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Manganese in PDB 5d09: Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase PHE211ALA Variant

Enzymatic activity of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase PHE211ALA Variant

All present enzymatic activity of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase PHE211ALA Variant:
2.5.1.54;

Protein crystallography data

The structure of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase PHE211ALA Variant, PDB code: 5d09 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) 100.45 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.675, 135.727, 149.356, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 25.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase PHE211ALA Variant (pdb code 5d09). 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 PHE211ALA Variant, PDB code: 5d09:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5d09

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Manganese binding site 1 out of 4 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase PHE211ALA 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 PHE211ALA Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:37.5
occ:1.00
 O A:HOH557 1.8 25.0 1.0
OE2 A:GLU304 1.9 37.6 1.0
NE2 A:HIS270 2.2 40.2 1.0
OD2 A:ASP324 2.3 32.9 1.0
SG A:CYS63 2.5 32.4 1.0
CD A:GLU304 2.9 35.7 1.0
CD2 A:HIS270 3.1 39.3 1.0
OE1 A:GLU304 3.2 36.2 1.0
CE1 A:HIS270 3.2 38.5 1.0
CG A:ASP324 3.2 35.1 1.0
CB A:ASP324 3.5 34.8 1.0
CB A:CYS63 3.6 33.0 1.0
O2' A:PEP402 3.6 58.1 1.0
CA A:CYS63 4.2 31.6 1.0
CG A:GLU304 4.3 33.0 1.0
NH2 A:ARG94 4.3 30.8 1.0
C1 A:PEP402 4.3 61.1 1.0
CG A:HIS270 4.3 40.2 1.0
ND1 A:HIS270 4.3 37.9 1.0
OD1 A:ASP324 4.4 39.2 1.0
NZ A:LYS99 4.4 53.8 1.0
C2 A:PEP402 4.5 63.2 1.0
C3 A:PEP402 4.6 62.3 1.0
CG A:LYS99 4.7 52.5 1.0
CA A:ASP324 4.7 34.7 1.0
N A:ASP324 4.8 33.4 1.0
O A:CYS63 4.8 32.5 1.0
C A:CYS63 4.9 31.0 1.0
CZ A:ARG94 5.0 29.5 1.0

Manganese binding site 2 out of 4 in 5d09

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Manganese binding site 2 out of 4 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase PHE211ALA 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 PHE211ALA Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:38.2
occ:1.00
 OD2 B:ASP324 2.0 32.3 1.0
O B:HOH570 2.0 36.6 1.0
OE2 B:GLU304 2.0 35.6 1.0
SG B:CYS63 2.4 40.0 1.0
NE2 B:HIS270 2.5 42.0 1.0
CD B:GLU304 3.0 33.5 1.0
CG B:ASP324 3.0 33.1 1.0
OE1 B:GLU304 3.2 34.4 1.0
CE1 B:HIS270 3.3 40.5 1.0
CB B:CYS63 3.4 38.2 1.0
CD2 B:HIS270 3.5 41.0 1.0
CB B:ASP324 3.5 32.5 1.0
NH1 B:ARG94 3.9 39.6 1.0
CA B:CYS63 4.1 36.4 1.0
OD1 B:ASP324 4.1 33.1 1.0
O B:HOH582 4.3 36.8 1.0
CG B:GLU304 4.4 31.9 1.0
ND1 B:HIS270 4.5 44.0 1.0
CG B:HIS270 4.6 42.0 1.0
O B:CYS63 4.6 35.0 1.0
N B:ASP324 4.7 34.6 1.0
CA B:ASP324 4.7 33.0 1.0
C B:CYS63 4.7 35.9 1.0
CZ B:ARG94 4.8 37.2 1.0
CB B:LYS99 5.0 52.7 1.0

Manganese binding site 3 out of 4 in 5d09

Go back to Manganese Binding Sites List in 5d09
Manganese binding site 3 out of 4 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase PHE211ALA 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 PHE211ALA Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:42.0
occ:1.00
 OE2 C:GLU304 1.9 34.0 1.0
OD2 C:ASP324 2.0 41.7 1.0
O C:HOH582 2.2 45.2 1.0
NE2 C:HIS270 2.4 38.9 1.0
SG C:CYS63 2.6 39.9 1.0
CD C:GLU304 2.8 34.3 1.0
CG C:ASP324 3.0 42.6 1.0
OE1 C:GLU304 3.0 35.8 1.0
CD2 C:HIS270 3.3 37.7 1.0
CE1 C:HIS270 3.4 38.8 1.0
CB C:ASP324 3.5 41.9 1.0
CB C:CYS63 3.6 38.4 1.0
NH2 C:ARG94 3.9 43.6 1.0
OD1 C:ASP324 4.1 48.7 1.0
CA C:CYS63 4.2 35.7 1.0
O C:HOH573 4.2 50.5 1.0
CG C:GLU304 4.2 31.4 1.0
O C:HOH576 4.3 37.9 1.0
CG C:HIS270 4.4 38.5 1.0
ND1 C:HIS270 4.4 38.7 1.0
CA C:ASP324 4.7 39.7 1.0
O C:CYS63 4.7 34.3 1.0
CZ C:ARG94 4.8 41.7 1.0
N C:ASP324 4.8 38.9 1.0
C C:CYS63 4.8 34.5 1.0

Manganese binding site 4 out of 4 in 5d09

Go back to Manganese Binding Sites List in 5d09
Manganese binding site 4 out of 4 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase PHE211ALA 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 PHE211ALA Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:57.0
occ:1.00
 OD2 D:ASP324 2.0 48.2 1.0
OE2 D:GLU304 2.1 43.0 1.0
NE2 D:HIS270 2.3 58.6 1.0
SG D:CYS63 2.6 55.2 1.0
CG D:ASP324 3.1 51.8 1.0
CD D:GLU304 3.1 45.0 1.0
CE1 D:HIS270 3.2 59.2 1.0
CD2 D:HIS270 3.3 58.7 1.0
OE1 D:GLU304 3.5 47.2 1.0
CB D:ASP324 3.7 53.2 1.0
CB D:CYS63 3.7 47.5 1.0
NH2 D:ARG94 3.8 49.0 1.0
CD D:LYS99 4.0 97.8 1.0
OD1 D:ASP324 4.1 52.4 1.0
CA D:CYS63 4.2 43.6 1.0
ND1 D:HIS270 4.4 59.9 1.0
CG D:GLU304 4.4 40.5 1.0
CG D:HIS270 4.4 61.7 1.0
O D:HOH558 4.5 32.8 1.0
CE D:LYS99 4.6 98.8 1.0
O D:CYS63 4.7 41.1 1.0
CZ D:ARG94 4.7 48.2 1.0
C D:CYS63 4.8 41.1 1.0
N D:ASP324 4.9 47.7 1.0
CA D:ASP324 4.9 52.0 1.0

Reference:

L.C.Heyes, E.J.Parker. Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase PHE211ALA Variant at 2.35 Angstroms Resolution To Be Published.
Page generated: Sat Oct 5 23:51:12 2024

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