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

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

All present enzymatic activity of Crystal Structure of 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 R117Q Mutant of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 4jtk 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) 41.31 / 1.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.470, 85.420, 162.710, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.6

Other elements in 4jtk:

The structure of Crystal Structure of 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 R117Q Mutant of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Synthase (KDO8PS) From Neisseria Meningitidis (pdb code 4jtk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of R117Q Mutant of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 4jtk:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4jtk

Go back to Chlorine Binding Sites List in 4jtk
Chlorine binding site 1 out of 4 in the Crystal Structure of 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 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:34.0
occ:1.00
 O B:HOH519 2.9 42.5 1.0
N B:GLN138 3.1 18.6 1.0
NH1 B:ARG165 3.1 27.0 1.0
NE2 B:GLN138 3.4 28.6 1.0
CG B:GLN138 3.4 24.7 1.0
CA B:PRO137 3.5 17.6 1.0
CD B:GLN138 3.8 28.2 1.0
C B:PRO137 3.8 17.4 1.0
CB B:ALA113 3.9 17.9 1.0
CB B:GLN138 3.9 19.9 1.0
NH2 B:ARG165 3.9 26.2 1.0
CZ B:ARG165 4.0 25.2 1.0
CB B:PRO137 4.1 17.8 1.0
CA B:GLN138 4.1 19.5 1.0
CE2 B:PHE139 4.6 28.4 1.0
CD2 B:PHE139 4.6 26.2 1.0
N B:PRO137 4.8 17.8 1.0
O B:LYS136 4.8 16.0 1.0
OE1 B:GLN138 4.8 33.3 1.0
N B:PHE139 5.0 20.9 1.0
CD1 D:PHE139 5.0 28.4 1.0
O B:PRO137 5.0 18.4 1.0

Chlorine binding site 2 out of 4 in 4jtk

Go back to Chlorine Binding Sites List in 4jtk
Chlorine binding site 2 out of 4 in the Crystal Structure of 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 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:40.1
occ:1.00
 NH2 C:ARG165 2.9 32.2 0.5
N C:GLN138 3.1 19.2 1.0
NE2 C:GLN138 3.1 38.6 1.0
CG C:GLN138 3.4 28.7 1.0
NH1 C:ARG165 3.4 32.5 0.5
NE C:ARG165 3.5 32.5 0.5
CZ C:ARG165 3.5 31.0 0.5
CA C:PRO137 3.7 20.5 1.0
CD C:GLN138 3.7 38.7 1.0
CB C:GLN138 3.8 24.8 1.0
CB C:ALA113 3.8 25.1 1.0
CD C:ARG165 3.8 29.2 0.5
C C:PRO137 3.9 19.0 1.0
CA C:GLN138 4.0 19.9 1.0
CZ C:ARG165 4.1 31.5 0.5
CB C:PRO137 4.3 22.0 1.0
NH2 C:ARG165 4.5 30.2 0.5
NE C:ARG165 4.7 29.6 0.5
O C:LYS136 4.7 18.7 1.0
CG C:ARG165 4.8 26.7 0.5
CE2 C:PHE139 4.8 33.0 1.0
CD2 C:PHE139 4.9 31.0 1.0
OE1 C:GLN138 4.9 37.8 1.0
N C:PRO137 4.9 21.5 1.0
NH1 C:ARG165 5.0 31.3 0.5
C C:ALA113 5.0 23.0 1.0
CA C:ALA113 5.0 21.5 1.0

Chlorine binding site 3 out of 4 in 4jtk

Go back to Chlorine Binding Sites List in 4jtk
Chlorine binding site 3 out of 4 in the Crystal Structure of 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 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
 N D:GLN138 3.2 16.7 1.0
NE2 D:GLN138 3.3 28.4 1.0
CG D:GLN138 3.4 21.6 1.0
NE D:ARG165 3.5 38.6 1.0
CB D:ALA113 3.7 23.2 1.0
CB D:GLN138 3.8 18.7 1.0
CE1 D:PHE114 3.8 28.5 1.0
O D:HOH482 3.8 40.4 1.0
CD1 D:PHE114 3.8 27.1 1.0
NH2 D:ARG165 3.8 38.8 1.0
CD D:GLN138 3.9 26.7 1.0
CA D:PRO137 3.9 20.0 1.0
CZ D:ARG165 3.9 36.2 1.0
C D:PRO137 4.0 17.1 1.0
CA D:GLN138 4.1 17.2 1.0
CD D:ARG165 4.2 28.4 1.0
CB D:PRO137 4.4 20.4 1.0
C D:ALA113 4.6 22.2 1.0
N D:PHE114 4.7 20.8 1.0
CA D:ALA113 4.8 21.5 1.0
CD2 D:PHE139 4.8 29.6 1.0
CE2 D:PHE139 4.8 30.3 1.0
O D:ALA113 4.8 22.4 1.0
CZ B:PHE139 4.9 30.4 1.0
O D:LYS136 4.9 19.6 1.0

Chlorine binding site 4 out of 4 in 4jtk

Go back to Chlorine Binding Sites List in 4jtk
Chlorine binding site 4 out of 4 in the Crystal Structure of 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 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:33.2
occ:1.00
 NZ D:LYS135 3.2 33.4 1.0
NE2 D:GLN110 3.2 28.1 1.0
CE1 D:HIS199 3.5 30.2 1.0
CE D:LYS135 3.8 33.2 1.0
CZ D:PHE234 3.8 24.9 1.0
CE D:LYS52 3.9 38.3 1.0
OE2 D:GLU236 3.9 43.1 1.0
NZ D:LYS52 3.9 39.1 1.0
CE1 D:PHE234 3.9 26.4 1.0
ND1 D:HIS199 4.0 27.7 1.0
O D:HOH438 4.1 32.2 1.0
NE2 D:HIS199 4.4 30.5 1.0
CD D:GLN110 4.4 27.4 1.0
OD2 D:ASP196 4.6 19.7 1.0
O D:HOH401 4.7 19.6 1.0
O D:HOH407 4.7 25.6 1.0
OE1 D:GLN110 4.8 26.9 1.0
CD D:LYS52 4.8 33.8 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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