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Chlorine in PDB 4usm: Wcbl Complex with Glycerol Bound to Sugar Site

Enzymatic activity of Wcbl Complex with Glycerol Bound to Sugar Site

All present enzymatic activity of Wcbl Complex with Glycerol Bound to Sugar Site:
2.7.1.167;

Protein crystallography data

The structure of Wcbl Complex with Glycerol Bound to Sugar Site, PDB code: 4usm was solved by M.Vivoli, M.N.Isupov, R.Nicholas, A.Hill, A.Scott, P.Kosma, J.Prior, N.J.Harmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.16 / 1.82
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 101.050, 115.890, 167.400, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Wcbl Complex with Glycerol Bound to Sugar Site (pdb code 4usm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Wcbl Complex with Glycerol Bound to Sugar Site, PDB code: 4usm:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4usm

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Chlorine binding site 1 out of 8 in the Wcbl Complex with Glycerol Bound to Sugar Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Wcbl Complex with Glycerol Bound to Sugar Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:21.9
occ:1.00
 O A:HOH2353 2.9 29.6 1.0
O A:HOH2504 2.9 32.4 1.0
O A:HOH2228 3.2 23.8 1.0
N A:GLY117 3.2 15.3 1.0
NH2 A:ARG13 3.2 16.1 1.0
CA A:GLY115 3.5 15.7 1.0
C A:GLY115 3.5 14.4 1.0
N A:LEU116 3.7 14.7 1.0
CA A:GLY117 3.7 12.7 1.0
O A:HOH2232 3.9 25.2 1.0
O A:GLY115 3.9 15.3 1.0
C1 A:GOL400 4.0 29.9 1.0
O1 A:GOL400 4.0 25.6 1.0
N A:GLY115 4.1 15.3 1.0
CA A:GLY299 4.2 19.0 1.0
CZ A:ARG13 4.2 21.1 1.0
O A:HOH2355 4.3 33.8 1.0
C A:LEU116 4.3 16.4 1.0
NH1 A:ARG13 4.4 17.7 1.0
OD2 A:ASP163 4.4 17.8 1.0
CL A:CL402 4.4 19.8 1.0
CA A:LEU116 4.5 13.7 1.0
N A:ALA300 4.8 16.1 1.0
C A:GLY117 4.8 13.3 1.0
N A:SER118 4.9 12.7 1.0
O A:HOH2231 5.0 15.3 1.0

Chlorine binding site 2 out of 8 in 4usm

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Chlorine binding site 2 out of 8 in the Wcbl Complex with Glycerol Bound to Sugar Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Wcbl Complex with Glycerol Bound to Sugar Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:19.8
occ:1.00
 OG A:SER118 3.0 16.8 1.0
N A:LEU116 3.2 14.7 1.0
N A:SER118 3.2 12.7 1.0
N A:SER114 3.4 16.2 1.0
O A:HOH2232 3.4 25.2 1.0
N A:GLY115 3.4 15.3 1.0
CB A:SER118 3.5 15.0 1.0
N A:GLY117 3.6 15.3 1.0
CB A:SER114 3.6 16.2 1.0
O A:HOH2228 3.8 23.8 1.0
CA A:SER114 3.8 16.6 1.0
C A:SER114 3.9 16.1 1.0
O A:PRO111 3.9 20.9 1.0
CA A:LEU116 3.9 13.7 1.0
CA A:SER118 3.9 15.8 1.0
C A:LEU116 3.9 16.4 1.0
O A:HOH2227 4.1 40.5 1.0
CB A:LEU116 4.1 14.1 1.0
C A:GLY115 4.2 14.4 1.0
C A:GLY117 4.3 13.3 1.0
CA A:GLY115 4.3 15.7 1.0
N A:GLY113 4.3 21.6 1.0
CL A:CL401 4.4 21.9 1.0
CA A:GLY117 4.4 12.7 1.0
C A:GLY113 4.5 20.3 1.0
OG A:SER114 4.5 18.1 1.0
CA A:GLY113 4.8 19.6 1.0
O A:SER114 4.8 20.2 1.0
O A:LEU116 4.8 12.9 1.0
N A:SER119 4.9 14.7 1.0
C A:ALA112 4.9 23.0 1.0
C A:SER118 4.9 15.2 1.0
C A:PRO111 4.9 26.2 1.0
O A:HOH2504 5.0 32.4 1.0
CG A:LEU116 5.0 12.7 1.0

