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Chlorine in PDB 2qkf: Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

Enzymatic activity of Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

All present enzymatic activity of Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis:
2.5.1.55;

Protein crystallography data

The structure of Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 2qkf was solved by F.C.Cochrane, M.L.Patchett, G.B.Jameson, E.J.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.515, 85.295, 162.686, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 23.5

Other elements in 2qkf:

The structure of Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis (pdb code 2qkf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 2qkf:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 2qkf

Go back to Chlorine Binding Sites List in 2qkf
Chlorine binding site 1 out of 5 in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis


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 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl281

b:41.9
occ:1.00
 NH2 B:ARG165 2.8 31.6 0.5
NH1 D:ARG117 3.0 51.4 1.0
N B:GLN138 3.1 25.4 1.0
NE2 B:GLN138 3.3 35.9 1.0
CG B:GLN138 3.5 31.8 1.0
CZ B:ARG165 3.5 30.8 0.5
NH1 B:ARG165 3.5 31.3 0.5
NH2 D:ARG117 3.6 52.3 1.0
NE B:ARG165 3.6 32.6 0.5
CD B:ARG165 3.7 32.0 0.5
CB B:ALA113 3.7 31.9 1.0
CA B:PRO137 3.7 28.8 1.0
CZ D:ARG117 3.7 51.4 1.0
CB B:GLN138 3.8 29.6 1.0
C B:PRO137 3.9 26.8 1.0
CD B:GLN138 3.9 34.0 1.0
CA B:GLN138 4.1 27.6 1.0
CB B:PRO137 4.4 27.8 1.0
CZ B:ARG165 4.6 32.8 0.5
O B:LYS136 4.7 23.3 1.0
CG B:ARG165 4.7 30.2 0.5
NE B:ARG165 4.7 29.8 0.5
O B:HOH391 4.8 38.8 1.0
C B:ALA113 4.8 30.9 1.0
CD2 B:PHE139 4.8 37.9 1.0
CE2 B:PHE139 4.8 38.8 1.0
N B:PHE114 4.8 32.9 1.0
N B:PRO137 4.9 26.6 1.0
CA B:ALA113 4.9 31.0 1.0
NE D:ARG117 5.0 49.7 1.0

Chlorine binding site 2 out of 5 in 2qkf

Go back to Chlorine Binding Sites List in 2qkf
Chlorine binding site 2 out of 5 in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis


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 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl281

b:41.6
occ:1.00
 N C:GLN138 3.3 30.8 1.0
NE2 C:GLN138 3.4 34.8 1.0
CG C:GLN138 3.4 33.2 1.0
NE C:ARG165 3.5 38.5 1.0
CB C:ALA113 3.7 33.8 1.0
CB C:GLN138 3.8 32.5 1.0
NH1 A:ARG117 3.9 46.5 0.5
CA C:PRO137 3.9 30.6 1.0
CD C:GLN138 3.9 34.4 1.0
C C:PRO137 4.1 27.3 1.0
CZ C:ARG165 4.1 39.4 1.0
CD C:ARG165 4.2 35.4 1.0
NH2 C:ARG165 4.2 40.0 1.0
CA C:GLN138 4.2 29.5 1.0
CB C:PRO137 4.5 31.9 1.0
N C:PHE114 4.6 36.3 1.0
C C:ALA113 4.6 33.6 1.0
CE2 C:PHE139 4.7 42.7 1.0
CA C:ALA113 4.8 31.5 1.0
CD2 C:PHE139 4.8 42.6 1.0
O C:LYS136 4.9 23.1 1.0
CZ A:ARG117 4.9 46.7 0.5

Chlorine binding site 3 out of 5 in 2qkf

Go back to Chlorine Binding Sites List in 2qkf
Chlorine binding site 3 out of 5 in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis


