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Manganese in PDB 5czt: Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176ALA Variant

Enzymatic activity of Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176ALA Variant

All present enzymatic activity of Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176ALA Variant:
2.5.1.54;

Protein crystallography data

The structure of Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176ALA Variant, PDB code: 5czt 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) 76.41 / 2.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.647, 140.828, 77.266, 90.00, 98.56, 90.00
R / Rfree (%) 17.1 / 20.6

Other elements in 5czt:

The structure of Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176ALA Variant also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176ALA Variant (pdb code 5czt). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176ALA Variant, PDB code: 5czt:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5czt

Go back to Manganese Binding Sites List in 5czt
Manganese binding site 1 out of 4 in the Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176ALA Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176ALA Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:35.6
occ:1.00
 O A:HOH642 1.8 33.4 1.0
OE2 A:GLU304 1.9 39.3 1.0
OD2 A:ASP324 2.2 38.4 1.0
NE2 A:HIS270 2.4 38.1 1.0
SG A:CYS63 2.6 34.4 1.0
CD A:GLU304 2.9 36.7 1.0
OE1 A:GLU304 3.2 34.8 1.0
CG A:ASP324 3.2 40.6 1.0
CD2 A:HIS270 3.3 38.9 1.0
CE1 A:HIS270 3.4 36.2 1.0
CB A:CYS63 3.5 34.9 1.0
CB A:ASP324 3.6 39.3 1.0
NH2 A:ARG94 3.8 33.6 1.0
O A:HOH539 4.1 31.8 1.0
CA A:CYS63 4.1 32.0 1.0
CD A:LYS99 4.2 59.6 1.0
NZ A:LYS99 4.2 62.2 1.0
CE A:LYS99 4.3 60.0 1.0
OD1 A:ASP324 4.3 44.2 1.0
CG A:GLU304 4.3 34.3 1.0
O A:HOH599 4.4 31.8 1.0
CG A:HIS270 4.4 38.0 1.0
ND1 A:HIS270 4.4 35.2 1.0
O A:CYS63 4.6 33.9 1.0
C A:CYS63 4.7 32.7 1.0
CZ A:ARG94 4.8 30.7 1.0
CA A:ASP324 4.8 39.5 1.0
N A:ASP324 4.8 39.9 1.0

Manganese binding site 2 out of 4 in 5czt

Go back to Manganese Binding Sites List in 5czt
Manganese binding site 2 out of 4 in the Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176ALA Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176ALA Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:30.7
occ:1.00
 OE2 B:GLU304 2.0 27.5 1.0
O B:HOH601 2.1 27.2 1.0
OD2 B:ASP324 2.2 34.2 1.0
NE2 B:HIS270 2.3 30.0 1.0
SG B:CYS63 2.5 29.0 1.0
CD B:GLU304 2.9 28.2 1.0
CG B:ASP324 3.0 33.7 1.0
OE1 B:GLU304 3.2 30.3 1.0
CE1 B:HIS270 3.2 29.8 1.0
CD2 B:HIS270 3.3 31.3 1.0
CB B:ASP324 3.4 33.7 1.0
CB B:CYS63 3.5 28.4 1.0
NH1 B:ARG94 3.9 28.7 1.0
CA B:CYS63 4.1 27.4 1.0
OD1 B:ASP324 4.1 35.6 1.0
O B:HOH593 4.3 29.1 1.0
ND1 B:HIS270 4.3 29.8 1.0
CG B:GLU304 4.3 27.5 1.0
CG B:HIS270 4.4 29.9 1.0
O B:HOH581 4.4 35.5 1.0
CA B:ASP324 4.6 34.9 1.0
O B:CYS63 4.7 25.5 1.0
C B:CYS63 4.8 26.5 1.0
N B:ASP324 4.8 33.2 1.0
O B:HOH602 4.8 38.4 1.0
CZ B:ARG94 4.8 28.9 1.0
CG B:LYS99 4.9 44.8 1.0

Manganese binding site 3 out of 4 in 5czt

Go back to Manganese Binding Sites List in 5czt
Manganese binding site 3 out of 4 in the Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176ALA Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176ALA Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:22.0
occ:1.00
 O C:HOH669 2.0 20.4 1.0
OE2 C:GLU304 2.0 22.7 1.0
OD2 C:ASP324 2.1 21.9 1.0
NE2 C:HIS270 2.2 21.5 1.0
SG C:CYS63 2.6 21.2 1.0
CD C:GLU304 2.9 21.5 1.0
CG C:ASP324 3.0 22.3 1.0
CE1 C:HIS270 3.1 21.2 1.0
OE1 C:GLU304 3.2 22.5 1.0
CD2 C:HIS270 3.2 21.9 1.0
CB C:ASP324 3.4 22.7 1.0
CB C:CYS63 3.5 19.7 1.0
NH2 C:ARG94 3.9 26.0 1.0
O C:HOH577 4.0 35.8 1.0
OD1 C:ASP324 4.1 23.6 1.0
O C:HOH569 4.1 23.3 1.0
CA C:CYS63 4.2 19.5 1.0
ND1 C:HIS270 4.2 21.3 1.0
O C:HOH619 4.3 18.7 1.0
CG C:HIS270 4.3 21.5 1.0
CG C:GLU304 4.3 20.8 1.0
O C:HOH707 4.4 46.9 1.0
O C:CYS63 4.7 19.5 1.0
CZ C:ARG94 4.7 25.8 1.0
CA C:ASP324 4.7 22.5 1.0
CG C:LYS99 4.8 49.2 1.0
C C:CYS63 4.8 19.3 1.0
N C:ASP324 4.9 23.1 1.0
CD C:LYS99 4.9 53.1 1.0

Manganese binding site 4 out of 4 in 5czt

Go back to Manganese Binding Sites List in 5czt
Manganese binding site 4 out of 4 in the Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176ALA Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176ALA Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:28.5
occ:1.00
 OD2 D:ASP324 2.0 22.6 1.0
O D:HOH639 2.2 24.0 1.0
OE2 D:GLU304 2.2 30.0 1.0
NE2 D:HIS270 2.2 29.2 1.0
SG D:CYS63 2.5 30.0 1.0
CD D:GLU304 3.0 27.4 1.0
CG D:ASP324 3.0 25.0 1.0
OE1 D:GLU304 3.1 24.8 1.0
CE1 D:HIS270 3.2 29.9 1.0
CD2 D:HIS270 3.2 28.9 1.0
CB D:CYS63 3.4 29.4 1.0
CB D:ASP324 3.4 24.9 1.0
NH2 D:ARG94 3.9 27.6 1.0
CA D:CYS63 4.1 28.3 1.0
OD1 D:ASP324 4.1 23.3 1.0
O D:HOH602 4.2 30.3 1.0
O D:HOH596 4.3 25.7 1.0
ND1 D:HIS270 4.3 29.5 1.0
CG D:HIS270 4.3 29.0 1.0
CG D:GLU304 4.4 27.0 1.0
CE D:LYS99 4.6 40.6 1.0
CA D:ASP324 4.7 25.6 1.0
O D:CYS63 4.7 25.6 1.0
N D:ASP324 4.8 25.4 1.0
C D:CYS63 4.8 26.4 1.0
CD D:LYS99 4.8 40.5 1.0
CZ D:ARG94 4.8 28.8 1.0
CG D:LYS99 4.9 37.6 1.0

Reference:

L.C.Heyes, E.J.Parker. Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176ALA Variant at 2.04 Angstroms Resolution To Be Published.
Page generated: Sat Aug 16 17:07:31 2025

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