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Manganese in PDB 5d05: Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase LYS107ALA Variant Regulated

Enzymatic activity of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase LYS107ALA Variant Regulated

All present enzymatic activity of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase LYS107ALA Variant Regulated:
2.5.1.54;

Protein crystallography data

The structure of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase LYS107ALA Variant Regulated, PDB code: 5d05 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) 74.46 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.331, 141.027, 76.028, 90.00, 97.02, 90.00
R / Rfree (%) 15 / 17.6

Other elements in 5d05:

The structure of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase LYS107ALA Variant Regulated also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase LYS107ALA Variant Regulated (pdb code 5d05). 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 LYS107ALA Variant Regulated, PDB code: 5d05:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5d05

Go back to Manganese Binding Sites List in 5d05
Manganese binding site 1 out of 4 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase LYS107ALA 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 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase LYS107ALA Variant Regulated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:18.7
occ:1.00
 OE2 A:GLU304 2.1 18.6 1.0
OD2 A:ASP324 2.1 17.5 1.0
O A:HOH521 2.2 17.9 1.0
NE2 A:HIS270 2.2 17.8 1.0
SG A:CYS63 2.6 19.4 1.0
CD A:GLU304 3.0 18.0 1.0
CG A:ASP324 3.1 20.3 1.0
OE1 A:GLU304 3.1 19.0 1.0
CD2 A:HIS270 3.2 17.5 1.0
CE1 A:HIS270 3.2 18.0 1.0
CB A:ASP324 3.4 20.1 1.0
CB A:CYS63 3.6 18.2 1.0
NH2 A:ARG94 3.7 16.3 1.0
O3P A:PEP403 4.1 18.9 1.0
CA A:CYS63 4.1 18.3 1.0
OD1 A:ASP324 4.2 20.5 1.0
CE A:LYS99 4.2 22.1 1.0
O A:HOH672 4.3 20.8 1.0
O A:HOH646 4.3 18.6 1.0
ND1 A:HIS270 4.3 18.0 1.0
CG A:HIS270 4.3 18.1 1.0
CG A:GLU304 4.4 18.4 1.0
CD A:LYS99 4.5 22.4 1.0
CZ A:ARG94 4.6 15.7 1.0
O A:CYS63 4.7 17.1 1.0
NZ A:LYS99 4.7 26.5 1.0
CA A:ASP324 4.7 20.4 1.0
C A:CYS63 4.8 18.1 1.0
C3 A:PEP403 4.8 22.8 1.0
O2 A:PEP403 4.8 18.7 1.0
N A:ASP324 4.8 20.6 1.0
CG A:LYS99 5.0 21.1 1.0

Manganese binding site 2 out of 4 in 5d05

Go back to Manganese Binding Sites List in 5d05
Manganese binding site 2 out of 4 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase LYS107ALA 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 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase LYS107ALA Variant Regulated within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:17.5
occ:1.00
 OE2 B:GLU304 1.9 17.7 1.0
OD2 B:ASP324 2.1 18.4 1.0
O B:HOH519 2.2 17.1 1.0
NE2 B:HIS270 2.3 17.2 1.0
SG B:CYS63 2.6 17.9 1.0
CD B:GLU304 2.9 18.0 1.0
CG B:ASP324 3.1 19.7 1.0
OE1 B:GLU304 3.2 18.1 1.0
CD2 B:HIS270 3.2 18.8 1.0
CE1 B:HIS270 3.3 17.9 1.0
CB B:ASP324 3.5 19.0 1.0
CB B:CYS63 3.5 17.8 1.0
NH1 B:ARG94 3.8 16.3 1.0
CE B:LYS99 4.1 22.8 1.0
O3P B:PEP404 4.1 18.5 1.0
CA B:CYS63 4.1 17.4 1.0
OD1 B:ASP324 4.2 20.3 1.0
O B:HOH618 4.2 17.7 1.0
CG B:GLU304 4.3 16.9 1.0
CD B:LYS99 4.3 22.6 1.0
O B:HOH675 4.3 21.5 1.0
CG B:HIS270 4.4 17.9 1.0
ND1 B:HIS270 4.4 17.3 1.0
NZ B:LYS99 4.6 26.1 1.0
CZ B:ARG94 4.7 16.0 1.0
CA B:ASP324 4.7 19.0 1.0
O B:CYS63 4.7 17.2 1.0
C3 B:PEP404 4.7 21.0 1.0
C B:CYS63 4.8 17.3 1.0
N B:ASP324 4.8 18.2 1.0
O2 B:PEP404 4.8 19.8 1.0
CG B:LYS99 4.9 21.0 1.0

