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Manganese in PDB 5dcd: Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated (Tyrosine)

Enzymatic activity of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated (Tyrosine)

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

Protein crystallography data

The structure of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated (Tyrosine), PDB code: 5dcd was solved by L.C.Heyes, E.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.23 / 2.31
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.938, 141.292, 74.675, 90.00, 96.28, 90.00
R / Rfree (%) 19.4 / 23.9

Manganese Binding Sites:

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

Manganese binding site 1 out of 4 in 5dcd

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Manganese binding site 1 out of 4 in the Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated (Tyrosine)


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

b:32.8
occ:1.00
 OE2 A:GLU304 2.0 32.0 1.0
O A:HOH580 2.0 34.6 1.0
OD2 A:ASP324 2.0 29.6 1.0
NE2 A:HIS270 2.4 28.4 1.0
SG A:CYS63 2.6 31.7 1.0
CD A:GLU304 2.9 32.0 1.0
CG A:ASP324 3.1 31.4 1.0
OE1 A:GLU304 3.2 34.0 1.0
CE1 A:HIS270 3.4 28.3 1.0
CD2 A:HIS270 3.4 28.0 1.0
CB A:CYS63 3.6 34.4 1.0
CB A:ASP324 3.7 32.4 1.0
O A:HOH545 4.0 38.2 1.0
NH2 A:ARG94 4.0 34.9 1.0
OD1 A:ASP324 4.2 32.0 1.0
NZ A:LYS99 4.2 58.5 1.0
CA A:CYS63 4.2 33.8 1.0
CG A:GLU304 4.3 31.1 1.0
O A:HOH573 4.4 32.8 1.0
ND1 A:HIS270 4.5 30.4 1.0
O A:HOH587 4.5 45.9 1.0
CG A:HIS270 4.5 29.2 1.0
CD A:LYS99 4.5 55.5 1.0
O A:CYS63 4.8 34.2 1.0
CZ A:ARG94 4.8 34.6 1.0
CE A:LYS99 4.9 59.4 1.0
C A:CYS63 4.9 33.6 1.0
CA A:ASP324 4.9 32.9 1.0
CAA A:TMO403 4.9 47.3 1.0
N A:ASP324 5.0 33.3 1.0

Manganese binding site 2 out of 4 in 5dcd

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Manganese binding site 2 out of 4 in the Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated (Tyrosine)


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

b:62.1
occ:1.00
 OE2 B:GLU304 2.0 53.6 1.0
OD2 B:ASP324 2.3 66.4 1.0
SG B:CYS63 2.6 56.5 1.0
NE2 B:HIS270 2.8 55.6 1.0
CD B:GLU304 3.0 53.9 1.0
CG B:ASP324 3.2 69.5 1.0
OE1 B:GLU304 3.4 54.7 1.0
CB B:ASP324 3.5 69.4 1.0
CE1 B:HIS270 3.6 54.9 1.0
CD2 B:HIS270 3.7 56.1 1.0
CB B:CYS63 3.7 56.5 1.0
NH2 B:ARG94 3.9 48.6 1.0
NZ B:LYS99 4.1 73.4 1.0
CA B:CYS63 4.3 54.0 1.0
OD1 B:ASP324 4.3 71.8 1.0
CG B:LYS99 4.4 69.2 1.0
CG B:GLU304 4.4 51.5 1.0
O B:CYS63 4.7 51.3 1.0
CZ B:ARG94 4.7 47.1 1.0
ND1 B:HIS270 4.7 55.5 1.0
CA B:ASP324 4.8 71.4 1.0
CG B:HIS270 4.8 56.1 1.0
CE B:LYS99 4.8 75.0 1.0
CAD B:TMO402 4.9 47.2 1.0
C B:CYS63 4.9 52.8 1.0
N B:ASP324 4.9 68.0 1.0

Manganese binding site 3 out of 4 in 5dcd

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Manganese binding site 3 out of 4 in the Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated (Tyrosine)


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

b:40.8
occ:1.00
 OE2 C:GLU304 1.9 38.3 1.0
OD2 C:ASP324 2.2 38.8 1.0
NE2 C:HIS270 2.3 42.1 1.0
O C:HOH573 2.4 43.4 1.0
SG C:CYS63 2.7 43.8 1.0
CD C:GLU304 2.9 38.3 1.0
CG C:ASP324 3.2 41.9 1.0
CE1 C:HIS270 3.2 41.3 1.0
CD2 C:HIS270 3.2 43.9 1.0
OE1 C:GLU304 3.3 41.2 1.0
CB C:ASP324 3.6 43.3 1.0
CB C:CYS63 3.7 40.5 1.0
NH2 C:ARG94 3.9 38.5 1.0
CA C:CYS63 4.3 38.6 1.0
CG C:GLU304 4.3 36.1 1.0
O C:HOH572 4.3 48.0 1.0
ND1 C:HIS270 4.3 43.2 1.0
OD1 C:ASP324 4.3 43.2 1.0
CG C:HIS270 4.3 43.0 1.0
O C:HOH534 4.5 45.0 1.0
O C:CYS63 4.6 39.4 1.0
CA C:ASP324 4.8 45.6 1.0
C C:CYS63 4.8 38.7 1.0
CZ C:ARG94 4.8 36.5 1.0
N C:ASP324 4.8 45.5 1.0

Manganese binding site 4 out of 4 in 5dcd

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Manganese binding site 4 out of 4 in the Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated (Tyrosine)


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

b:48.7
occ:1.00
 OD2 D:ASP324 2.0 41.6 1.0
OE2 D:GLU304 2.0 43.1 1.0
NE2 D:HIS270 2.4 49.3 1.0
SG D:CYS63 2.8 46.7 1.0
CD D:GLU304 3.0 41.0 1.0
CG D:ASP324 3.1 45.5 1.0
CD2 D:HIS270 3.2 49.5 1.0
OE1 D:GLU304 3.3 42.8 1.0
CE1 D:HIS270 3.4 48.1 1.0
CB D:ASP324 3.5 47.0 1.0
NH2 D:ARG94 3.7 51.8 1.0
CB D:CYS63 3.8 44.5 1.0
OD1 D:ASP324 4.1 47.3 1.0
CG D:LYS99 4.4 56.1 1.0
CG D:GLU304 4.4 38.1 1.0
CA D:CYS63 4.4 41.6 1.0
CG D:HIS270 4.4 48.6 1.0
ND1 D:HIS270 4.5 47.8 1.0
O D:HOH553 4.6 51.3 1.0
CE D:LYS99 4.7 59.6 1.0
CZ D:ARG94 4.7 49.0 1.0
O D:CYS63 4.8 40.1 1.0
CA D:ASP324 4.8 47.6 1.0
CD D:LYS99 4.8 58.2 1.0
N D:ASP324 4.9 47.0 1.0
C D:CYS63 5.0 39.5 1.0

Reference:

L.C.Heyes, E.J.Parker. Structure of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep at 2.05 Angstroms To Be Published.
Page generated: Sat Oct 5 23:53:57 2024

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