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Chlorine in PDB 3qpz: Crystal Structure of the N59A Mutant of the 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

Enzymatic activity of Crystal Structure of the N59A Mutant of the 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

All present enzymatic activity of Crystal Structure of the N59A Mutant of the 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 the N59A Mutant of the 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 3qpz was solved by T.M.Allison, G.B.Jameson, E.J.Parker, F.C.Cochrane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.93 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.642, 85.368, 162.624, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.5

Other elements in 3qpz:

The structure of Crystal Structure of the N59A Mutant of the 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 the N59A Mutant of the 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis (pdb code 3qpz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of the N59A Mutant of the 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 3qpz:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3qpz

Go back to Chlorine Binding Sites List in 3qpz
Chlorine binding site 1 out of 8 in the Crystal Structure of the N59A Mutant of the 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 the N59A Mutant of the 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl281

b:30.0
occ:1.00
 NZ A:LYS135 3.1 32.1 1.0
NE2 A:GLN110 3.2 31.6 1.0
CE A:LYS52 3.4 37.1 1.0
CE1 A:HIS199 3.4 31.3 1.0
CZ A:PHE234 3.4 34.5 1.0
CE2 A:PHE234 3.7 34.8 1.0
CE A:LYS135 3.9 32.9 1.0
ND1 A:HIS199 3.9 30.1 1.0
NZ A:LYS52 3.9 37.9 1.0
O A:HOH325 4.0 33.0 1.0
OE2 A:GLU236 4.0 48.9 1.0
CD A:GLN110 4.3 30.9 1.0
NE2 A:HIS199 4.4 30.4 1.0
OD2 A:ASP196 4.4 27.6 1.0
OE1 A:GLN110 4.5 31.6 1.0
CE1 A:PHE234 4.6 34.0 1.0
CD A:LYS52 4.6 36.9 1.0
O A:HOH288 4.9 41.7 1.0
CD2 A:PHE234 5.0 34.4 1.0

Chlorine binding site 2 out of 8 in 3qpz

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Chlorine binding site 2 out of 8 in the Crystal Structure of the N59A Mutant of the 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 the N59A Mutant of the 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl282

b:30.0
occ:1.00
 NE2 A:GLN138 3.1 36.2 1.0
N A:GLN138 3.3 28.6 1.0
CB A:ALA113 3.4 34.0 1.0
O A:HOH621 3.4 43.5 1.0
CG A:GLN138 3.5 33.1 1.0
CE1 A:PHE114 3.6 38.8 1.0
NE A:ARG165 3.6 35.6 1.0
CD1 A:PHE114 3.7 38.3 1.0
CB A:GLN138 3.7 31.1 1.0
CD A:GLN138 3.8 34.6 1.0
CD A:ARG165 4.1 32.4 1.0
CA A:PRO137 4.1 31.5 1.0
CZ A:ARG165 4.1 36.5 1.0
CA A:GLN138 4.2 29.4 1.0
C A:PRO137 4.2 27.1 1.0
NH2 A:ARG165 4.4 38.5 1.0
C A:ALA113 4.4 32.0 1.0
CA A:ALA113 4.5 32.1 1.0
N A:PHE114 4.6 31.8 1.0
CB A:PRO137 4.7 31.6 1.0
CZ A:PHE114 4.7 38.6 1.0
O A:ALA113 4.8 31.3 1.0
CG A:PHE114 4.9 38.7 1.0
NH1 A:ARG165 4.9 36.5 1.0
O A:LYS136 4.9 25.7 1.0

Chlorine binding site 3 out of 8 in 3qpz

Go back to Chlorine Binding Sites List in 3qpz
Chlorine binding site 3 out of 8 in the Crystal Structure of the N59A Mutant of the 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 the N59A Mutant of the 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl282

b:30.0
occ:1.00
 NZ B:LYS135 3.2 36.3 1.0
NZ B:LYS52 3.3 31.7 1.0
O B:HOH364 3.3 54.4 1.0
CZ B:PHE234 3.3 28.1 1.0
NE2 B:GLN110 3.4 26.2 1.0
CE2 B:PHE234 3.4 27.6 1.0
O B:HOH653 3.5 46.1 1.0
O B:HOH681 3.7 42.7 1.0
CD B:LYS52 3.9 29.8 1.0
O B:HOH464 4.0 30.2 1.0
CE B:LYS52 4.0 30.5 1.0
O B:HOH363 4.1 44.1 1.0
CG B:GLU236 4.2 38.4 1.0
CD B:GLN110 4.4 24.3 1.0
CE B:LYS135 4.6 35.9 1.0
CG B:LYS52 4.6 28.1 1.0
CE1 B:PHE234 4.6 27.4 1.0
CD B:GLU236 4.6 38.5 1.0
OE1 B:GLN110 4.6 23.3 1.0
OE2 B:GLU236 4.7 36.0 1.0
O B:HOH295 4.7 21.5 1.0
CD2 B:PHE234 4.8 27.2 1.0

