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Chlorine in PDB 5d04: Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant Regulated

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

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

Protein crystallography data

The structure of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant Regulated, PDB code: 5d04 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) 75.43 / 1.70
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 73.620, 75.430, 143.939, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 17.8

Other elements in 5d04:

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

Manganese (Mn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant Regulated (pdb code 5d04). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant Regulated, PDB code: 5d04:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5d04

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Chlorine binding site 1 out of 6 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant Regulated


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 Regulated within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl402

b:42.0
occ:1.00
 O C:HOH508 2.6 26.8 1.0
OD2 C:ASP200 2.7 19.5 1.0
NH2 C:ARG175 2.9 14.2 1.0
OG1 D:THR102 3.3 25.9 1.0
CB C:ASP200 3.4 17.8 1.0
NH1 C:ARG175 3.4 14.5 1.0
CG C:ASP200 3.5 19.0 1.0
CZ C:ARG175 3.6 13.6 1.0
O D:HOH567 3.9 25.8 1.0
CA C:ILE197 4.3 17.6 1.0
CG C:GLU170 4.3 13.5 1.0
OE2 C:GLU170 4.4 14.9 1.0
CG2 C:ILE197 4.6 19.5 1.0
CB D:THR102 4.6 26.6 1.0
OD1 C:ASP200 4.7 20.7 1.0
O C:ILE197 4.7 16.2 1.0
O C:LYS196 4.7 17.6 1.0
CB C:ILE197 4.8 18.4 1.0
CG2 D:THR102 4.8 26.5 1.0
NZ C:LYS196 4.8 35.6 1.0
CD C:GLU170 4.8 15.0 1.0
CA C:ASP200 4.9 17.6 1.0
NE C:ARG175 4.9 13.3 1.0
C C:ILE197 5.0 17.3 1.0

Chlorine binding site 2 out of 6 in 5d04

Go back to Chlorine Binding Sites List in 5d04
Chlorine binding site 2 out of 6 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant Regulated


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 Regulated within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:25.9
occ:1.00
 O C:HOH725 3.0 21.1 1.0
O C:HOH704 3.1 36.5 1.0
NZ C:LYS188 3.1 18.4 1.0
NE C:ARG236 3.2 19.9 1.0
NH1 C:ARG236 3.4 21.5 1.0
CG C:HIS270 3.6 19.0 1.0
ND1 C:HIS270 3.7 18.7 1.0
CZ C:ARG236 3.8 21.5 1.0
CB C:HIS270 3.8 19.8 1.0
CD C:LYS188 3.8 17.7 1.0
CE C:LYS188 3.9 18.1 1.0
CD2 C:HIS270 4.1 19.6 1.0
O C:HOH757 4.2 31.9 1.0
CD C:ARG236 4.3 19.1 1.0
CE1 C:HIS270 4.3 19.0 1.0
CG C:ARG236 4.3 18.2 1.0
OD2 C:ASP267 4.3 17.9 1.0
CB C:ARG236 4.4 17.8 1.0
NE2 C:HIS270 4.5 18.9 1.0
O C:HOH574 4.7 25.9 1.0
O C:HOH667 4.7 34.1 1.0
O C:HOH733 4.7 22.4 1.0
CB C:ALA166 4.8 16.4 1.0
NH2 C:ARG167 5.0 28.7 1.0

Chlorine binding site 3 out of 6 in 5d04

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Chlorine binding site 3 out of 6 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant Regulated


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 Regulated within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:33.0
occ:1.00
 O C:HOH733 2.8 22.4 1.0
O C:HOH574 3.0 25.9 1.0
OH C:TYR96 3.0 17.9 1.0
NZ C:LYS188 3.3 18.4 1.0
CE C:LYS188 3.4 18.1 1.0
CE2 C:TYR96 3.5 16.1 1.0
CB C:ALA163 3.6 15.0 1.0
CD C:LYS188 3.6 17.7 1.0
CZ C:TYR96 3.7 16.7 1.0
SD C:MET302 3.9 24.9 1.0
O C:HOH735 3.9 26.1 1.0
CE C:MET302 4.3 20.3 1.0
NH1 C:ARG94 4.4 21.0 1.0
CG C:LYS188 4.6 17.5 1.0
O C:HOH725 4.7 21.1 1.0
OE1 C:GLU145 4.7 16.9 1.0
CD2 C:TYR96 4.7 15.9 1.0
CA C:GLY165 5.0 14.2 1.0

