 4.5 17.1 1.0
CZ C:ARG217 4.5 17.8 1.0
O C:GLY212 4.5 24.8 1.0
O C:HOH803 4.8 28.2 1.0
CG C:LEU213 4.8 16.0 1.0
CB C:ARG172 4.9 27.5 1.0
O C:GLU214 5.0 14.3 1.0

Chlorine binding site 6 out of 10 in 8ori

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Chlorine binding site 6 out of 10 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic)


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

b:37.4
occ:1.00
 N C:GLY37 3.0 13.6 1.0
O C:HOH526 3.9 37.6 1.0
CG C:PRO4 3.9 16.4 1.0
CA C:LEU36 3.9 14.1 1.0
CA C:GLY37 3.9 14.9 1.0
C C:LEU36 4.0 13.0 1.0
CD C:PRO4 4.0 15.2 1.0
CG2 C:THR0 4.2 45.9 1.0
CD2 C:LEU36 4.4 20.9 1.0
CB C:PRO4 4.4 15.5 1.0
CB C:LEU36 4.5 16.6 1.0
O C:HOH623 4.6 21.7 1.0
C C:GLY37 5.0 14.4 1.0

Chlorine binding site 7 out of 10 in 8ori

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Chlorine binding site 7 out of 10 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic)


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 Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl405

b:30.9
occ:1.00
 O C:HOH950 3.0 42.6 1.0
O C:HOH891 3.1 27.3 1.0
N C:ALA129 3.1 13.0 1.0
O C:HOH695 3.4 23.4 1.0
CB C:ALA129 3.8 13.2 1.0
CB C:THR128 3.8 15.6 1.0
CA C:THR128 3.8 14.4 1.0
C C:THR128 3.9 13.4 1.0
CG2 C:VAL101 4.0 17.2 1.0
CA C:ALA129 4.0 12.9 1.0
CG2 C:THR128 4.6 19.5 1.0
OG1 C:THR128 4.7 16.4 1.0
O C:HOH932 4.8 42.8 1.0
O C:HOH720 4.9 17.1 1.0

Chlorine binding site 8 out of 10 in 8ori

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Chlorine binding site 8 out of 10 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic)


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 Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl403

b:28.6
occ:1.00
 NH1 D:ARG172 2.9 66.2 1.0
N D:GLU214 3.4 26.1 1.0
CZ D:ARG172 3.5 61.8 1.0
CD D:ARG217 3.7 17.5 1.0
CG D:ARG172 3.8 33.3 1.0
NH1 D:ARG217 3.8 22.3 1.0
CG D:GLU214 3.9 43.9 1.0
CA D:LEU213 3.9 23.9 1.0
CB D:GLU214 4.0 35.0 1.0
CB D:ARG217 4.0 16.2 1.0
NE D:ARG172 4.1 53.3 1.0
CD2 D:LEU213 4.1 22.3 1.0
O D:HOH781 4.1 37.3 1.0
C D:LEU213 4.2 24.3 1.0
CD D:ARG172 4.2 42.6 1.0
NH2 D:ARG172 4.2 64.6 1.0
CA D:GLU214 4.3 28.4 1.0
CG D:ARG217 4.3 17.2 1.0
NE D:ARG217 4.3 18.1 1.0
CB D:LEU213 4.4 19.9 1.0
CZ D:ARG217 4.4 19.9 1.0
O D:GLY212 4.7 32.9 1.0
CG D:LEU213 4.9 20.9 1.0
O D:GLU214 5.0 20.7 1.0

Chlorine binding site 9 out of 10 in 8ori

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Chlorine binding site 9 out of 10 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic)


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 Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl404

b:14.6
occ:1.00
 O D:HOH525 3.2 41.2 0.5
O D:HOH639 3.2 16.4 1.0
NH2 D:ARG198 3.2 11.3 0.6
N D:LEU32 3.3 13.9 1.0
O D:HOH882 3.5 36.8 1.0
CB D:LEU32 3.8 13.1 1.0
CA D:LYS31 4.1 14.9 1.0
CA D:LEU32 4.1 13.4 1.0
C D:LYS31 4.2 13.2 1.0
CZ D:ARG198 4.2 11.5 0.6
NH1 D:ARG198 4.4 12.2 0.6
CG D:LYS31 4.5 20.8 1.0
O D:GLY30 4.6 19.5 1.0
O D:LEU32 4.6 20.2 1.0
CB D:LYS31 4.8 16.0 1.0
C D:LEU32 4.9 15.3 1.0

Chlorine binding site 10 out of 10 in 8ori

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Chlorine binding site 10 out of 10 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic)


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 Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl405

b:51.5
occ:1.00
 NH1 D:ARG122 3.1 18.0 1.0
O D:HOH579 3.5 26.6 1.0
CD D:ARG122 3.7 15.6 1.0
CA D:GLN119 3.7 14.3 1.0
N D:GLN119 4.1 13.5 1.0
CB D:GLN119 4.1 15.0 1.0
O D:HOH686 4.2 36.0 1.0
CZ D:ARG122 4.2 15.9 1.0
CG2 D:ILE118 4.3 15.6 1.0
CG D:GLN119 4.3 23.1 1.0
NE D:ARG122 4.4 15.3 1.0
C D:ILE118 4.5 14.1 1.0
O D:ILE118 4.5 15.7 1.0
O D:HOH803 4.8 30.8 1.0
CG D:ARG122 4.9 14.4 1.0
CB D:ARG122 4.9 15.5 1.0
O D:HOH942 5.0 29.3 1.0
C D:GLN119 5.0 14.1 1.0

Reference:

J.I.Loch, P.Worsztynowicz, J.Sliwiak, M.Grzechowiak, B.Imiolczyk, K.Pokrywka, M.Chwastyk, M.Gilski, M.Jaskolski. Rhizobium Etli Has Two L-Asparaginases with Low Sequence Identity But Similar Structure and Catalytic Center. Acta Crystallogr D Struct V. 79 775 2023BIOL.
ISSN: ISSN 2059-7983
PubMed: 37494066
DOI: 10.1107/S2059798323005648
Page generated: Tue Jul 30 11:16:09 2024

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