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 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl282

b:36.9
occ:1.00
 NE2 C:GLN110 3.2 26.8 1.0
NZ C:LYS135 3.2 34.7 1.0
CE C:LYS52 3.3 31.0 0.5
CE1 C:HIS199 3.5 30.4 1.0
CZ C:PHE234 3.5 34.9 1.0
NZ C:LYS52 3.7 30.9 0.5
NZ C:LYS52 3.7 26.3 0.5
CE2 C:PHE234 3.7 34.8 1.0
CE C:LYS135 3.9 34.9 1.0
CE C:LYS52 3.9 27.0 0.5
OE2 C:GLU236 3.9 38.4 1.0
O C:HOH311 3.9 37.4 1.0
ND1 C:HIS199 4.0 29.0 1.0
CD C:GLN110 4.3 25.8 1.0
NE2 C:HIS199 4.4 29.7 1.0
OE1 C:GLN110 4.6 26.4 1.0
CD C:LYS52 4.7 30.4 0.5
NZ C:LYS57 4.7 43.3 0.5
OD2 C:ASP196 4.7 26.0 1.0
CD C:LYS52 4.7 27.1 0.5
O C:HOH375 4.7 35.9 1.0
CE1 C:PHE234 4.8 34.7 1.0

Chlorine binding site 4 out of 5 in 2qkf

Go back to Chlorine Binding Sites List in 2qkf
Chlorine binding site 4 out of 5 in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis


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 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl281

b:35.7
occ:1.00
 NZ D:LYS135 3.1 32.5 1.0
NE2 D:GLN110 3.3 27.4 1.0
CE1 D:HIS199 3.4 29.0 1.0
CZ D:PHE234 3.5 27.2 1.0
NZ D:LYS52 3.7 33.9 1.0
CE D:LYS52 3.7 34.0 1.0
CE2 D:PHE234 3.8 26.9 1.0
ND1 D:HIS199 3.9 26.7 1.0
CE D:LYS135 3.9 32.2 1.0
OE2 D:GLU236 4.0 39.8 1.0
O D:HOH320 4.2 29.7 1.0
NE2 D:HIS199 4.3 27.6 1.0
CD D:GLN110 4.3 28.3 1.0
OE1 D:GLN110 4.5 30.5 1.0
OD2 D:ASP196 4.5 27.8 1.0
CE1 D:PHE234 4.7 27.2 1.0
CD D:LYS52 4.7 33.5 1.0
O D:HOH295 4.8 34.0 1.0
O D:HOH319 4.9 34.6 1.0

Chlorine binding site 5 out of 5 in 2qkf

Go back to Chlorine Binding Sites List in 2qkf
Chlorine binding site 5 out of 5 in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis


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 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl282

b:48.1
occ:1.00
 NE2 D:GLN138 2.8 39.4 1.0
N D:GLN138 3.1 28.1 1.0
CG D:GLN138 3.2 36.2 1.0
CD D:GLN138 3.4 38.6 1.0
CB D:ALA113 3.6 33.1 1.0
CB D:GLN138 3.6 34.0 1.0
CE1 D:PHE114 3.6 34.7 0.5
CD1 D:PHE114 3.8 34.7 0.5
CA D:PRO137 3.9 28.6 1.0
NE D:ARG165 3.9 35.1 1.0
CA D:GLN138 4.0 30.9 1.0
C D:PRO137 4.0 24.0 1.0
CD D:ARG165 4.2 32.6 1.0
CZ D:ARG165 4.3 36.4 1.0
CB D:PRO137 4.5 29.2 1.0
C D:ALA113 4.6 33.7 1.0
OE1 D:GLN138 4.6 40.5 1.0
NH2 D:ARG165 4.7 37.5 1.0
CA D:ALA113 4.7 31.9 1.0
N D:PHE114 4.7 34.0 0.5
N D:PHE114 4.7 33.5 0.5
CD2 D:PHE139 4.7 37.2 1.0
CE2 D:PHE139 4.8 38.0 1.0
O D:LYS136 4.9 23.8 1.0
O D:ALA113 4.9 34.6 1.0
CZ D:PHE114 4.9 34.8 0.5
N D:PHE139 5.0 30.5 1.0
NH1 D:ARG165 5.0 35.4 1.0

Reference:

F.C.Cochrane, M.L.Patchett, G.B.Jameson, E.J.Parker. Re-Establishing A Metal-Binding Scaffold with Full Activity in the Metal-Independent KDO8P Synthase From Neisseria Meningitidis To Be Published.
Page generated: Sat Jul 20 10:48:36 2024

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