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

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

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

Protein crystallography data

The structure of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated (Tryptophan), PDB code: 5dce 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) 75.37 / 2.23
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.432, 138.042, 75.868, 90.00, 96.58, 90.00
R / Rfree (%) 19.2 / 23.8

Manganese Binding Sites:

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

Manganese binding site 1 out of 4 in 5dce

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


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

b:41.0
occ:1.00
 OD2 A:ASP324 1.8 34.3 1.0
O A:HOH547 2.0 38.6 1.0
OE2 A:GLU304 2.0 37.8 1.0
NE2 A:HIS270 2.4 36.4 1.0
SG A:CYS63 2.6 34.8 1.0
CG A:ASP324 2.9 36.4 1.0
CD A:GLU304 2.9 36.4 1.0
OE1 A:GLU304 3.2 37.3 1.0
CD2 A:HIS270 3.3 35.6 1.0
CE1 A:HIS270 3.4 37.1 1.0
CB A:ASP324 3.5 35.5 1.0
CB A:CYS63 3.6 35.8 1.0
OD1 A:ASP324 4.0 32.8 1.0
CA A:CYS63 4.2 34.7 1.0
O A:HOH555 4.2 40.9 1.0
O A:HOH562 4.3 62.7 1.0
CG A:GLU304 4.3 36.7 1.0
NH2 A:ARG94 4.3 39.8 1.0
O A:HOH544 4.4 45.6 1.0
CG A:HIS270 4.4 37.7 1.0
ND1 A:HIS270 4.5 38.4 1.0
O A:HOH560 4.5 42.7 1.0
CA A:ASP324 4.7 36.0 1.0
N A:ASP324 4.8 37.0 1.0
O A:CYS63 4.8 30.2 1.0
C A:CYS63 4.8 33.4 1.0

Manganese binding site 2 out of 4 in 5dce

Go back to Manganese Binding Sites List in 5dce
Manganese binding site 2 out of 4 in the Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated (Tryptophan)


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

b:70.6
occ:1.00
 OE2 B:GLU304 1.8 48.5 1.0
OD2 B:ASP324 2.1 76.3 1.0
NE2 B:HIS270 2.4 61.6 1.0
SG B:CYS63 2.5 57.7 1.0
CD B:GLU304 2.8 54.9 1.0
CG B:ASP324 3.0 71.6 1.0
CD2 B:HIS270 3.2 64.6 1.0
OE1 B:GLU304 3.3 60.5 1.0
CB B:ASP324 3.4 69.5 1.0
CE1 B:HIS270 3.4 60.5 1.0
CB B:CYS63 3.6 56.9 1.0
NH1 B:ARG94 4.0 47.0 1.0
OD1 B:ASP324 4.1 72.5 1.0
CG B:GLU304 4.1 54.0 1.0
CA B:CYS63 4.2 55.4 1.0
O B:HOH546 4.3 53.9 1.0
CG B:HIS270 4.4 64.9 1.0
ND1 B:HIS270 4.4 63.5 1.0
CA B:ASP324 4.6 72.1 1.0
O B:CYS63 4.7 52.9 1.0
N B:ASP324 4.8 72.5 1.0
C B:CYS63 4.8 55.1 1.0
CZ B:ARG94 4.9 48.9 1.0

Manganese binding site 3 out of 4 in 5dce

Go back to Manganese Binding Sites List in 5dce
Manganese binding site 3 out of 4 in the Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated (Tryptophan)


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

b:64.2
occ:1.00
 OE2 C:GLU304 1.9 54.6 1.0
OD2 C:ASP324 2.2 69.1 1.0
NE2 C:HIS270 2.3 63.2 1.0
SG C:CYS63 2.4 54.2 1.0
O C:HOH555 2.6 60.4 1.0
CD C:GLU304 2.8 55.9 1.0
OE1 C:GLU304 3.0 55.8 1.0
CD2 C:HIS270 3.1 64.8 1.0
CG C:ASP324 3.2 70.7 1.0
CE1 C:HIS270 3.2 62.5 1.0
CB C:ASP324 3.5 68.8 1.0
CB C:CYS63 3.6 55.9 1.0
CG C:GLU304 4.2 53.6 1.0
NH2 C:ARG94 4.2 51.1 1.0
CA C:CYS63 4.2 53.4 1.0
CG C:HIS270 4.3 65.6 1.0
OD1 C:ASP324 4.3 76.9 1.0
ND1 C:HIS270 4.3 62.2 1.0
O C:HOH548 4.4 46.1 1.0
O C:CYS63 4.8 50.4 1.0
CA C:ASP324 4.8 67.8 1.0
N C:ASP324 4.9 67.4 1.0
C C:CYS63 4.9 51.8 1.0
CZ C:ARG94 4.9 49.4 1.0

Manganese binding site 4 out of 4 in 5dce

Go back to Manganese Binding Sites List in 5dce
Manganese binding site 4 out of 4 in the Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated (Tryptophan)


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

b:65.6
occ:1.00
 OD2 D:ASP324 1.8 48.9 1.0
OE2 D:GLU304 1.9 56.5 1.0
NE2 D:HIS270 2.5 59.9 1.0
SG D:CYS63 2.5 52.2 1.0
CG D:ASP324 3.0 51.6 1.0
CD D:GLU304 3.0 55.5 1.0
CD2 D:HIS270 3.4 59.1 1.0
OE1 D:GLU304 3.4 55.9 1.0
CE1 D:HIS270 3.5 61.3 1.0
CB D:CYS63 3.5 52.9 1.0
CB D:ASP324 3.6 53.8 1.0
O D:HOH546 3.8 60.8 1.0
NH2 D:ARG94 4.0 56.1 1.0
OD1 D:ASP324 4.0 50.3 1.0
CA D:CYS63 4.1 52.2 1.0
CG D:GLU304 4.3 54.8 1.0
CG D:HIS270 4.6 60.4 1.0
ND1 D:HIS270 4.6 59.6 1.0
O D:CYS63 4.6 48.0 1.0
C D:CYS63 4.7 51.4 1.0
CZ D:ARG94 4.8 57.3 1.0
CA D:ASP324 4.9 54.0 1.0
N D:ASP324 4.9 51.8 1.0

Reference:

P.J.Cross, L.C.Heyes, S.Zhang, A.R.Nazmi, E.J.Parker. The Functional Unit of Neisseria Meningitidis 3-Deoxy--Arabino-Heptulosonate 7-Phosphate Synthase Is Dimeric. Plos One V. 11 45187 2016.
ISSN: ESSN 1932-6203
PubMed: 26828675
DOI: 10.1371/JOURNAL.PONE.0145187
Page generated: Sat Oct 5 23:53:57 2024

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