Chlorine in PDB 3stc: Crystal Structure of Loop 7 Truncated Mutant of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

Enzymatic activity of Crystal Structure of Loop 7 Truncated Mutant of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

All present enzymatic activity of Crystal Structure of Loop 7 Truncated 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 Loop 7 Truncated Mutant of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 3stc was solved by T.M.Allison, 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) 36.56 / 1.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.780, 85.760, 163.220, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.5

Other elements in 3stc:

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

Chlorine binding site 1 out of 7 in 3stc

Go back to Chlorine Binding Sites List in 3stc
Chlorine binding site 1 out of 7 in the Crystal Structure of Loop 7 Truncated 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 Loop 7 Truncated 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
A:Cl270

b:44.8
occ:1.00
 N A:GLN138 3.2 29.5 1.0
CG A:GLN138 3.4 32.0 1.0
CE2 A:PHE114 3.4 48.5 1.0
NE2 A:GLN138 3.6 39.8 1.0
CD2 A:PHE114 3.6 46.7 1.0
CB A:ALA113 3.7 33.2 1.0
CB A:GLN138 3.8 30.8 1.0
CA A:PRO137 3.9 30.0 1.0
C A:PRO137 4.0 29.0 1.0
CD A:GLN138 4.0 35.3 1.0
CA A:GLN138 4.1 30.4 1.0
NE A:ARG165 4.1 49.9 1.0
CD A:ARG165 4.1 40.6 1.0
CZ A:ARG165 4.4 50.6 1.0
CB A:PRO137 4.5 32.2 1.0
NH2 A:ARG165 4.6 55.9 1.0
CE1 A:PHE139 4.6 43.5 1.0
CD1 A:PHE139 4.7 42.4 1.0
C A:ALA113 4.7 35.5 1.0
CZ A:PHE114 4.7 48.9 1.0
N A:PHE114 4.8 35.6 1.0
CA A:ALA113 4.9 31.8 1.0
O A:ALA113 4.9 34.0 1.0
O A:LYS136 5.0 26.9 1.0
NH1 A:ARG165 5.0 49.6 1.0

Chlorine binding site 2 out of 7 in 3stc

Go back to Chlorine Binding Sites List in 3stc
Chlorine binding site 2 out of 7 in the Crystal Structure of Loop 7 Truncated 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 Loop 7 Truncated 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:Cl270

b:30.5
occ:1.00
 NH1 B:ARG165 3.1 32.0 1.0
N B:GLN138 3.2 20.0 1.0
CG B:GLN138 3.4 23.7 1.0
CA B:PRO137 3.6 19.4 1.0
NH2 B:ARG165 3.6 32.5 1.0
CB B:ALA113 3.8 17.8 1.0
CZ B:ARG165 3.8 31.4 1.0
C B:PRO137 3.9 19.5 1.0
NE2 B:GLN138 3.9 29.3 1.0
CB B:GLN138 3.9 22.1 1.0
CB B:PRO137 4.1 19.1 1.0
CA B:GLN138 4.2 21.6 1.0
CD B:GLN138 4.2 27.8 1.0
O D:HOH686 4.6 29.2 1.0
O B:LYS136 4.8 18.4 1.0
N B:PRO137 4.8 18.6 1.0
CD2 B:PHE139 5.0 30.7 1.0

Chlorine binding site 3 out of 7 in 3stc

Go back to Chlorine Binding Sites List in 3stc
Chlorine binding site 3 out of 7 in the Crystal Structure of Loop 7 Truncated 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 Loop 7 Truncated 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:Cl271

b:25.7
occ:0.67
 O B:HOH674 1.8 18.8 0.3
NZ B:LYS135 2.9 35.1 1.0
NE2 B:GLN110 3.3 26.2 1.0
CZ B:PHE223 3.3 19.7 1.0
O B:HOH660 3.5 28.4 1.0
CE2 B:PHE223 3.6 19.2 1.0
NZ B:LYS52 3.7 19.5 1.0
O B:HOH310 3.8 32.0 1.0
CE B:LYS135 3.8 31.9 1.0
CD B:LYS52 4.0 18.3 1.0
O B:HOH272 4.2 30.1 1.0
CE B:LYS52 4.2 18.4 1.0
O B:HOH661 4.2 42.9 1.0
CD B:GLN110 4.4 22.8 1.0
CG B:GLU225 4.5 34.4 1.0
CE1 B:PHE223 4.6 19.6 1.0
O B:HOH311 4.6 17.9 1.0
OE1 B:GLN110 4.6 20.9 1.0
CG B:LYS52 4.7 17.2 1.0
OE1 B:GLU225 4.7 32.6 1.0
O B:HOH491 4.8 43.8 1.0
CD B:GLU225 4.8 36.0 1.0
CD B:LYS135 4.9 29.0 1.0
CD2 B:PHE223 5.0 18.9 1.0

Chlorine binding site 4 out of 7 in 3stc

Go back to Chlorine Binding Sites List in 3stc
Chlorine binding site 4 out of 7 in the Crystal Structure of Loop 7 Truncated 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 Loop 7 Truncated 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:Cl270

b:34.0
occ:1.00
 N C:GLN138 3.3 25.0 1.0
NE2 C:GLN138 3.3 32.0 1.0
CG C:GLN138 3.4 29.1 1.0
NE C:ARG165 3.5 42.2 1.0
CB C:ALA113 3.6 25.2 1.0
NH2 C:ARG165 3.8 44.8 1.0
CD C:GLN138 3.9 31.9 1.0
CA C:PRO137 3.9 24.2 1.0
CZ C:ARG165 3.9 42.0 1.0
CB C:GLN138 3.9 27.1 1.0
C C:PRO137 4.1 23.6 1.0
CA C:GLN138 4.2 25.6 1.0
CD C:ARG165 4.3 32.9 1.0
CB C:PRO137 4.5 25.0 1.0
CE1 C:PHE139 4.7 40.5 1.0
CD1 C:PHE139 4.8 39.1 1.0
NH1 C:ARG165 4.9 40.3 1.0
CA C:ALA113 4.9 25.1 1.0
C C:ALA113 4.9 25.8 1.0
O C:LYS136 5.0 22.7 1.0