Chlorine binding site 4 out of 6 in 5d04

Go back to Chlorine Binding Sites List in 5d04
Chlorine binding site 4 out of 6 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant Regulated


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 Regulated within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl405

b:23.3
occ:1.00
 O D:HOH573 2.8 28.1 1.0
O D:HOH580 3.0 14.5 1.0
O D:HOH836 3.1 27.9 1.0
N C:LYS216 3.2 12.1 1.0
O C:HOH726 3.4 17.3 1.0
CB C:THR215 3.7 12.4 1.0
CA C:THR215 3.8 11.8 1.0
CG C:LYS216 3.8 13.2 1.0
C C:THR215 4.0 12.0 1.0
CB C:LYS216 4.0 12.7 1.0
CA C:LYS216 4.2 12.2 1.0
CB D:VAL15 4.2 18.7 1.0
CG1 D:VAL15 4.3 18.6 1.0
CG2 C:THR215 4.3 12.8 1.0
O D:HOH510 4.4 20.4 1.0
NE2 C:GLN153 4.6 11.7 1.0
CG2 D:VAL15 4.9 17.8 1.0
O D:VAL15 4.9 20.3 1.0
OG1 C:THR215 4.9 12.2 1.0
CD C:LYS216 5.0 12.9 1.0
OD2 D:ASP9 5.0 16.9 1.0

Chlorine binding site 5 out of 6 in 5d04

Go back to Chlorine Binding Sites List in 5d04
Chlorine binding site 5 out of 6 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant Regulated


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant Regulated within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:19.7
occ:1.00
 O D:HOH749 3.0 36.1 1.0
O D:HOH727 3.0 14.1 1.0
NZ D:LYS188 3.1 13.2 1.0
NE D:ARG236 3.2 12.5 1.0
NH2 D:ARG236 3.3 15.3 1.0
CG D:HIS270 3.6 11.4 1.0
CD D:LYS188 3.7 13.2 1.0
CB D:HIS270 3.7 11.2 1.0
CZ D:ARG236 3.8 13.5 1.0
ND1 D:HIS270 3.8 11.3 1.0
CE D:LYS188 3.9 13.4 1.0
CD2 D:HIS270 4.0 11.4 1.0
CG D:ARG236 4.3 11.6 1.0
CD D:ARG236 4.3 12.1 1.0
O D:HOH814 4.3 25.4 1.0
CE1 D:HIS270 4.3 11.3 1.0
CB D:ARG236 4.5 11.4 1.0
OD2 D:ASP267 4.5 10.4 1.0
NE2 D:HIS270 4.5 11.5 1.0
O D:HOH756 4.6 27.0 1.0
CB D:ALA166 4.6 11.4 1.0
O D:HOH603 4.7 21.8 1.0
O D:HOH763 4.8 19.2 1.0
NH1 D:ARG167 5.0 26.6 1.0

Chlorine binding site 6 out of 6 in 5d04

Go back to Chlorine Binding Sites List in 5d04
Chlorine binding site 6 out of 6 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant Regulated


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant Regulated within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl403

b:30.4
occ:1.00
 O D:HOH763 2.8 19.2 1.0
O D:HOH603 2.9 21.8 1.0
OH D:TYR96 3.0 13.0 1.0
NZ D:LYS188 3.3 13.2 1.0
CE D:LYS188 3.4 13.4 1.0
CE2 D:TYR96 3.5 11.7 1.0
CB D:ALA163 3.6 12.1 1.0
CD D:LYS188 3.7 13.2 1.0
CZ D:TYR96 3.7 11.7 1.0
O D:HOH781 3.9 21.6 1.0
SD D:MET302 4.1 18.3 1.0
CE D:MET302 4.4 16.1 1.0
NH1 D:ARG94 4.5 15.6 1.0
CG D:LYS188 4.5 13.2 1.0
O D:HOH727 4.7 14.1 1.0
OE1 D:GLU145 4.7 12.6 1.0
CD2 D:TYR96 4.8 11.6 1.0
CA D:GLY165 4.9 10.7 1.0

Reference:

L.C.Heyes, E.J.Parker. Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant Regulated at 1.70 Angstroms Resolution To Be Published.
Page generated: Fri Jul 26 06:25:57 2024

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