Manganese binding site 3 out of 4 in 5d05

Go back to Manganese Binding Sites List in 5d05
Manganese binding site 3 out of 4 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase LYS107ALA 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 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase LYS107ALA Variant Regulated within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:16.1
occ:1.00
 OD2 C:ASP324 2.1 17.0 1.0
OE2 C:GLU304 2.1 16.8 1.0
O C:HOH516 2.2 17.4 1.0
NE2 C:HIS270 2.3 15.9 1.0
SG C:CYS63 2.6 17.1 1.0
CD C:GLU304 2.9 15.7 1.0
CG C:ASP324 3.1 18.7 1.0
OE1 C:GLU304 3.2 16.7 1.0
CE1 C:HIS270 3.2 14.7 1.0
CD2 C:HIS270 3.3 15.8 1.0
CB C:ASP324 3.5 18.0 1.0
CB C:CYS63 3.6 17.3 1.0
NH2 C:ARG94 3.7 16.7 1.0
O1P C:PEP403 4.1 17.0 1.0
CA C:CYS63 4.1 16.3 1.0
OD1 C:ASP324 4.1 19.6 1.0
CE C:LYS99 4.2 23.3 1.0
O C:HOH675 4.3 17.6 1.0
O C:HOH706 4.3 17.4 1.0
ND1 C:HIS270 4.3 15.0 1.0
CG C:GLU304 4.3 14.9 1.0
CD C:LYS99 4.3 23.8 1.0
CG C:HIS270 4.4 14.8 1.0
NZ C:LYS99 4.6 26.3 1.0
CZ C:ARG94 4.6 15.8 1.0
O C:CYS63 4.7 15.4 1.0
CA C:ASP324 4.7 18.5 1.0
C C:CYS63 4.8 16.7 1.0
C3 C:PEP403 4.8 21.2 1.0
O2 C:PEP403 4.8 19.6 1.0
N C:ASP324 4.8 18.8 1.0
CG C:LYS99 4.9 22.1 1.0

Manganese binding site 4 out of 4 in 5d05

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Manganese binding site 4 out of 4 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase LYS107ALA 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 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase LYS107ALA Variant Regulated within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:27.7
occ:1.00
 OE2 D:GLU304 2.1 32.0 1.0
OD2 D:ASP324 2.1 28.1 1.0
O D:HOH506 2.3 20.9 1.0
NE2 D:HIS270 2.3 28.4 1.0
SG D:CYS63 2.6 27.4 1.0
CD D:GLU304 2.9 30.6 1.0
OE1 D:GLU304 3.0 31.2 1.0
CG D:ASP324 3.1 29.6 1.0
CD2 D:HIS270 3.2 27.4 1.0
CE1 D:HIS270 3.3 27.8 1.0
CB D:ASP324 3.5 29.2 1.0
CB D:CYS63 3.6 26.9 1.0
NH2 D:ARG94 3.7 25.4 1.0
O2P D:PEP404 4.0 25.5 1.0
NZ D:LYS99 4.1 38.8 1.0
CA D:CYS63 4.1 26.5 1.0
OD1 D:ASP324 4.2 29.0 1.0
O D:HOH632 4.3 27.5 1.0
CG D:GLU304 4.3 30.2 1.0
O D:HOH572 4.4 26.8 1.0
CG D:HIS270 4.4 27.6 1.0
ND1 D:HIS270 4.4 27.8 1.0
CD D:LYS99 4.5 34.3 1.0
CZ D:ARG94 4.6 25.6 1.0
O D:CYS63 4.7 24.8 1.0
CE D:LYS99 4.8 38.0 1.0
C D:CYS63 4.8 26.5 1.0
CA D:ASP324 4.8 29.9 1.0
N D:ASP324 4.8 30.1 1.0
C3 D:PEP404 4.8 28.8 1.0
O2 D:PEP404 4.9 28.2 1.0
CG D:LYS99 5.0 32.4 1.0

Reference:

L.C.Heyes, E.J.Parker. Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase LYS107ALA Variant Regulated at 1.75 Angstroms Resolution To Be Published.
Page generated: Sat Oct 5 23:50:41 2024

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