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Chlorine in PDB 5d03: Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant

Enzymatic activity of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant

All present enzymatic activity of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant:
2.5.1.54;

Protein crystallography data

The structure of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant, PDB code: 5d03 was solved by L.C.Heyes, E.J.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.53 / 1.84
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.256, 135.622, 75.989, 90.00, 96.27, 90.00
R / Rfree (%) 16.2 / 19.7

Other elements in 5d03:

The structure of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant (pdb code 5d03). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant, PDB code: 5d03:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5d03

Go back to Chlorine Binding Sites List in 5d03
Chlorine binding site 1 out of 4 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:53.7
occ:1.00
 OG1 A:THR102 3.2 31.8 1.0
NH2 A:ARG101 3.7 31.9 1.0
N A:THR102 3.7 26.3 1.0
NE A:ARG101 3.7 30.4 1.0
O A:HOH531 3.8 28.7 1.0
CB A:THR102 3.9 31.9 1.0
CZ A:ARG101 4.2 31.8 1.0
O A:HOH648 4.2 40.5 1.0
CA A:ARG101 4.4 23.2 1.0
CA A:THR102 4.5 29.0 1.0
C A:ARG101 4.6 25.8 1.0
CB A:ARG101 4.8 24.9 1.0
CD A:ARG101 4.8 28.6 1.0
O A:HOH698 5.0 42.6 1.0

Chlorine binding site 2 out of 4 in 5d03

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Chlorine binding site 2 out of 4 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:46.7
occ:1.00
 O C:TYR96 2.9 30.0 1.0
N C:LEU109 2.9 34.6 1.0
O C:ILE65 3.2 33.9 1.0
CA C:GLY108 3.3 39.3 1.0
CA C:PHE97 3.3 32.0 1.0
C C:PHE97 3.4 34.2 1.0
O C:PHE97 3.5 37.7 1.0
C C:GLY108 3.6 38.0 1.0
CH2 C:TRP106 3.7 43.1 1.0
C C:TYR96 3.8 27.5 1.0
CB C:LEU109 3.8 39.5 1.0
N C:ILE65 3.9 27.8 1.0
N C:PHE97 4.0 30.9 1.0
CA C:LEU109 4.0 36.2 1.0
CB C:SER64 4.0 28.8 1.0
C C:ILE65 4.2 31.1 1.0
CZ3 C:TRP106 4.2 43.2 1.0
N C:GLU98 4.2 34.3 1.0
CG C:LYS99 4.3 31.1 1.0
CZ2 C:TRP106 4.4 42.4 1.0
CA C:ILE65 4.5 29.0 1.0
CA C:SER64 4.5 28.1 1.0
CB C:PHE97 4.6 32.6 1.0
C C:SER64 4.6 28.2 1.0
CD C:LYS99 4.6 30.3 1.0
N C:GLY108 4.6 41.8 1.0
CD1 C:PHE97 4.6 29.6 1.0
CB C:ILE65 4.7 28.6 1.0
O C:GLY108 4.8 40.5 1.0
OG C:SER64 4.9 28.1 1.0

Chlorine binding site 3 out of 4 in 5d03

Go back to Chlorine Binding Sites List in 5d03
Chlorine binding site 3 out of 4 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl403

b:51.7
occ:1.00
 O D:TYR96 2.9 26.6 1.0
N D:LEU109 2.9 33.3 1.0
O D:ILE65 3.0 32.6 1.0
CA D:GLY108 3.3 31.4 1.0
CA D:PHE97 3.4 33.2 1.0
C D:PHE97 3.4 33.7 1.0
O D:PHE97 3.5 32.6 1.0
C D:GLY108 3.6 32.1 1.0
CH2 D:TRP106 3.6 38.7 1.0
N D:ILE65 3.7 32.8 1.0
CB D:SER64 3.8 31.6 1.0
C D:TYR96 3.8 29.4 1.0
CB D:LEU109 3.9 36.4 1.0
C D:ILE65 3.9 33.0 1.0
CA D:LEU109 4.0 33.8 1.0
N D:PHE97 4.0 31.7 1.0
CZ3 D:TRP106 4.1 37.7 1.0
N D:GLU98 4.2 31.3 1.0
CZ2 D:TRP106 4.2 36.7 1.0
CA D:ILE65 4.3 33.8 1.0
CG D:LYS99 4.3 30.8 1.0
CA D:SER64 4.3 31.3 1.0
C D:SER64 4.4 32.8 1.0
OG D:SER64 4.6 33.3 1.0
CB D:ILE65 4.6 34.4 1.0
N D:GLY108 4.6 32.1 1.0
CB D:PHE97 4.7 34.8 1.0
CD D:LYS99 4.7 29.4 1.0
O D:GLY108 4.8 33.3 1.0
CD1 D:PHE97 4.8 31.7 1.0

Chlorine binding site 4 out of 4 in 5d03

Go back to Chlorine Binding Sites List in 5d03
Chlorine binding site 4 out of 4 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl404

b:56.1
occ:1.00
 OG1 D:THR102 3.5 43.8 1.0
NH2 D:ARG101 3.6 45.4 1.0
NE D:ARG101 3.7 38.9 1.0
O D:HOH592 3.8 36.2 1.0
N D:THR102 3.9 39.9 1.0
CZ D:ARG101 4.1 42.9 1.0
CB D:THR102 4.2 42.2 1.0
O D:HOH609 4.2 42.6 1.0
CA D:ARG101 4.4 34.1 1.0
CA D:THR102 4.7 40.3 1.0
C D:ARG101 4.7 38.0 1.0
CB D:ARG101 4.8 33.2 1.0
CD D:ARG101 4.8 38.0 1.0

Reference:

L.C.Heyes, E.J.Parker. Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant at 1.84 Angstroms Resolution To Be Published.
Page generated: Sat Jul 12 01:03:02 2025

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