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Chlorine in PDB 5dcb: Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep

Enzymatic activity of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep

All present enzymatic activity of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep:
2.5.1.54;

Protein crystallography data

The structure of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep, PDB code: 5dcb 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) 74.96 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.458, 140.310, 75.500, 90.00, 96.89, 90.00
R / Rfree (%) 16.9 / 21.2

Other elements in 5dcb:

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

Chlorine binding site 1 out of 3 in 5dcb

Go back to Chlorine Binding Sites List in 5dcb
Chlorine binding site 1 out of 3 in the Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep


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 Regulated and Complexed with Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:33.6
occ:1.00
O B:HOH592 3.1 24.9 1.0
N A:LYS216 3.2 19.3 1.0
O A:HOH676 3.3 25.5 1.0
CB A:THR215 3.6 19.6 1.0
CA A:THR215 3.7 19.1 1.0
CG A:LYS216 3.8 20.8 1.0
C A:THR215 3.9 18.9 1.0
CB A:LYS216 4.1 20.5 1.0
CG1 B:VAL15 4.2 29.4 1.0
CA A:LYS216 4.2 20.2 1.0
CG2 A:THR215 4.3 20.1 1.0
CB B:VAL15 4.3 30.4 1.0
NE2 A:GLN153 4.6 20.1 1.0
OG1 A:THR215 4.7 19.9 1.0
CG2 B:VAL15 4.7 29.8 1.0
CD A:LYS216 4.9 20.6 1.0

Chlorine binding site 2 out of 3 in 5dcb

Go back to Chlorine Binding Sites List in 5dcb
Chlorine binding site 2 out of 3 in the Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep


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 Regulated and Complexed with Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:24.0
occ:1.00
O A:HOH708 3.0 33.7 1.0
O B:HOH671 3.1 14.8 1.0
O A:HOH608 3.1 16.4 1.0
O A:HOH625 3.2 41.3 1.0
N B:LYS216 3.2 18.8 1.0
CB B:THR215 3.7 17.5 1.0
CA B:THR215 3.7 17.5 1.0
C B:THR215 4.0 17.6 1.0
CG B:LYS216 4.0 20.7 1.0
CB B:LYS216 4.1 20.3 1.0
CG1 A:VAL15 4.1 27.2 1.0
CB A:VAL15 4.2 27.6 1.0
CA B:LYS216 4.3 19.4 1.0
CG2 B:THR215 4.3 18.1 1.0
O A:HOH526 4.5 29.7 1.0
CG2 A:VAL15 4.7 27.9 1.0
NE2 B:GLN153 4.8 17.9 1.0
O B:HOH694 4.9 28.4 1.0
OG1 B:THR215 4.9 17.6 1.0
O B:HOH695 4.9 32.6 1.0

Chlorine binding site 3 out of 3 in 5dcb

Go back to Chlorine Binding Sites List in 5dcb
Chlorine binding site 3 out of 3 in the Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep


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 Regulated and Complexed with Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl406

b:55.4
occ:1.00
O C:HOH505 3.2 24.0 1.0
O B:HOH514 3.3 23.7 1.0
CB D:HIS219 3.3 23.9 1.0
O C:HOH582 3.4 33.5 1.0
O B:HOH670 3.4 25.6 1.0
CB A:HIS219 3.7 24.3 1.0
CD2 A:HIS219 3.7 28.4 1.0
ND1 D:HIS219 3.8 27.1 1.0
CG D:HIS219 3.9 26.6 1.0
CG A:HIS219 4.0 27.8 1.0
CB A:ALA217 4.1 23.9 1.0
CB D:ALA217 4.1 21.8 1.0
O D:ALA217 4.3 20.8 1.0
CA D:HIS219 4.4 22.7 1.0
N D:HIS219 4.4 21.7 1.0
O A:ALA217 4.5 24.3 1.0
C D:ALA217 4.8 20.7 1.0
CA A:HIS219 4.8 22.8 1.0
OG1 D:THR215 4.8 18.4 1.0
N A:HIS219 4.8 22.2 1.0
OE1 C:GLU17 4.8 39.5 1.0
C A:ALA217 4.9 23.3 1.0
NE2 A:HIS219 4.9 30.8 1.0
CE1 D:HIS219 5.0 28.3 1.0

Reference:

L.C.Heyes, E.J.Parker. Structure of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep at 2.05 Angstroms To Be Published.
Page generated: Sat Dec 12 11:38:21 2020

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