Chlorine binding site 4 out of 8 in 3qpz

Go back to Chlorine Binding Sites List in 3qpz
Chlorine binding site 4 out of 8 in the Crystal Structure of the N59A Mutant of the 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 the N59A Mutant of the 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl283

b:30.0
occ:1.00
 NH1 B:ARG165 2.9 29.9 1.0
N B:GLN138 3.1 24.4 1.0
NE2 B:GLN138 3.4 32.0 1.0
CG B:GLN138 3.5 30.7 1.0
CA B:PRO137 3.6 25.1 1.0
NH2 B:ARG165 3.6 29.8 1.0
CZ B:ARG165 3.7 29.7 1.0
C B:PRO137 3.8 23.3 1.0
CB B:ALA113 3.8 26.8 1.0
CD B:GLN138 3.9 32.4 1.0
CB B:GLN138 3.9 29.8 1.0
CA B:GLN138 4.1 25.7 1.0
NH1 D:ARG117 4.2 53.3 1.0
CB B:PRO137 4.3 26.1 1.0
O B:HOH404 4.4 37.0 1.0
NH2 D:ARG117 4.6 53.9 1.0
O B:LYS136 4.6 21.6 1.0
CZ D:ARG117 4.7 52.8 1.0
N B:PRO137 4.8 25.5 1.0
CE2 B:PHE139 4.9 37.7 1.0
C B:ALA113 4.9 23.6 1.0
CD2 B:PHE139 4.9 37.0 1.0
N B:PHE114 5.0 24.4 1.0
NE B:ARG165 5.0 28.4 1.0
OE1 B:GLN138 5.0 34.2 1.0
CA B:ALA113 5.0 23.2 1.0

Chlorine binding site 5 out of 8 in 3qpz

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Chlorine binding site 5 out of 8 in the Crystal Structure of the N59A Mutant of the 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 the N59A Mutant of the 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:30.0
occ:1.00
 O C:HOH414 2.8 51.7 1.0
NZ C:LYS135 3.1 31.4 1.0
NE2 C:GLN110 3.2 24.8 1.0
CE1 C:HIS199 3.5 31.9 1.0
CZ C:PHE234 3.6 29.8 1.0
O C:HOH606 3.7 45.0 1.0
CE2 C:PHE234 3.8 29.6 1.0
O C:HOH689 3.9 43.4 1.0
NZ C:LYS52 3.9 37.7 1.0
CE C:LYS135 3.9 32.9 1.0
OE2 C:GLU236 3.9 38.0 1.0
ND1 C:HIS199 4.0 30.5 1.0
O C:HOH321 4.1 32.6 1.0
CD C:GLN110 4.3 24.4 1.0
NE2 C:HIS199 4.4 31.8 1.0
CE C:LYS52 4.6 36.0 1.0
CD C:LYS52 4.6 35.1 1.0
OE1 C:GLN110 4.6 23.8 1.0
OD2 C:ASP196 4.7 25.5 1.0
CE1 C:PHE234 4.9 29.3 1.0
O C:HOH493 4.9 33.8 1.0

