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Chlorine in PDB 6nxd: Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4

Enzymatic activity of Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4

All present enzymatic activity of Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4:
3.5.1.1;

Protein crystallography data

The structure of Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4, PDB code: 6nxd was solved by J.Lubkowski, A.Wlodawer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.17 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.315, 89.757, 93.083, 90.00, 117.03, 90.00
R / Rfree (%) 20.3 / 24.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4 (pdb code 6nxd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4, PDB code: 6nxd:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 6nxd

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Chlorine binding site 1 out of 10 in the Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1001

b:13.3
occ:1.00
 OG A:SER275 3.1 15.1 1.0
N C:ASP167 3.3 14.0 1.0
N C:GLY168 3.7 15.6 1.0
CB C:ASP167 3.7 14.2 1.0
C C:HIS165 3.7 14.3 1.0
CA C:HIS165 3.8 13.4 1.0
CB C:HIS165 3.8 11.8 1.0
C A:SER275 3.8 14.6 1.0
CA A:GLY276 3.8 15.6 1.0
N A:GLY276 3.8 15.2 1.0
N C:ALA166 3.8 14.1 1.0
CA C:ASP167 3.9 14.7 1.0
CB A:SER275 3.9 13.8 1.0
O A:SER275 4.0 13.3 1.0
C C:ASP167 4.0 16.2 1.0
O A:HOH1202 4.1 38.8 1.0
O C:HIS165 4.4 18.3 1.0
C C:ALA166 4.4 14.2 1.0
OD2 C:ASP167 4.4 16.9 1.0
CA A:SER275 4.5 13.9 1.0
CA C:GLY168 4.5 16.2 1.0
CG C:ASP167 4.6 15.3 1.0
ND1 C:HIS165 4.6 12.5 1.0
CA C:ALA166 4.6 13.5 1.0
CG C:HIS165 4.7 12.5 1.0
O C:HOH1217 4.9 34.4 1.0

Chlorine binding site 2 out of 10 in 6nxd

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Chlorine binding site 2 out of 10 in the Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1002

b:14.7
occ:1.00
 OG C:SER275 3.0 16.4 1.0
N A:ASP167 3.3 13.5 1.0
N A:GLY168 3.6 14.6 1.0
CB A:ASP167 3.7 14.9 1.0
CB A:HIS165 3.7 11.5 1.0
C A:HIS165 3.7 13.0 1.0
CA A:HIS165 3.7 12.8 1.0
N A:ALA166 3.8 14.3 1.0
CA A:ASP167 3.8 15.0 1.0
N C:GLY276 3.8 15.5 1.0
CA C:GLY276 3.8 17.5 1.0
C C:SER275 3.8 15.0 1.0
CB C:SER275 3.9 14.9 1.0
O C:SER275 3.9 13.8 1.0
C A:ASP167 4.0 15.1 1.0
O A:HIS165 4.3 12.9 1.0
C A:ALA166 4.3 13.9 1.0
OD2 A:ASP167 4.4 16.8 1.0
CA A:GLY168 4.4 15.5 1.0
CA C:SER275 4.5 14.5 1.0
CA A:ALA166 4.6 13.5 1.0
CG A:ASP167 4.6 16.8 1.0
CG A:HIS165 4.6 12.7 1.0
ND1 A:HIS165 4.7 12.1 1.0
O A:HOH1165 4.8 45.0 1.0

Chlorine binding site 3 out of 10 in 6nxd

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Chlorine binding site 3 out of 10 in the Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1003

b:21.6
occ:1.00
 O1 A:EDO1007 2.7 37.8 1.0
N A:GLY198 3.2 23.3 1.0
O A:HOH1160 3.3 31.5 1.0
N A:ASN107 3.3 19.1 1.0
C1 A:EDO1007 3.8 37.0 1.0
CA A:GLY198 4.0 21.9 1.0
CA A:ASN107 4.1 19.2 1.0
CD A:ARG331 4.1 16.1 1.0
CG A:GLU106 4.1 26.2 1.0
CA A:HIS197 4.1 25.9 1.0
C A:HIS197 4.1 23.4 1.0
CA A:GLU106 4.2 20.5 1.0
C A:GLU106 4.3 18.5 1.0
NE A:ARG331 4.3 18.6 1.0
O A:PRO196 4.3 31.3 1.0
OD1 A:ASN107 4.5 20.6 1.0
NH1 A:ARG331 4.5 19.9 1.0
CZ A:ARG331 4.5 18.7 1.0
O2 A:EDO1007 4.6 40.4 1.0
C2 A:EDO1007 4.6 37.7 1.0
O A:GLY198 4.7 20.1 1.0
CD2 A:HIS197 4.7 31.8 1.0
CB A:GLU106 4.7 24.6 1.0
OE1 A:GLU106 4.7 39.0 1.0
N A:HIS197 4.8 24.0 1.0
N A:LEU108 4.8 16.0 1.0
C A:GLY198 4.9 21.4 1.0
C A:PRO196 4.9 27.6 1.0
CD A:GLU106 4.9 30.0 1.0
C A:ASN107 5.0 18.2 1.0

Chlorine binding site 4 out of 10 in 6nxd

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Chlorine binding site 4 out of 10 in the Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1004

b:25.1
occ:1.00
 ND1 A:HIS70 3.4 24.1 1.0
CG A:GLU73 3.5 15.9 1.0
CG A:GLN69 3.7 25.5 1.0
NE2 A:GLN69 3.7 34.9 1.0
CB A:GLU73 3.8 16.8 1.0
CE1 A:HIS70 4.0 22.5 1.0
CA A:HIS70 4.1 16.8 1.0
O A:GLN69 4.2 12.5 1.0
CD A:GLN69 4.2 29.1 1.0
C A:GLN69 4.4 16.4 1.0
N A:HIS70 4.4 16.8 1.0
CG A:HIS70 4.5 21.7 1.0
CD A:GLU73 4.8 19.0 1.0
CB A:HIS70 4.8 19.4 1.0
CB A:GLN69 4.9 20.1 1.0

Chlorine binding site 5 out of 10 in 6nxd

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Chlorine binding site 5 out of 10 in the Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1001

b:13.8
occ:1.00
 O B:HOH1241 3.0 36.0 1.0
OG B:SER275 3.1 12.9 1.0
N D:ASP167 3.2 11.1 1.0
N D:GLY168 3.5 10.0 1.0
N D:ALA166 3.6 10.2 1.0
N B:GLY276 3.7 14.7 1.0
C D:HIS165 3.7 12.1 1.0
CA B:GLY276 3.7 15.0 1.0
C B:SER275 3.7 13.7 1.0
CA D:HIS165 3.7 12.2 1.0
CB D:ASP167 3.8 13.0 1.0
CB D:HIS165 3.8 13.9 1.0
CA D:ASP167 3.8 12.1 1.0
O B:SER275 3.8 13.6 1.0
CB B:SER275 4.0 12.9 1.0
C D:ASP167 4.0 11.3 1.0
O B:HOH1226 4.3 34.6 1.0
C D:ALA166 4.3 10.8 1.0
O D:HIS165 4.4 13.7 1.0
CA D:GLY168 4.4 10.1 1.0
OD2 D:ASP167 4.4 13.7 1.0
CA D:ALA166 4.5 10.7 1.0
CA B:SER275 4.5 13.6 1.0
CG D:ASP167 4.6 13.8 1.0
ND1 D:HIS165 4.6 18.9 1.0
CG D:HIS165 4.7 16.7 1.0
O D:HOH1225 4.7 38.6 1.0

Chlorine binding site 6 out of 10 in 6nxd

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Chlorine binding site 6 out of 10 in the Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1002

b:13.4
occ:1.00
 OG D:SER275 3.1 12.1 1.0
O B:HOH1242 3.2 31.4 1.0
N B:ASP167 3.3 10.8 1.0
N B:GLY168 3.6 11.6 1.0
N B:ALA166 3.6 10.4 1.0
C B:HIS165 3.7 13.2 1.0
CB B:ASP167 3.7 12.6 1.0
CA B:HIS165 3.7 12.7 1.0
CA D:GLY276 3.7 15.3 1.0
C D:SER275 3.8 15.0 1.0
CB B:HIS165 3.8 14.4 1.0
N D:GLY276 3.8 16.3 1.0
CA B:ASP167 3.8 11.7 1.0
O D:SER275 3.9 14.2 1.0
CB D:SER275 3.9 12.8 1.0
C B:ASP167 4.0 12.2 1.0
C B:ALA166 4.3 10.2 1.0
O B:HIS165 4.4 15.1 1.0
O B:HOH1185 4.4 36.0 1.0
CA B:GLY168 4.4 11.0 1.0
OD2 B:ASP167 4.4 13.4 1.0
O D:HOH1230 4.5 35.2 1.0
CA D:SER275 4.5 13.3 1.0
CA B:ALA166 4.5 10.7 1.0
CG B:ASP167 4.6 12.3 1.0
CG B:HIS165 4.7 17.4 1.0
ND1 B:HIS165 4.7 18.8 1.0

Chlorine binding site 7 out of 10 in 6nxd

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Chlorine binding site 7 out of 10 in the Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1003

