Chlorine in PDB 4jth: Crystal Structure of F114R/R117Q Mutant of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

Enzymatic activity of Crystal Structure of F114R/R117Q Mutant of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

All present enzymatic activity of Crystal Structure of F114R/R117Q Mutant 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 F114R/R117Q Mutant of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 4jth was solved by T.M.Allison, F.C.Cochrane, 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) 45.95 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.150, 85.990, 163.110, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.4

Other elements in 4jth:

The structure of Crystal Structure of F114R/R117Q Mutant 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 F114R/R117Q Mutant of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis (pdb code 4jth). 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 F114R/R117Q Mutant of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 4jth:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 4jth

Go back to Chlorine Binding Sites List in 4jth
Chlorine binding site 1 out of 5 in the Crystal Structure of F114R/R117Q Mutant 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 F114R/R117Q Mutant 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:Cl301

b:25.0
occ:1.00
 NH2 B:ARG165 3.1 45.0 1.0
NE B:ARG114 3.2 43.8 1.0
N B:GLN138 3.2 17.2 1.0
NH1 B:ARG165 3.4 51.7 1.0
CG B:GLN138 3.6 23.9 1.0
NE2 B:GLN138 3.7 32.4 1.0
CZ B:ARG165 3.7 45.3 1.0
CA B:PRO137 3.8 16.4 1.0
CB B:ALA113 3.8 19.4 1.0
CD B:ARG114 4.0 36.7 1.0
CB B:GLN138 4.0 19.7 1.0
C B:PRO137 4.0 16.2 1.0
NH1 B:ARG114 4.1 51.4 1.0
CZ B:ARG114 4.1 46.3 1.0
CD B:GLN138 4.1 30.0 1.0
CA B:GLN138 4.2 18.9 1.0
CE2 B:PHE139 4.3 28.6 1.0
CB B:PRO137 4.4 17.0 1.0
CG B:ARG114 4.5 31.9 1.0
CD2 B:PHE139 4.6 28.6 1.0
N B:ARG114 4.8 20.7 1.0
C B:ALA113 4.8 20.1 1.0
O B:LYS136 4.9 14.5 1.0
CA B:ALA113 4.9 18.2 1.0
NE B:ARG165 4.9 41.6 1.0
N B:PRO137 5.0 15.8 1.0

Chlorine binding site 2 out of 5 in 4jth

Go back to Chlorine Binding Sites List in 4jth
Chlorine binding site 2 out of 5 in the Crystal Structure of F114R/R117Q Mutant 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 F114R/R117Q Mutant 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:Cl301

b:25.0
occ:1.00
 NE C:ARG114 3.2 36.4 1.0
O C:HOH589 3.4 37.9 1.0
N C:GLN138 3.4 18.7 1.0
NE2 C:GLN138 3.4 26.4 1.0
CG C:GLN138 3.6 25.1 1.0
NE C:ARG165 3.6 40.9 1.0
CB C:ALA113 3.8 22.0 1.0
NH1 C:ARG114 3.9 35.0 1.0
CB C:GLN138 4.0 21.6 1.0
CA C:PRO137 4.0 17.7 1.0
CD C:GLN138 4.0 26.9 1.0
CZ C:ARG165 4.0 35.9 1.0
CZ C:ARG114 4.0 36.9 1.0
NH2 C:ARG165 4.1 40.9 1.0
CD C:ARG114 4.1 34.6 1.0
C C:PRO137 4.2 17.4 1.0
CD C:ARG165 4.3 31.3 1.0
CA C:GLN138 4.3 19.9 1.0
CE2 C:PHE139 4.4 31.8 1.0
CD2 C:PHE139 4.6 30.8 1.0
CB C:PRO137 4.6 18.9 1.0
CG C:ARG114 4.8 30.8 1.0
NH1 C:ARG165 4.9 38.6 1.0