Chlorine binding site 3 out of 8 in 4usm

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Chlorine binding site 3 out of 8 in the Wcbl Complex with Glycerol Bound to Sugar Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Wcbl Complex with Glycerol Bound to Sugar Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:33.8
occ:1.00
 O A:HOH2021 3.1 24.9 1.0
N A:GLY19 3.1 14.1 1.0
CL A:CL404 3.2 28.8 1.0
NZ A:LYS296 3.2 22.3 1.0
O A:HOH2018 3.3 37.9 1.0
C A:ALA17 3.3 13.5 1.0
CA A:ALA17 3.5 16.6 1.0
N A:ALA17 3.5 14.4 1.0
N A:GLY18 3.6 14.9 1.0
CA A:GLY19 3.6 16.8 1.0
O A:ALA17 3.7 13.7 1.0
CE A:LYS296 3.8 19.9 1.0
C A:GLY15 3.9 16.8 1.0
O A:GLY15 4.0 19.5 1.0
C A:LEU16 4.0 14.9 1.0
NZ A:LYS268 4.1 15.6 1.0
C A:GLY18 4.2 14.5 1.0
CA A:GLY15 4.2 14.9 1.0
N A:LEU16 4.2 14.6 1.0
O A:LEU16 4.4 14.2 1.0
CA A:GLY18 4.4 11.7 1.0
O A:SER298 4.5 29.4 1.0
O A:HOH2438 4.5 34.9 1.0
O A:HOH2429 4.5 31.5 1.0
C A:GLY19 4.6 16.5 1.0
O A:GLY19 4.7 14.5 1.0
CA A:LEU16 4.7 13.6 1.0

Chlorine binding site 4 out of 8 in 4usm

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Chlorine binding site 4 out of 8 in the Wcbl Complex with Glycerol Bound to Sugar Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Wcbl Complex with Glycerol Bound to Sugar Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:28.8
occ:1.00
 O A:HOH2438 2.8 34.9 1.0
O A:SER298 2.8 29.4 1.0
NE2 A:GLN162 3.1 16.7 1.0
CL A:CL403 3.2 33.8 1.0
O A:HOH2018 3.5 37.9 1.0
CA A:GLY15 3.7 14.9 1.0
O A:GLY299 3.8 15.5 1.0
CA A:GLY299 3.8 19.0 1.0
CA A:GLY19 3.9 16.8 1.0
C A:GLY299 3.9 19.9 1.0
C A:SER298 4.0 24.2 1.0
CD A:GLN162 4.2 24.1 1.0
NZ A:LYS268 4.2 15.6 1.0
C A:GLY15 4.4 16.8 1.0
N A:GLY299 4.5 18.3 1.0
N A:GLY19 4.5 14.1 1.0
NH2 A:ARG13 4.5 16.1 1.0
OE1 A:GLN162 4.5 25.3 1.0
CZ A:ARG13 4.6 21.1 1.0
C3 A:GOL400 4.6 35.0 1.0
N A:GLY15 4.6 11.8 1.0
NZ A:LYS296 4.7 22.3 1.0
O A:GLY15 4.7 19.5 1.0
NH1 A:ARG13 4.7 17.7 1.0
N A:ALA300 4.8 16.1 1.0
C A:GLY19 5.0 16.5 1.0

Chlorine binding site 5 out of 8 in 4usm

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Chlorine binding site 5 out of 8 in the Wcbl Complex with Glycerol Bound to Sugar Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Wcbl Complex with Glycerol Bound to Sugar Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:26.6
occ:1.00
 O B:HOH2275 2.9 32.7 1.0
O B:HOH2187 3.1 24.4 1.0
O B:HOH2068 3.2 38.9 1.0
NH2 B:ARG13 3.2 18.9 1.0
N B:GLY117 3.2 18.1 1.0
CA B:GLY115 3.5 19.5 1.0
C B:GLY115 3.5 17.1 1.0
N B:LEU116 3.7 18.0 1.0
CA B:GLY117 3.7 12.9 1.0
O B:GLY115 3.9 18.4 1.0
C1 B:GOL400 4.0 33.4 1.0
O1 B:GOL400 4.0 30.8 1.0
O B:HOH2190 4.0 22.5 1.0
N B:GLY115 4.1 19.9 1.0
O B:HOH2277 4.1 37.5 1.0
CZ B:ARG13 4.2 22.4 1.0
CA B:GLY299 4.2 26.4 1.0
C B:LEU116 4.3 20.0 1.0
NH1 B:ARG13 4.4 20.1 1.0
OD2 B:ASP163 4.4 22.1 1.0
CL B:CL402 4.4 21.8 1.0
CA B:LEU116 4.5 18.8 1.0
N B:ALA300 4.8 19.1 1.0
C B:GLY117 4.8 16.1 1.0
N B:SER118 5.0 16.5 1.0