b:19.7
occ:1.00
 O B:HOH1146 3.1 24.5 1.0
N B:LYS4 3.2 19.1 1.0
O2 B:EDO1008 3.2 28.9 1.0
O B:HOH1183 3.2 19.1 1.0
CA B:PRO47 3.6 14.5 1.0
CG B:LYS4 3.7 17.7 1.0
O1 B:EDO1008 3.7 42.1 1.0
CB B:LYS4 3.8 17.3 1.0
CB B:PRO47 3.8 14.8 1.0
CA B:LYS3 3.8 27.0 1.0
N B:PRO47 3.9 16.4 1.0
C B:LYS3 4.0 23.4 1.0
CA B:LYS4 4.1 16.6 1.0
O B:GLN2 4.1 38.4 1.0
CB B:ALA140 4.2 16.0 1.0
C B:MET46 4.3 18.7 1.0
O B:MET46 4.4 17.2 1.0
C2 B:EDO1008 4.4 37.5 1.0
CD B:LYS3 4.6 28.8 1.0
CG B:LYS3 4.6 28.1 1.0
CD B:PRO47 4.6 16.2 1.0
O B:LYS4 4.6 13.4 1.0
C1 B:EDO1008 4.7 37.7 1.0
N B:LYS3 4.7 31.0 1.0
O B:GLU45 4.8 21.4 1.0
CB B:LYS3 4.8 27.7 1.0
C B:GLN2 4.8 35.9 1.0
C B:LYS4 4.9 15.2 1.0
CD B:LYS4 4.9 17.5 1.0
CG B:PRO47 4.9 16.0 1.0
C B:PRO47 4.9 13.8 1.0

Chlorine binding site 8 out of 10 in 6nxd

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Chlorine binding site 8 out of 10 in the Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1004

b:21.1
occ:1.00
 N B:GLU201 3.4 19.9 1.0
CA B:GLY200 3.7 20.8 1.0
C B:GLY200 4.0 19.2 1.0
CB B:GLU201 4.3 23.1 1.0
CA B:GLU201 4.4 20.1 1.0
CG B:GLU201 5.0 25.8 1.0

Chlorine binding site 9 out of 10 in 6nxd

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Chlorine binding site 9 out of 10 in the Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1001

b:19.9
occ:1.00
 O C:HOH1211 3.0 32.9 1.0
N C:GLY198 3.2 22.4 1.0
N C:ASN107 3.4 19.6 1.0
CA C:GLY198 4.0 20.6 1.0
CD C:ARG331 4.1 16.2 1.0
CA C:HIS197 4.1 27.9 1.0
CA C:ASN107 4.1 19.4 1.0
C C:HIS197 4.1 25.3 1.0
CA C:GLU106 4.2 19.1 1.0
CG C:GLU106 4.2 24.2 1.0
O C:HOH1201 4.2 40.1 1.0
O C:PRO196 4.3 30.8 1.0
C C:GLU106 4.3 17.7 1.0
NE C:ARG331 4.3 17.5 1.0
OD1 C:ASN107 4.4 20.2 1.0
NH1 C:ARG331 4.4 18.2 1.0
CZ C:ARG331 4.6 18.2 1.0
CD2 C:HIS197 4.6 35.3 1.0
O C:GLY198 4.7 18.0 1.0
CB C:GLU106 4.8 21.4 1.0
N C:HIS197 4.8 26.7 1.0
N C:LEU108 4.8 18.7 1.0
C C:PRO196 4.9 27.8 1.0
C C:GLY198 4.9 19.6 1.0
C C:ASN107 5.0 20.4 1.0

Chlorine binding site 10 out of 10 in 6nxd

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Chlorine binding site 10 out of 10 in the Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Type I L-Asparaginase From Escherichia Coli in Complex with Citrate at pH 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1001

b:19.4
occ:1.00
 O D:HOH1130 3.1 16.9 1.0
O2 D:EDO1007 3.1 31.5 1.0
O D:HOH1179 3.2 22.3 1.0
N D:LYS4 3.2 19.4 1.0
CA D:PRO47 3.6 13.8 1.0
CG D:LYS4 3.7 19.3 1.0
CB D:LYS4 3.8 18.1 1.0
N D:PRO47 3.9 15.2 1.0
CB D:PRO47 3.9 13.9 1.0
CA D:LYS3 4.0 27.3 1.0
CD D:LYS3 4.0 29.8 1.0
C D:LYS3 4.1 24.6 1.0
CA D:LYS4 4.1 16.8 1.0
O D:GLN2 4.1 39.6 1.0
C D:MET46 4.2 17.5 1.0
CB D:ALA140 4.2 15.8 1.0
C2 D:EDO1007 4.2 37.0 1.0
O D:MET46 4.3 17.5 1.0
C1 D:EDO1007 4.4 37.8 1.0
O D:LYS4 4.7 13.6 1.0
CD D:PRO47 4.7 15.1 1.0
O D:GLU45 4.7 19.1 1.0
CG D:LYS3 4.7 30.1 1.0
O1 D:EDO1007 4.8 38.0 1.0
CD D:LYS4 4.8 20.7 1.0
C D:LYS4 4.9 15.8 1.0
N D:LYS3 4.9 30.7 1.0
CG D:PRO47 4.9 14.7 1.0
C D:GLN2 4.9 37.0 1.0
CB D:LYS3 4.9 28.1 1.0
C D:PRO47 4.9 13.6 1.0

Reference:

J.Lubkowski, W.Chan, A.Wlodawer. Opportunistic Complexes of E. Coli L-Asparaginases with Citrate Anions. Sci Rep V. 9 11070 2019.
ISSN: ESSN 2045-2322
PubMed: 31363102
DOI: 10.1038/S41598-019-46432-0
Page generated: Mon Jul 29 12:19:33 2024

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