Atomistry » Manganese » PDB 5cdn-5dcb » 5cz0
Atomistry »
  Manganese »
    PDB 5cdn-5dcb »
      5cz0 »

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

Go back to Manganese Binding Sites List in 5cz0
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

Go back to Manganese Binding Sites List in 5cz0
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy