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Chlorine in PDB 1k2x: Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene

Enzymatic activity of Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene

All present enzymatic activity of Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene:
3.5.1.1;

Protein crystallography data

The structure of Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene, PDB code: 1k2x was solved by D.Borek, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.50 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.296, 77.624, 148.152, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19.8

Other elements in 1k2x:

The structure of Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene (pdb code 1k2x). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene, PDB code: 1k2x:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 1k2x

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Chlorine binding site 1 out of 9 in the Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl803

b:21.3
occ:1.00
 O A:HOH883 3.2 27.1 1.0
O A:HOH906 3.3 28.4 1.0
NE2 A:GLN23 3.3 10.9 1.0
CD2 A:LEU22 3.8 7.5 1.0
CG A:GLN23 4.0 10.1 1.0
CD A:GLN23 4.2 11.0 1.0
CG A:LEU22 4.4 8.2 1.0
CB A:LEU22 4.4 9.2 1.0
N A:GLN23 5.0 9.5 1.0

Chlorine binding site 2 out of 9 in 1k2x

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Chlorine binding site 2 out of 9 in the Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene


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 Putative Asparaginase Encoded By Escherichia Coli Ybik Gene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl808

b:50.9
occ:1.00
 N A:SER147 3.1 12.9 1.0
O A:HOH916 3.4 30.1 1.0
CA A:THR146 3.6 10.1 1.0
OG A:SER147 3.6 16.9 1.0
C A:THR146 3.8 11.2 1.0
O A:HOH934 3.9 34.6 1.0
CB A:THR146 3.9 10.0 1.0
CB A:SER147 4.0 14.4 1.0
CA A:SER147 4.2 14.2 1.0
CG2 A:THR146 4.4 10.4 1.0
O A:HOH1015 4.5 42.4 1.0
O A:SER145 4.7 7.9 1.0
N A:THR146 4.8 9.0 1.0
N A:LEU148 5.0 15.7 1.0

Chlorine binding site 3 out of 9 in 1k2x

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Chlorine binding site 3 out of 9 in the Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene


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 Putative Asparaginase Encoded By Escherichia Coli Ybik Gene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl810

b:34.2
occ:1.00
 O A:HOH1038 2.8 41.8 1.0
N B:GLU293 3.2 10.0 1.0
N A:ALA14 3.5 13.6 1.0
CB B:THR292 3.6 8.8 1.0
CA A:ALA14 3.6 14.8 1.0
C A:GLY13 3.6 11.8 1.0
CG B:GLU293 3.6 14.8 1.0
O A:GLY13 3.7 11.0 1.0
CA B:THR292 3.7 9.1 1.0
CB A:ALA14 3.9 15.0 1.0
CB B:GLU293 3.9 11.2 1.0
CG2 B:THR292 3.9 9.7 1.0
C B:THR292 4.0 9.4 1.0
OE2 B:GLU293 4.0 24.7 1.0
CD B:GLU293 4.1 19.4 1.0
CA B:GLU293 4.2 10.6 1.0
CA A:GLY13 4.4 10.8 1.0
OG1 B:THR292 4.9 7.4 1.0
OE1 B:GLU293 5.0 22.0 1.0
C A:ALA14 5.0 16.2 1.0

Chlorine binding site 4 out of 9 in 1k2x

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Chlorine binding site 4 out of 9 in the Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene


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 Putative Asparaginase Encoded By Escherichia Coli Ybik Gene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl811

b:60.9
occ:1.00
 O A:HOH841 3.1 18.7 1.0
O A:HOH912 3.4 26.8 1.0
CB A:ARG104 3.6 6.7 1.0
CG1 A:VAL139 3.7 10.6 1.0
CD A:ARG104 3.9 9.1 1.0
CB A:GLU137 3.9 11.6 1.0
OE1 A:GLU137 4.0 22.4 1.0
O A:HOH877 4.1 23.0 1.0
CG A:ARG104 4.3 7.6 1.0
O A:HOH849 4.3 19.9 1.0
O A:HOH924 4.5 40.3 1.0
O A:GLU137 4.6 11.5 1.0
CD A:GLU137 4.6 18.2 1.0
CG A:GLU137 4.7 14.7 1.0
CA A:GLU137 4.9 11.0 1.0
C A:GLU137 4.9 11.2 1.0
CA A:ARG104 4.9 6.7 1.0
N A:ARG104 5.0 6.9 1.0

Chlorine binding site 5 out of 9 in 1k2x

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Chlorine binding site 5 out of 9 in the Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene


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 Putative Asparaginase Encoded By Escherichia Coli Ybik Gene within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl804

b:21.3
occ:1.00
 NE2 C:GLN23 3.2 9.5 1.0
CD2 C:LEU22 3.9 6.2 1.0
CG C:GLN23 4.0 8.3 1.0
CB C:LEU22 4.0 6.6 1.0
CD C:GLN23 4.1 9.6 1.0
CG C:LEU22 4.2 6.6 1.0
N C:GLN23 4.6 6.6 1.0

