Atomistry » Chlorine » PDB 6nvh-6o0v » 6nxd
Atomistry »
  Chlorine »
    PDB 6nvh-6o0v »
      6nxd »

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

Go back to Chlorine Binding Sites List in 6nxd
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

Go back to Chlorine Binding Sites List in 6nxd
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

Go back to Chlorine Binding Sites List in 6nxd
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

Go back to Chlorine Binding Sites List in 6nxd
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

Go back to Chlorine Binding Sites List in 6nxd
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

Go back to Chlorine Binding Sites List in 6nxd
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

Go back to Chlorine Binding Sites List in 6nxd
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

Go back to Chlorine Binding Sites List in 6nxd
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

Go back to Chlorine Binding Sites List in 6nxd
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

Go back to Chlorine Binding Sites List in 6nxd
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: Sat Jul 12 17:32:26 2025

Last articles

Cl in 7RN2
Cl in 7RLR
Cl in 7RN1
Cl in 7RMZ
Cl in 7RMT
Cl in 7RME
Cl in 7RMD
Cl in 7RLS
Cl in 7RM2
Cl in 7RMB
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy