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Manganese in PDB 5cz0: Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU98ALA Variant

Enzymatic activity of Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU98ALA Variant

All present enzymatic activity of Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU98ALA Variant:
2.5.1.54;

Protein crystallography data

The structure of Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU98ALA Variant, PDB code: 5cz0 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) 75.63 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.850, 135.250, 76.040, 90.00, 95.95, 90.00
R / Rfree (%) 20 / 26.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU98ALA Variant (pdb code 5cz0). 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 GLU98ALA Variant, PDB code: 5cz0:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5cz0

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Manganese binding site 1 out of 4 in the Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU98ALA 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 GLU98ALA Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:39.5
occ:1.00
 OE2 A:GLU304 2.0 32.6 1.0
O A:HOH524 2.1 29.7 1.0
OD2 A:ASP324 2.3 33.3 1.0
NE2 A:HIS270 2.4 27.2 1.0
SG A:CYS63 2.5 33.9 1.0
CD A:GLU304 3.0 33.3 1.0
CG A:ASP324 3.2 32.9 1.0
CD2 A:HIS270 3.2 27.7 1.0
OE1 A:GLU304 3.3 32.7 1.0
O1 A:PEP403 3.5 52.6 1.0
CB A:CYS63 3.5 32.4 1.0
CE1 A:HIS270 3.5 27.7 1.0
CB A:ASP324 3.6 34.4 1.0
C2 A:EDO405 4.1 55.5 1.0
OD1 A:ASP324 4.2 31.1 1.0
NZ A:LYS99 4.2 39.5 1.0
O A:HOH533 4.2 29.4 1.0
CA A:CYS63 4.3 31.4 1.0
NH2 A:ARG94 4.3 33.9 1.0
C1 A:PEP403 4.4 55.8 1.0
CG A:GLU304 4.4 33.9 1.0
CG A:HIS270 4.5 28.3 1.0
C2 A:PEP403 4.5 57.8 1.0
ND1 A:HIS270 4.6 27.5 1.0
N A:ASP324 4.8 33.4 1.0
CA A:ASP324 4.8 34.6 1.0
C3 A:PEP403 4.9 54.6 1.0
O2 A:PEP403 4.9 56.0 1.0

Manganese binding site 2 out of 4 in 5cz0

Go back to Manganese Binding Sites List in 5cz0
Manganese binding site 2 out of 4 in the Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU98ALA 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 GLU98ALA Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:60.2
occ:1.00
 OE2 B:GLU304 2.0 38.5 1.0
NE2 B:HIS270 2.5 58.8 1.0
OD2 B:ASP324 2.6 62.6 1.0
SG B:CYS63 2.6 48.1 1.0
CD B:GLU304 3.1 40.5 1.0
OE1 B:GLU304 3.4 41.5 1.0
CG B:ASP324 3.4 63.6 1.0
CE1 B:HIS270 3.4 58.1 1.0
CD2 B:HIS270 3.5 59.5 1.0
CB B:ASP324 3.7 59.8 1.0
CB B:CYS63 3.8 49.1 1.0
NH1 B:ARG94 3.8 41.3 1.0
NZ B:LYS99 4.0 66.3 1.0
O2' B:PEP402 4.1 66.1 1.0
C1 B:PEP402 4.2 65.9 1.0
C2 B:PEP402 4.3 74.0 1.0
CG B:GLU304 4.4 41.8 1.0
CA B:CYS63 4.4 50.1 1.0
OD1 B:ASP324 4.5 64.0 1.0
ND1 B:HIS270 4.5 58.4 1.0
C3 B:PEP402 4.6 75.0 1.0
CG B:HIS270 4.6 58.2 1.0
O1 B:PEP402 4.7 55.2 1.0
O B:CYS63 4.8 49.9 1.0
CZ B:ARG94 4.8 38.9 1.0
CE B:LYS99 4.8 67.5 1.0
O2 B:PEP402 4.8 79.4 1.0
C B:CYS63 4.9 50.7 1.0
CA B:ASP324 4.9 61.7 1.0
N B:ASP324 4.9 61.9 1.0

Manganese binding site 3 out of 4 in 5cz0

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Manganese binding site 3 out of 4 in the Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU98ALA 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 GLU98ALA Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:53.9
occ:1.00
 OE2 C:GLU304 2.0 45.9 1.0
OD2 C:ASP324 2.3 66.6 1.0
NE2 C:HIS270 2.3 49.2 1.0
SG C:CYS63 2.4 52.5 1.0
O C:HOH504 2.4 33.8 1.0
CD C:GLU304 2.8 45.4 1.0
OE1 C:GLU304 3.0 48.8 1.0
CD2 C:HIS270 3.2 51.2 1.0
CG C:ASP324 3.2 65.2 1.0
CE1 C:HIS270 3.3 50.1 1.0
CB C:CYS63 3.5 48.0 1.0
CB C:ASP324 3.6 63.8 1.0
O2' C:PEP402 3.8 54.5 1.0
CA C:CYS63 4.1 46.7 1.0
CG C:GLU304 4.2 42.0 1.0
NH2 C:ARG94 4.3 38.6 1.0
OD1 C:ASP324 4.3 66.8 1.0
CG C:HIS270 4.3 52.1 1.0
ND1 C:HIS270 4.4 50.0 1.0
C1 C:PEP402 4.6 56.3 1.0
O C:CYS63 4.8 48.0 1.0
CA C:ASP324 4.8 63.3 1.0
O C:HOH509 4.9 47.1 1.0
C C:CYS63 4.9 47.8 1.0
N C:ASP324 5.0 64.3 1.0
C2 C:PEP402 5.0 64.6 1.0

Manganese binding site 4 out of 4 in 5cz0

Go back to Manganese Binding Sites List in 5cz0
Manganese binding site 4 out of 4 in the Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU98ALA 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 GLU98ALA Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:49.7
occ:1.00
 OE2 D:GLU304 2.1 48.8 1.0
OD2 D:ASP324 2.1 48.9 1.0
NE2 D:HIS270 2.4 45.2 1.0
SG D:CYS63 2.6 41.3 1.0
CD D:GLU304 3.1 49.4 1.0
CG D:ASP324 3.1 50.7 1.0
O1 D:PEP403 3.3 48.9 1.0
CD2 D:HIS270 3.3 46.1 1.0
CE1 D:HIS270 3.4 46.2 1.0
OE1 D:GLU304 3.4 51.4 1.0
CB D:ASP324 3.7 49.5 1.0
CB D:CYS63 3.7 39.6 1.0
NZ D:LYS99 3.8 50.4 1.0
OD1 D:ASP324 4.1 53.3 1.0
NH2 D:ARG94 4.1 45.0 1.0
C1 D:PEP403 4.2 59.5 1.0
CA D:CYS63 4.2 40.0 1.0
C2 D:PEP403 4.2 65.0 1.0
CG D:GLU304 4.4 48.2 1.0
CG D:HIS270 4.5 47.6 1.0
ND1 D:HIS270 4.5 46.0 1.0
C3 D:PEP403 4.6 65.8 1.0
O D:CYS63 4.6 42.5 1.0
O2 D:PEP403 4.6 68.0 1.0
CE D:LYS99 4.7 51.2 1.0
C D:CYS63 4.8 40.7 1.0
CA D:ASP324 4.9 49.2 1.0
CZ D:ARG94 5.0 44.8 1.0
N D:ASP324 5.0 50.2 1.0

Reference:

L.C.Heyes, E.J.Parker. NMEDAH7PS E98A Variant at 2.5 Angstroms Resolution To Be Published.
Page generated: Sat Oct 5 23:48:50 2024

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