Chlorine binding site 6 out of 9 in 1k2x

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Chlorine binding site 6 out of 9 in the Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene


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 Putative Asparaginase Encoded By Escherichia Coli Ybik Gene within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl807

b:40.1
occ:1.00
 O C:HOH897 3.0 32.5 1.0
NH1 C:ARG104 3.1 16.0 1.0
O C:HOH859 3.5 28.8 1.0
CG1 C:VAL139 3.5 10.9 1.0
CD C:ARG104 3.6 10.9 1.0
OE1 C:GLU137 3.8 25.6 1.0
CZ C:ARG104 4.1 14.0 1.0
CD1 C:ILE143 4.1 12.2 0.5
CD1 C:ILE143 4.2 13.8 0.5
NE C:ARG104 4.3 11.3 1.0
CD C:GLU137 4.3 21.1 1.0
CG C:ARG104 4.4 9.1 1.0
O C:HOH969 4.5 40.6 1.0
CB C:ARG104 4.5 7.6 1.0
OE2 C:GLU137 4.7 24.6 1.0
CB C:VAL139 4.8 10.3 1.0

Chlorine binding site 7 out of 9 in 1k2x

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Chlorine binding site 7 out of 9 in the Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene


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 Putative Asparaginase Encoded By Escherichia Coli Ybik Gene within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl809

b:38.5
occ:1.00
 N C:SER147 3.2 12.0 1.0
O C:HOH836 3.3 21.9 1.0
OG C:SER147 3.4 17.3 1.0
CA C:THR146 3.6 10.2 1.0
CB C:THR146 3.8 10.2 1.0
C C:THR146 3.9 11.0 1.0
O C:HOH865 3.9 28.5 1.0
CB C:SER147 4.1 13.4 1.0
CA C:SER147 4.2 13.1 1.0
CG2 C:THR146 4.4 10.0 1.0
O C:SER145 4.7 8.6 1.0
O C:HOH937 4.7 49.0 1.0
O C:HOH845 4.8 25.5 1.0
N C:THR146 4.8 9.3 1.0

Chlorine binding site 8 out of 9 in 1k2x

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Chlorine binding site 8 out of 9 in the Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene


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 Putative Asparaginase Encoded By Escherichia Coli Ybik Gene within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl805

b:30.8
occ:1.00
 NE D:ARG262 3.2 11.7 1.0
NH2 D:ARG262 3.3 14.0 1.0
NZ D:LYS267 3.3 10.1 1.0
O B:HOH356 3.4 34.3 1.0
CE1 B:TYR251 3.6 6.2 1.0
OH B:TYR251 3.7 6.1 1.0
CZ D:ARG262 3.7 12.8 1.0
CD D:LYS267 3.7 10.7 1.0
CE D:LYS267 3.8 13.1 1.0
CZ B:TYR251 4.1 6.1 1.0
CD2 D:LEU248 4.3 8.6 1.0
CD D:ARG262 4.3 10.8 1.0
CG D:ARG262 4.3 9.5 1.0
CG D:LYS267 4.6 9.6 1.0
CD1 B:TYR251 4.7 6.0 1.0
O D:HOH833 4.8 29.2 1.0
NH1 D:ARG262 5.0 12.2 1.0

Chlorine binding site 9 out of 9 in 1k2x

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Chlorine binding site 9 out of 9 in the Crystal Structure of Putative Asparaginase Encoded By Escherichia Coli Ybik Gene


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 Putative Asparaginase Encoded By Escherichia Coli Ybik Gene within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl806

b:31.2
occ:1.00
 N D:GLU293 3.2 9.5 1.0
O C:HOH928 3.3 20.2 1.0
O D:HOH870 3.4 46.4 1.0
CB D:THR292 3.6 8.9 1.0
CA D:THR292 3.8 9.1 1.0
CB D:GLU293 3.9 10.1 1.0
CG2 D:THR292 3.9 9.8 1.0
C D:THR292 4.0 9.2 1.0
O C:HOH949 4.0 37.2 1.0
CA D:GLU293 4.1 9.9 1.0
O C:GLY13 4.2 18.5 1.0
CA C:GLY13 4.4 14.4 1.0
C C:GLY13 4.7 16.8 1.0
OG1 D:THR292 4.9 8.1 1.0
O C:ILE15 5.0 18.5 1.0
N D:GLY294 5.0 8.8 1.0

Reference:

K.Michalska, D.Borek, A.Hernandez-Santoyo, M.Jaskolski. Crystal Packing of Plant-Type L-Asparaginase From Escherichia Coli. Acta Crystallogr.,Sect.D V. 64 309 2008.
ISSN: ISSN 0907-4449
PubMed: 18323626
DOI: 10.1107/S0907444907068072
Page generated: Fri Jul 19 23:07:39 2024

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