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Manganese 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:

Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase VAL223ALA Variant, PDB code: 5d03:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5d03

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Manganese 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 Manganese with other atoms in the Mn 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:Mn401

b:23.8
occ:1.00
 O A:HOH549 2.1 25.9 1.0
OE2 A:GLU304 2.1 22.2 1.0
OD2 A:ASP324 2.1 23.6 1.0
NE2 A:HIS270 2.4 24.6 1.0
SG A:CYS63 2.6 21.1 1.0
O2' A:PEP402 2.9 29.8 1.0
CD A:GLU304 3.0 22.2 1.0
CG A:ASP324 3.1 24.1 1.0
OE1 A:GLU304 3.2 22.6 1.0
CD2 A:HIS270 3.3 24.8 1.0
CE1 A:HIS270 3.3 24.7 1.0
CB A:ASP324 3.6 22.3 1.0
CB A:CYS63 3.6 20.8 1.0
C1 A:PEP402 3.8 28.2 1.0
NZ A:LYS99 4.0 20.4 1.0
OD1 A:ASP324 4.1 23.6 1.0
NH2 A:ARG94 4.2 22.5 1.0
CA A:CYS63 4.2 20.4 1.0
O A:HOH582 4.3 28.0 1.0
C2 A:PEP402 4.3 27.6 1.0
CG A:GLU304 4.4 22.7 1.0
ND1 A:HIS270 4.4 24.3 1.0
CG A:HIS270 4.4 23.7 1.0
O1 A:PEP402 4.5 28.4 1.0
C3 A:PEP402 4.6 26.1 1.0
CE A:LYS99 4.8 20.5 1.0
O A:CYS63 4.8 20.0 1.0
CA A:ASP324 4.8 22.4 1.0
C A:CYS63 4.9 19.4 1.0
N A:ASP324 4.9 21.6 1.0
O2 A:PEP402 4.9 26.3 1.0
O A:HOH698 5.0 42.6 1.0
CZ A:ARG94 5.0 22.2 1.0

Manganese binding site 2 out of 4 in 5d03

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Manganese 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 Manganese with other atoms in the Mn 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
B:Mn401

b:32.3
occ:1.00
 OE2 B:GLU304 1.9 26.5 1.0
OD2 B:ASP324 2.3 36.0 1.0
NE2 B:HIS270 2.3 28.8 1.0
O B:HOH639 2.4 42.5 1.0
SG B:CYS63 2.6 28.6 1.0
O1 B:PEP402 2.8 35.1 1.0
CD B:GLU304 2.9 29.0 1.0
CG B:ASP324 3.1 34.8 1.0
CE1 B:HIS270 3.2 29.1 1.0
OE1 B:GLU304 3.2 32.2 1.0
CD2 B:HIS270 3.3 29.3 1.0
CB B:ASP324 3.5 33.3 1.0
CB B:CYS63 3.6 27.7 1.0
C1 B:PEP402 3.7 32.2 1.0
NZ B:LYS99 4.1 28.0 1.0
NH1 B:ARG94 4.2 25.8 1.0
C2 B:PEP402 4.2 33.9 1.0
OD1 B:ASP324 4.2 32.5 1.0
CA B:CYS63 4.2 28.2 1.0
CG B:GLU304 4.3 27.4 1.0
ND1 B:HIS270 4.4 26.6 1.0
CG B:HIS270 4.4 28.6 1.0
O B:HOH663 4.4 31.4 1.0
C3 B:PEP402 4.5 30.3 1.0
O2' B:PEP402 4.5 33.7 1.0
CA B:ASP324 4.8 33.2 1.0
O2 B:PEP402 4.8 30.9 1.0
O B:CYS63 4.8 25.7 1.0
N B:ASP324 4.9 32.9 1.0
C B:CYS63 4.9 27.8 1.0
CZ B:ARG94 5.0 25.6 1.0

Manganese binding site 3 out of 4 in 5d03

Go back to Manganese Binding Sites List in 5d03
Manganese 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 Manganese with other atoms in the Mn 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
C:Mn401

b:34.7
occ:1.00
 OE2 C:GLU304 2.0 30.9 1.0
O C:HOH510 2.1 32.4 1.0
OD2 C:ASP324 2.2 34.5 1.0
NE2 C:HIS270 2.3 32.5 1.0
SG C:CYS63 2.6 34.9 1.0
CD C:GLU304 2.9 31.4 1.0
OE1 C:GLU304 3.1 30.6 1.0
CG C:ASP324 3.2 39.8 1.0
CE1 C:HIS270 3.2 30.4 1.0
CD2 C:HIS270 3.3 31.8 1.0
O1 C:PEP402 3.4 28.3 1.0
CB C:ASP324 3.6 40.1 1.0
CB C:CYS63 3.6 31.8 1.0
NH2 C:ARG94 4.0 26.0 1.0
NZ C:LYS99 4.2 32.5 1.0
C1 C:PEP402 4.2 25.6 1.0
O C:HOH574 4.2 37.8 1.0
CA C:CYS63 4.2 29.4 1.0
OD1 C:ASP324 4.2 43.3 1.0
CG C:GLU304 4.3 27.8 1.0
ND1 C:HIS270 4.3 29.4 1.0
CG C:HIS270 4.4 30.9 1.0
C2 C:PEP402 4.6 31.5 1.0
O C:CYS63 4.8 25.5 1.0
CA C:ASP324 4.8 40.8 1.0
O2' C:PEP402 4.8 27.1 1.0
CZ C:ARG94 4.8 26.0 1.0
C C:CYS63 4.9 27.2 1.0
N C:ASP324 4.9 40.5 1.0
C3 C:PEP402 4.9 37.6 1.0

Manganese binding site 4 out of 4 in 5d03

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Manganese 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 Manganese with other atoms in the Mn 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:Mn401

b:34.4
occ:1.00
 OD2 D:ASP324 1.9 32.2 1.0
OE2 D:GLU304 2.1 35.9 1.0
O D:HOH520 2.4 40.7 1.0
NE2 D:HIS270 2.4 30.8 1.0
SG D:CYS63 2.6 33.2 1.0
O2' D:PEP402 2.7 36.2 1.0
CD D:GLU304 3.0 33.8 1.0
CG D:ASP324 3.0 34.3 1.0
OE1 D:GLU304 3.1 32.9 1.0
CE1 D:HIS270 3.3 31.2 1.0
CD2 D:HIS270 3.4 33.0 1.0
CB D:ASP324 3.5 32.4 1.0
C1 D:PEP402 3.6 35.5 1.0
CB D:CYS63 3.7 32.0 1.0
NZ D:LYS99 4.0 29.1 1.0
O D:HOH652 4.0 46.9 1.0
OD1 D:ASP324 4.1 32.1 1.0
NH2 D:ARG94 4.1 32.4 1.0
CA D:CYS63 4.2 31.6 1.0
C2 D:PEP402 4.3 37.6 1.0
CG D:GLU304 4.4 34.4 1.0
O1 D:PEP402 4.4 34.0 1.0
ND1 D:HIS270 4.4 32.1 1.0
CG D:HIS270 4.5 32.8 1.0
O D:HOH632 4.5 31.7 1.0
C3 D:PEP402 4.7 35.4 1.0
O D:CYS63 4.7 32.5 1.0
CA D:ASP324 4.8 33.1 1.0
CE D:LYS99 4.9 29.0 1.0
C D:CYS63 4.9 32.3 1.0
N D:ASP324 4.9 33.7 1.0
CZ D:ARG94 4.9 32.7 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 Aug 16 17:07:52 2025

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