Chlorine binding site 3 out of 5 in 4jth

Go back to Chlorine Binding Sites List in 4jth
Chlorine binding site 3 out of 5 in the Crystal Structure of F114R/R117Q Mutant 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 F114R/R117Q Mutant 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:Cl302

b:32.1
occ:1.00
 NE2 C:GLN110 3.2 22.2 1.0
NZ C:LYS135 3.2 28.6 1.0
CZ C:PHE234 3.5 27.4 1.0
CE1 C:HIS199 3.6 24.2 1.0
CE C:LYS52 3.7 28.4 1.0
CE1 C:PHE234 3.7 28.9 1.0
CE C:LYS135 3.8 28.2 1.0
NZ C:LYS52 3.9 29.5 1.0
OE2 C:GLU236 4.0 28.4 1.0
ND1 C:HIS199 4.1 23.0 1.0
O C:HOH424 4.2 23.4 1.0
CD C:GLN110 4.3 20.7 1.0
NE2 C:HIS199 4.6 24.0 1.0
OD2 C:ASP196 4.6 16.9 1.0
OE1 C:GLN110 4.6 20.6 1.0
CD C:LYS52 4.7 25.3 1.0
O C:HOH480 4.8 24.9 1.0
CE2 C:PHE234 4.8 24.6 1.0

Chlorine binding site 4 out of 5 in 4jth

Go back to Chlorine Binding Sites List in 4jth
Chlorine binding site 4 out of 5 in the Crystal Structure of F114R/R117Q Mutant 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 F114R/R117Q Mutant 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:Cl301

b:29.9
occ:1.00
 NZ D:LYS135 3.2 29.1 1.0
NE2 D:GLN110 3.3 19.8 1.0
CE1 D:HIS199 3.4 23.6 1.0
CZ D:PHE234 3.7 21.5 1.0
CE D:LYS52 3.7 32.5 1.0
CE1 D:PHE234 3.8 21.4 1.0
NZ D:LYS52 3.8 32.6 1.0
OE2 D:GLU236 3.9 39.3 1.0
ND1 D:HIS199 4.0 22.3 1.0
CE D:LYS135 4.0 26.0 1.0
O D:HOH435 4.2 23.4 1.0
NE2 D:HIS199 4.3 24.4 1.0
CD D:GLN110 4.4 20.0 1.0
OD2 D:ASP196 4.5 18.0 1.0
O D:HOH412 4.7 25.8 1.0
CD D:LYS52 4.7 31.2 1.0
OE1 D:GLN110 4.7 19.8 1.0
CE2 D:PHE234 5.0 19.9 1.0

Chlorine binding site 5 out of 5 in 4jth

Go back to Chlorine Binding Sites List in 4jth
Chlorine binding site 5 out of 5 in the Crystal Structure of F114R/R117Q Mutant 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 F114R/R117Q Mutant 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:Cl302

b:47.9
occ:1.00
 NE2 D:GLN138 3.0 46.6 1.0
CG D:GLN138 3.1 28.6 1.0
N D:GLN138 3.2 18.4 1.0
CB D:GLN138 3.5 22.6 1.0
CD D:GLN138 3.5 40.6 1.0
NE D:ARG165 3.6 39.0 1.0
CB D:ALA113 3.7 20.5 1.0
CA D:GLN138 4.0 19.4 1.0
CA D:PRO137 4.0 17.2 1.0
CZ D:ARG165 4.0 41.2 1.0
C D:PRO137 4.0 16.7 1.0
NH2 D:ARG165 4.1 46.1 1.0
CD D:ARG165 4.2 29.8 1.0
CE2 D:PHE139 4.5 29.3 1.0
CD2 D:PHE139 4.5 24.6 1.0
C D:ALA113 4.7 22.4 1.0
CB D:PRO137 4.7 19.4 1.0
N D:ARG114 4.7 22.9 1.0
OE1 D:GLN138 4.8 37.3 1.0
NH1 D:ARG165 4.8 40.8 1.0
CA D:ALA113 4.8 20.1 1.0
CG D:ARG114 4.9 36.3 1.0
O D:LYS136 4.9 15.7 1.0
N D:PHE139 5.0 21.8 1.0
C D:GLN138 5.0 19.3 1.0

Reference:

T.M.Allison, F.C.Cochrane, G.B.Jameson, E.J.Parker. Examining the Role of Intersubunit Contacts in Catalysis By 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase. Biochemistry V. 52 4676 2013.
ISSN: ISSN 0006-2960
PubMed: 23746359
DOI: 10.1021/BI400521F
Page generated: Sun Jul 21 17:43:38 2024

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