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

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

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

Protein crystallography data

The structure of Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU98ALA Variant Regulated, PDB code: 5czs 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) 74.06 / 2.42
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.322, 142.326, 74.591, 90.00, 96.84, 90.00
R / Rfree (%) 19.1 / 24.6

Manganese Binding Sites:

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

Manganese binding site 1 out of 4 in 5czs

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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 Regulated


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 Regulated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:27.9
occ:1.00
 O A:HOH549 1.9 28.3 1.0
OE2 A:GLU304 2.0 25.2 1.0
OD2 A:ASP324 2.0 24.8 1.0
NE2 A:HIS270 2.2 25.2 1.0
SG A:CYS63 2.8 25.2 1.0
CD A:GLU304 2.9 25.4 1.0
CE1 A:HIS270 3.0 25.7 1.0
CG A:ASP324 3.1 24.7 1.0
CD2 A:HIS270 3.2 25.8 1.0
OE1 A:GLU304 3.2 24.9 1.0
O1 A:PEP402 3.4 50.6 0.8
CB A:ASP324 3.5 25.4 1.0
CB A:CYS63 3.7 25.1 1.0
O1 A:EDO404 4.0 47.9 1.0
ND1 A:HIS270 4.1 26.4 1.0
C1 A:PEP402 4.2 48.5 0.8
OD1 A:ASP324 4.2 24.2 1.0
CG A:HIS270 4.3 26.2 1.0
CA A:CYS63 4.3 24.9 1.0
CG A:GLU304 4.3 25.7 1.0
NH2 A:ARG94 4.3 28.4 1.0
C2 A:PEP402 4.3 46.6 0.8
C3 A:PEP402 4.4 45.2 0.8
O A:HOH524 4.6 23.7 1.0
O A:CYS63 4.7 25.6 1.0
CA A:ASP324 4.8 26.0 1.0
N A:ASP324 4.9 25.5 1.0
C A:CYS63 4.9 25.1 1.0
O2 A:PEP402 5.0 52.0 0.8
C2 A:EDO404 5.0 47.3 1.0

Manganese binding site 2 out of 4 in 5czs

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Manganese binding site 2 out of 4 in the Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU98ALA Variant Regulated


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 Regulated within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:43.2
occ:1.00
 OE2 B:GLU304 2.0 37.2 1.0
OD2 B:ASP324 2.3 40.8 1.0
NE2 B:HIS270 2.3 35.4 1.0
SG B:CYS63 2.5 38.6 1.0
CD B:GLU304 3.0 38.9 1.0
CE1 B:HIS270 3.2 35.4 1.0
CG B:ASP324 3.2 40.7 1.0
CD2 B:HIS270 3.3 37.3 1.0
OE1 B:GLU304 3.3 37.5 1.0
CB B:ASP324 3.5 41.1 1.0
CB B:CYS63 3.6 39.7 1.0
C3 B:PEP402 4.0 58.2 0.8
CA B:CYS63 4.1 38.4 1.0
NH1 B:ARG94 4.2 33.4 1.0
ND1 B:HIS270 4.3 36.9 1.0
C2 B:PEP402 4.3 57.4 0.8
OD1 B:ASP324 4.4 41.9 1.0
CG B:HIS270 4.4 39.0 1.0
CG B:GLU304 4.4 36.9 1.0
O1 B:PEP402 4.5 48.0 0.8
O B:CYS63 4.6 35.1 1.0
C B:CYS63 4.7 37.3 1.0
CA B:ASP324 4.8 41.3 1.0
C1 B:PEP402 4.8 56.9 0.8
N B:ASP324 4.8 39.2 1.0
O2 B:PEP402 4.9 60.4 0.8
CZ B:ARG94 5.0 34.2 1.0

Manganese binding site 3 out of 4 in 5czs

Go back to Manganese Binding Sites List in 5czs
Manganese binding site 3 out of 4 in the Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU98ALA Variant Regulated


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 Regulated within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:32.6
occ:1.00
 OE2 C:GLU304 1.8 29.2 1.0
O C:HOH520 1.8 20.7 1.0
OD2 C:ASP324 2.1 33.7 1.0
NE2 C:HIS270 2.4 29.6 1.0
SG C:CYS63 2.6 28.8 1.0
CD C:GLU304 2.7 28.5 1.0
CG C:ASP324 3.0 35.4 1.0
OE1 C:GLU304 3.1 28.0 1.0
CE1 C:HIS270 3.2 29.3 1.0
CB C:ASP324 3.3 36.4 1.0
CD2 C:HIS270 3.4 30.7 1.0
CB C:CYS63 3.4 30.0 1.0
CA C:CYS63 4.0 29.4 1.0
O C:HOH529 4.0 17.0 1.0
NH2 C:ARG94 4.0 28.9 1.0
CG C:GLU304 4.1 27.7 1.0
OD1 C:ASP324 4.2 35.5 1.0
O C:HOH568 4.3 37.8 1.0
ND1 C:HIS270 4.3 30.4 1.0
CG C:HIS270 4.4 31.0 1.0
O2' C:PEP402 4.5 36.5 0.8
O C:CYS63 4.5 29.0 1.0
CA C:ASP324 4.6 37.8 1.0
C C:CYS63 4.7 29.5 1.0
C3 C:PEP402 4.7 34.4 0.8
N C:ASP324 4.7 36.5 1.0
C2 C:PEP402 4.7 34.3 0.8
CZ C:ARG94 4.8 28.2 1.0
C1 C:PEP402 4.8 32.6 0.8

Manganese binding site 4 out of 4 in 5czs

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Manganese binding site 4 out of 4 in the Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU98ALA Variant Regulated


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 Regulated within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:38.7
occ:1.00
 OE2 D:GLU304 2.0 32.7 1.0
O D:HOH567 2.0 32.9 1.0
OD2 D:ASP324 2.2 34.3 1.0
NE2 D:HIS270 2.3 31.9 1.0
SG D:CYS63 2.6 33.6 1.0
CD D:GLU304 3.0 33.0 1.0
CG D:ASP324 3.1 34.1 1.0
CD2 D:HIS270 3.2 32.9 1.0
CE1 D:HIS270 3.3 32.6 1.0
OE1 D:GLU304 3.3 35.8 1.0
CB D:ASP324 3.4 33.0 1.0
CB D:CYS63 3.7 32.4 1.0
O D:HOH565 3.9 43.6 1.0
NH2 D:ARG94 4.1 38.4 1.0
O1 D:PEP402 4.2 49.7 0.8
O D:HOH558 4.2 34.5 1.0
OD1 D:ASP324 4.3 36.6 1.0
CA D:CYS63 4.3 31.9 1.0
CG D:GLU304 4.3 32.1 1.0
CG D:HIS270 4.4 33.9 1.0
O D:HOH550 4.4 34.1 1.0
ND1 D:HIS270 4.4 32.4 1.0
C2 D:PEP402 4.5 45.8 0.8
C1 D:PEP402 4.5 46.3 0.8
C3 D:PEP402 4.5 45.7 0.8
CA D:ASP324 4.7 32.4 1.0
O D:CYS63 4.7 31.6 1.0
N D:ASP324 4.8 31.3 1.0
C D:CYS63 4.9 31.6 1.0
CZ D:ARG94 4.9 37.7 1.0

Reference:

L.C.Heyes, E.J.Parker. Structure of Neisseria Meningitidis 3 Dexy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU98ALA Variant at 2.42 Angstroms Resolution To Be Published.
Page generated: Sat Oct 5 23:49:17 2024

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