Chlorine binding site 5 out of 7 in 3stc

Go back to Chlorine Binding Sites List in 3stc
Chlorine binding site 5 out of 7 in the Crystal Structure of Loop 7 Truncated 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 Loop 7 Truncated 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:Cl271

b:27.2
occ:1.00
 NE2 C:GLN110 3.3 20.5 1.0
NZ C:LYS135 3.3 28.0 1.0
CE1 C:HIS199 3.5 22.8 1.0
CZ C:PHE223 3.6 21.7 1.0
CE2 C:PHE223 3.7 21.7 1.0
CE C:LYS135 3.7 28.1 1.0
CE C:LYS52 3.7 24.1 1.0
NZ C:LYS52 3.8 24.8 1.0
OE2 C:GLU225 3.9 26.0 1.0
ND1 C:HIS199 4.0 21.9 1.0
O C:HOH326 4.3 29.1 1.0
CD C:GLN110 4.3 20.3 1.0
OE1 C:GLN110 4.6 19.9 1.0
NE2 C:HIS199 4.6 23.5 1.0
NZ C:LYS57 4.6 58.9 1.0
CD C:LYS52 4.6 22.9 1.0
OD2 C:ASP196 4.7 20.3 1.0
CE1 C:PHE223 4.8 21.0 1.0
O C:HOH394 4.9 33.0 1.0
OG C:SER54 4.9 21.6 0.5

Chlorine binding site 6 out of 7 in 3stc

Go back to Chlorine Binding Sites List in 3stc
Chlorine binding site 6 out of 7 in the Crystal Structure of Loop 7 Truncated 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 6 of Crystal Structure of Loop 7 Truncated 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:Cl270

b:40.9
occ:1.00
 NE2 D:GLN138 2.7 30.7 1.0
NH2 D:ARG165 2.9 41.8 1.0
N D:GLN138 3.1 21.5 1.0
CG D:GLN138 3.3 26.8 1.0
CD D:GLN138 3.5 31.4 1.0
CB D:ALA113 3.6 25.1 1.0
CB D:GLN138 3.7 24.4 1.0
CE1 D:PHE114 3.8 37.5 1.0
CA D:PRO137 3.9 21.3 1.0
CD1 D:PHE114 3.9 39.1 1.0
C D:PRO137 4.0 20.8 1.0
CZ D:ARG165 4.0 40.0 1.0
CA D:GLN138 4.0 21.4 1.0
CD D:ARG165 4.2 32.7 1.0
O D:HOH547 4.4 42.6 1.0
CB D:PRO137 4.5 21.5 1.0
NE D:ARG165 4.5 39.6 1.0
CE1 D:PHE139 4.5 29.1 1.0
CD1 D:PHE139 4.6 27.3 1.0
C D:ALA113 4.7 30.4 1.0
OE1 D:GLN138 4.7 35.0 1.0
O D:HOH420 4.7 34.3 1.0
CA D:ALA113 4.8 28.0 1.0
N D:PHE114 4.9 30.3 1.0
O D:LYS136 4.9 19.0 1.0
O D:ALA113 5.0 31.3 1.0
NH1 D:ARG165 5.0 40.9 1.0

Chlorine binding site 7 out of 7 in 3stc

Go back to Chlorine Binding Sites List in 3stc
Chlorine binding site 7 out of 7 in the Crystal Structure of Loop 7 Truncated 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 7 of Crystal Structure of Loop 7 Truncated 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:Cl271

b:32.6
occ:1.00
 NE2 D:GLN110 3.3 24.5 1.0
NZ D:LYS135 3.3 33.9 1.0
O D:HOH552 3.4 45.4 1.0
CE1 D:HIS199 3.4 33.3 1.0
CZ D:PHE223 3.6 22.4 1.0
NZ D:LYS52 3.6 32.9 1.0
CE D:LYS52 3.7 33.6 1.0
CE2 D:PHE223 3.9 22.5 1.0
CE D:LYS135 3.9 29.3 1.0
OE2 D:GLU225 3.9 33.8 1.0
ND1 D:HIS199 4.1 29.5 1.0
NE2 D:HIS199 4.2 33.9 1.0
O D:HOH665 4.4 25.4 1.0
CD D:GLN110 4.4 25.9 1.0
OD2 D:ASP196 4.6 21.1 1.0
OE1 D:GLN110 4.6 24.2 1.0
CD D:LYS52 4.7 31.9 1.0
CE1 D:PHE223 4.8 22.3 1.0
OG D:SER54 4.9 37.8 1.0
O D:HOH292 5.0 28.5 1.0
O D:HOH276 5.0 20.2 1.0

Reference:

T.M.Allison, R.D.Hutton, W.Jiao, B.J.Gloyne, E.B.Nimmo, G.B.Jameson, E.J.Parker. An Extended (Beta)7(Alpha)7 Substrate-Binding Loop Is Essential For Efficient Catalysis By 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase Biochemistry V. 50 9318 2011.
ISSN: ISSN 0006-2960
PubMed: 21942786
DOI: 10.1021/BI201231E
Page generated: Sat Dec 12 10:10:55 2020

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