Chlorine binding site 6 out of 8 in 3qpz

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Chlorine binding site 6 out of 8 in the Crystal Structure of the N59A Mutant of the 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 6 of Crystal Structure of the N59A Mutant of the 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl283

b:30.0
occ:1.00
 N C:GLN138 3.3 28.9 1.0
O A:HOH710 3.3 48.6 1.0
NE2 C:GLN138 3.3 36.0 1.0
CG C:GLN138 3.4 34.5 1.0
NE C:ARG165 3.4 38.4 1.0
CB C:ALA113 3.6 29.2 1.0
CB C:GLN138 3.8 33.0 1.0
CD C:GLN138 3.8 35.6 1.0
CA C:PRO137 3.9 29.3 1.0
NH2 A:ARG117 4.0 45.7 0.5
CZ C:ARG165 4.0 39.7 1.0
C C:PRO137 4.1 25.7 1.0
CD C:ARG165 4.1 36.2 1.0
NH1 A:ARG117 4.1 45.7 0.5
NH2 C:ARG165 4.1 39.8 1.0
CA C:GLN138 4.1 29.2 1.0
CB C:PRO137 4.5 29.9 1.0
CZ A:ARG117 4.5 45.4 0.5
C C:ALA113 4.6 27.0 1.0
N C:PHE114 4.7 28.4 0.5
N C:PHE114 4.7 30.2 0.5
CA C:ALA113 4.8 27.3 1.0
O C:LYS136 4.8 22.6 1.0
CE2 C:PHE139 4.9 43.4 1.0
CD2 C:PHE139 4.9 43.0 1.0

Chlorine binding site 7 out of 8 in 3qpz

Go back to Chlorine Binding Sites List in 3qpz
Chlorine binding site 7 out of 8 in the Crystal Structure of the N59A Mutant of the 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 7 of Crystal Structure of the N59A Mutant of the 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:30.0
occ:1.00
 NZ D:LYS135 3.1 30.2 1.0
NE2 D:GLN110 3.2 26.3 1.0
CE1 D:HIS199 3.4 27.5 1.0
CZ D:PHE234 3.6 24.3 1.0
CE D:LYS52 3.7 30.4 1.0
NZ D:LYS52 3.8 30.0 1.0
CE2 D:PHE234 3.9 24.6 1.0
CE D:LYS135 3.9 30.1 1.0
ND1 D:HIS199 3.9 26.1 1.0
O D:HOH356 4.1 31.2 1.0
OE2 D:GLU236 4.1 37.0 1.0
CD D:GLN110 4.3 26.9 1.0
NE2 D:HIS199 4.4 26.3 1.0
OE1 D:GLN110 4.5 27.8 1.0
OD2 D:ASP196 4.6 24.9 1.0
CE1 D:PHE234 4.7 24.5 1.0
O D:HOH297 4.8 26.4 1.0
CD D:LYS52 4.8 29.9 1.0
O D:HOH355 4.8 27.5 1.0

Chlorine binding site 8 out of 8 in 3qpz

Go back to Chlorine Binding Sites List in 3qpz
Chlorine binding site 8 out of 8 in the Crystal Structure of the N59A Mutant of the 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 8 of Crystal Structure of the N59A Mutant of the 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl283

b:30.0
occ:1.00
 N D:GLN138 3.2 22.9 1.0
NE2 D:GLN138 3.5 32.4 1.0
CG D:GLN138 3.5 29.4 1.0
CB D:ALA113 3.5 28.7 1.0
NE D:ARG165 3.7 35.5 1.0
CB D:GLN138 3.7 27.9 1.0
O D:HOH461 3.8 36.7 1.0
CE1 D:PHE114 3.9 32.9 1.0
CA D:PRO137 3.9 25.8 1.0
CD1 D:PHE114 3.9 32.8 1.0
CD D:GLN138 4.0 30.9 1.0
C D:PRO137 4.0 22.1 1.0
CA D:GLN138 4.1 25.5 1.0
CD D:ARG165 4.2 32.4 1.0
CZ D:ARG165 4.3 36.8 1.0
CB D:PRO137 4.4 27.4 1.0
C D:ALA113 4.5 26.2 1.0
NH2 D:ARG165 4.5 38.0 1.0
CA D:ALA113 4.6 26.3 1.0
O D:ALA113 4.7 27.1 1.0
N D:PHE114 4.7 25.1 1.0
CE1 B:PHE139 4.8 37.8 1.0
CZ B:PHE139 4.8 38.4 1.0
O D:LYS136 5.0 22.5 1.0

Reference:

T.M.Allison, R.D.Hutton, F.C.Cochrane, J.A.Yeoman, G.B.Jameson, E.J.Parker. Targeting the Role of A Key Conserved Motif For Substrate Selection and Catalysis By 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase Biochemistry V. 50 3686 2011.
ISSN: ISSN 0006-2960
PubMed: 21438567
DOI: 10.1021/BI200251F
Page generated: Sat Dec 12 10:05:08 2020

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