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Manganese in PDB 4umc: Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water

Enzymatic activity of Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water

All present enzymatic activity of Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water:
2.5.1.54;

Protein crystallography data

The structure of Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water, PDB code: 4umc was solved by L.C.Heyes, S.Reichau, P.J.Cross, E.J.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.99 / 2.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.421, 137.013, 76.476, 90.00, 96.48, 90.00
R / Rfree (%) 20.255 / 23.038

Manganese Binding Sites:

The binding sites of Manganese atom in the Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water (pdb code 4umc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water, PDB code: 4umc:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4umc

Go back to Manganese Binding Sites List in 4umc
Manganese binding site 1 out of 4 in the Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1350

b:28.4
occ:1.00
 OD2 A:ASP324 2.0 28.0 1.0
OE2 A:GLU304 2.1 29.3 1.0
O2' A:PEQ1352 2.3 36.5 1.0
NE2 A:HIS270 2.3 29.0 1.0
SG A:CYS63 2.6 31.0 1.0
CG A:ASP324 3.0 29.1 1.0
CD A:GLU304 3.1 28.5 1.0
C1 A:PEQ1352 3.1 39.3 1.0
CD2 A:HIS270 3.3 29.6 1.0
CE1 A:HIS270 3.3 28.9 1.0
OE1 A:GLU304 3.4 27.7 1.0
CB A:ASP324 3.5 30.2 1.0
CB A:CYS63 3.6 29.9 1.0
O1 A:PEQ1352 3.7 36.0 1.0
C2 A:PEQ1352 4.0 40.0 1.0
NZ A:LYS99 4.1 23.8 1.0
OD1 A:ASP324 4.1 28.8 1.0
C3 A:PEQ1352 4.1 40.8 1.0
O A:HOH2087 4.3 27.2 1.0
CA A:CYS63 4.3 29.9 1.0
NH2 A:ARG94 4.3 25.0 1.0
ND1 A:HIS270 4.4 30.3 1.0
CG A:HIS270 4.4 30.3 1.0
CG A:GLU304 4.4 28.4 1.0
O2 A:PEQ1352 4.5 39.6 1.0
CA A:ASP324 4.8 30.5 1.0
CE A:LYS99 4.9 23.7 1.0
N A:ASP324 4.9 29.1 1.0
O A:CYS63 4.9 29.0 1.0
C A:CYS63 5.0 30.3 1.0

Manganese binding site 2 out of 4 in 4umc

Go back to Manganese Binding Sites List in 4umc
Manganese binding site 2 out of 4 in the Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1351

b:36.6
occ:1.00
 OE2 B:GLU304 1.9 33.6 1.0
OD2 B:ASP324 2.0 37.2 1.0
O2' B:PEQ1352 2.3 44.9 1.0
NE2 B:HIS270 2.5 34.8 1.0
SG B:CYS63 2.6 31.2 1.0
CD B:GLU304 2.9 33.7 1.0
CG B:ASP324 3.0 38.7 1.0
C1 B:PEQ1352 3.3 46.8 1.0
OE1 B:GLU304 3.3 32.7 1.0
CD2 B:HIS270 3.3 35.4 1.0
CB B:ASP324 3.4 37.6 1.0
CB B:CYS63 3.5 33.1 1.0
CE1 B:HIS270 3.5 34.5 1.0
C3 B:PEQ1352 3.9 46.0 1.0
O1 B:PEQ1352 3.9 46.8 1.0
NZ B:LYS99 4.1 38.2 1.0
OD1 B:ASP324 4.1 39.5 1.0
CA B:CYS63 4.2 32.5 1.0
NH2 B:ARG94 4.2 33.0 1.0
C2 B:PEQ1352 4.2 43.3 1.0
CG B:GLU304 4.3 33.2 1.0
O B:HOH2064 4.3 33.9 1.0
O B:HOH2055 4.5 29.3 1.0
CG B:HIS270 4.5 36.3 1.0
ND1 B:HIS270 4.6 35.6 1.0
CA B:ASP324 4.6 38.2 1.0
N B:ASP324 4.7 38.3 1.0
O B:CYS63 4.9 32.5 1.0
O2 B:PEQ1352 4.9 41.4 1.0
C B:CYS63 4.9 32.3 1.0
CE B:LYS99 4.9 38.0 1.0