Chlorine binding site 6 out of 8 in 4usm

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Chlorine binding site 6 out of 8 in the Wcbl Complex with Glycerol Bound to Sugar Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Wcbl Complex with Glycerol Bound to Sugar Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:21.8
occ:1.00
 OG B:SER118 3.0 20.4 1.0
N B:LEU116 3.2 18.0 1.0
N B:SER118 3.2 16.5 1.0
N B:SER114 3.4 19.7 1.0
N B:GLY115 3.5 19.9 1.0
CB B:SER118 3.5 16.4 1.0
CB B:SER114 3.5 20.8 1.0
O B:HOH2190 3.6 22.5 1.0
N B:GLY117 3.6 18.1 1.0
O B:HOH2187 3.7 24.4 1.0
CA B:SER114 3.7 20.2 1.0
CA B:LEU116 3.8 18.8 1.0
C B:SER114 3.9 18.0 1.0
O B:PRO111 3.9 22.5 1.0
C B:LEU116 3.9 20.0 1.0
CA B:SER118 3.9 18.1 1.0
CB B:LEU116 4.0 16.7 1.0
O B:HOH2186 4.0 45.8 1.0
C B:GLY115 4.2 17.1 1.0
CA B:GLY115 4.3 19.5 1.0
C B:GLY117 4.3 16.1 1.0
N B:GLY113 4.3 26.1 1.0
CA B:GLY117 4.4 12.9 1.0
CL B:CL401 4.4 26.6 1.0
OG B:SER114 4.4 21.2 1.0
C B:GLY113 4.5 25.0 1.0
O B:LEU116 4.8 17.1 1.0
O B:SER114 4.8 23.5 1.0
CA B:GLY113 4.8 25.3 1.0
C B:ALA112 4.9 24.2 1.0
N B:SER119 4.9 18.9 1.0
CG B:LEU116 4.9 14.4 1.0
C B:PRO111 4.9 28.1 1.0
C B:SER118 4.9 16.5 1.0
CA B:ALA112 5.0 37.3 1.0

Chlorine binding site 7 out of 8 in 4usm

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Chlorine binding site 7 out of 8 in the Wcbl Complex with Glycerol Bound to Sugar Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Wcbl Complex with Glycerol Bound to Sugar Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:37.0
occ:1.00
 NZ B:LYS296 2.9 19.4 0.3
O B:HOH2020 3.0 29.0 1.0
N B:GLY19 3.1 18.0 1.0
NZ B:LYS296 3.2 15.9 0.7
O B:HOH2017 3.2 47.3 1.0
CL B:CL404 3.3 31.6 1.0
C B:ALA17 3.4 18.2 1.0
CA B:ALA17 3.5 18.7 1.0
N B:ALA17 3.6 15.6 1.0
N B:GLY18 3.6 18.0 1.0
CA B:GLY19 3.6 17.9 1.0
O B:ALA17 3.7 17.4 1.0
CE B:LYS296 3.8 14.6 0.7
C B:GLY15 3.9 15.0 1.0
O B:GLY15 4.0 20.6 1.0
CE B:LYS296 4.0 20.0 0.3
C B:LEU16 4.0 17.1 1.0
NZ B:LYS268 4.1 21.7 1.0
C B:GLY18 4.2 16.8 1.0
CA B:GLY15 4.3 14.0 1.0
N B:LEU16 4.3 17.2 1.0
O B:LEU16 4.4 19.3 1.0
CA B:GLY18 4.4 13.0 1.0
O B:SER298 4.5 39.4 1.0
O B:HOH2334 4.5 31.1 1.0
O B:GLY19 4.6 20.1 1.0
C B:GLY19 4.6 20.5 1.0
CA B:LEU16 4.7 13.6 1.0

Chlorine binding site 8 out of 8 in 4usm

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Chlorine binding site 8 out of 8 in the Wcbl Complex with Glycerol Bound to Sugar Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Wcbl Complex with Glycerol Bound to Sugar Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:31.6
occ:1.00
 O B:SER298 2.8 39.4 1.0
NE2 B:GLN162 3.1 22.6 1.0
CL B:CL403 3.3 37.0 1.0
O B:HOH2017 3.4 47.3 1.0
O B:GLY299 3.7 19.7 1.0
CA B:GLY15 3.7 14.0 1.0
CA B:GLY299 3.8 26.4 1.0
C B:GLY299 3.8 23.6 1.0
CA B:GLY19 3.9 17.9 1.0
C B:SER298 4.0 32.4 1.0
CD B:GLN162 4.2 26.0 1.0
NZ B:LYS268 4.3 21.7 1.0
NH2 B:ARG13 4.4 18.9 1.0
N B:GLY299 4.4 19.8 1.0
OE1 B:GLN162 4.4 25.5 1.0
C3 B:GOL400 4.4 39.2 1.0
CZ B:ARG13 4.5 22.4 1.0
C B:GLY15 4.5 15.0 1.0
N B:GLY19 4.5 18.0 1.0
N B:GLY15 4.6 15.8 1.0
N B:ALA300 4.7 19.1 1.0
NH1 B:ARG13 4.7 20.1 1.0
O B:GLY15 4.7 20.6 1.0
NZ B:LYS296 4.8 15.9 0.7
NE B:ARG13 5.0 21.4 1.0

Reference:

M.Vivoli, M.N.Isupov, R.Nicholas, A.Hill, A.E.Scott, P.Kosma, J.L.Prior, N.J.Harmer. Unraveling the B.Pseudomallei Heptokinase Wcbl: From Structure to Drug Discovery. Chem.Biol. V. 22 1622 2015.
ISSN: ISSN 1074-5521
PubMed: 26687481
DOI: 10.1016/J.CHEMBIOL.2015.10.015
Page generated: Fri Jul 26 02:27:08 2024

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