Manganese binding site 3 out of 4 in 4umc

Go back to Manganese Binding Sites List in 4umc
Manganese binding site 3 out of 4 in the Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1350

b:39.2
occ:1.00
 OE2 C:GLU304 2.0 33.0 1.0
OD2 C:ASP324 2.0 42.5 1.0
O2' C:PEQ1351 2.3 41.6 1.0
NE2 C:HIS270 2.5 33.4 1.0
SG C:CYS63 2.6 37.5 1.0
CD C:GLU304 3.0 31.4 1.0
CG C:ASP324 3.1 44.8 1.0
C1 C:PEQ1351 3.3 44.3 1.0
CD2 C:HIS270 3.3 35.1 1.0
OE1 C:GLU304 3.3 30.7 1.0
CB C:ASP324 3.5 43.8 1.0
CB C:CYS63 3.5 37.6 1.0
CE1 C:HIS270 3.6 33.7 1.0
O1 C:PEQ1351 4.0 36.2 1.0
C3 C:PEQ1351 4.0 46.6 1.0
NZ C:LYS99 4.1 36.4 1.0
C2 C:PEQ1351 4.2 45.3 1.0
OD1 C:ASP324 4.2 46.4 1.0
CA C:CYS63 4.2 36.2 1.0
O C:HOH2055 4.2 33.4 1.0
NH2 C:ARG94 4.2 33.9 1.0
CG C:GLU304 4.3 30.4 1.0
CG C:HIS270 4.5 36.3 1.0
O2 C:PEQ1351 4.6 47.3 1.0
ND1 C:HIS270 4.6 34.5 1.0
CA C:ASP324 4.8 43.9 1.0
N C:ASP324 4.8 43.2 1.0
O C:CYS63 4.8 36.0 1.0
C C:CYS63 4.9 36.3 1.0
CE C:LYS99 4.9 37.4 1.0
CZ C:ARG94 4.9 33.8 1.0

Manganese binding site 4 out of 4 in 4umc

Go back to Manganese Binding Sites List in 4umc
Manganese binding site 4 out of 4 in the Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1350

b:40.8
occ:1.00
 OD2 D:ASP324 1.9 36.2 1.0
OE2 D:GLU304 2.1 39.5 1.0
O2' D:PEQ1352 2.1 38.0 1.0
SG D:CYS63 2.5 39.4 1.0
NE2 D:HIS270 2.6 36.1 1.0
CG D:ASP324 2.9 37.4 1.0
CD D:GLU304 3.1 38.6 1.0
C1 D:PEQ1352 3.3 39.6 1.0
CB D:ASP324 3.3 38.7 1.0
OE1 D:GLU304 3.4 36.7 1.0
CD2 D:HIS270 3.4 35.9 1.0
CB D:CYS63 3.5 41.7 1.0
CE1 D:HIS270 3.6 37.3 1.0
C3 D:PEQ1352 3.6 43.8 1.0
NZ D:LYS99 4.0 36.5 1.0
C2 D:PEQ1352 4.0 42.4 1.0
OD1 D:ASP324 4.1 38.7 1.0
CA D:CYS63 4.2 41.4 1.0
O D:HOH2038 4.2 33.7 1.0
O1 D:PEQ1352 4.2 39.5 1.0
NH2 D:ARG94 4.3 42.3 1.0
CG D:GLU304 4.4 39.3 1.0
CA D:ASP324 4.6 38.8 1.0
CG D:HIS270 4.6 37.1 1.0
ND1 D:HIS270 4.6 36.8 1.0
N D:ASP324 4.7 37.9 1.0
O2 D:PEQ1352 4.7 43.6 1.0
CE D:LYS99 4.8 36.6 1.0
O D:CYS63 4.8 42.8 1.0
C D:CYS63 4.9 40.8 1.0

Reference:

L.C.Heyes, S.Reichau, P.J.Cross, G.B.Jameson, E.J.Parker. Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino- Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water. Bioorg.Chem. 2014.
ISSN: ESSN 1090-2120
PubMed: 25245459
DOI: 10.1016/J.BIOORG.2014.08.003
Page generated: Sat Oct 5 21:21:14 2024

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