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Manganese in PDB 4uma: 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: 4uma 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) 73.04 / 1.76
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.495, 136.501, 76.157, 90.00, 96.41, 90.00
R / Rfree (%) 19.061 / 21.44

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 4uma). 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: 4uma:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4uma

Go back to Manganese Binding Sites List in 4uma
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:20.9
occ:1.00
OD2 A:ASP324 2.0 25.1 1.0
OE2 A:GLU304 2.0 21.4 1.0
NE2 A:HIS270 2.3 22.9 1.0
OAD A:GZ31351 2.3 23.9 1.0
SG A:CYS63 2.6 20.6 1.0
CD A:GLU304 2.9 23.2 1.0
CAI A:GZ31351 2.9 22.9 1.0
CG A:ASP324 3.0 23.8 1.0
OE1 A:GLU304 3.1 24.0 1.0
CD2 A:HIS270 3.2 22.2 1.0
CE1 A:HIS270 3.3 23.4 1.0
OAB A:GZ31351 3.3 23.5 1.0
CB A:ASP324 3.4 23.4 1.0
CB A:CYS63 3.6 19.7 1.0
CAH A:GZ31351 4.0 26.0 1.0
O A:HOH2219 4.0 29.3 1.0
OD1 A:ASP324 4.1 26.0 1.0
NH2 A:ARG94 4.2 21.6 1.0
NZ A:LYS99 4.2 19.2 1.0
CA A:CYS63 4.2 19.5 1.0
CG A:GLU304 4.3 23.7 1.0
O A:HOH2194 4.4 25.0 1.0
ND1 A:HIS270 4.4 22.3 1.0
CG A:HIS270 4.4 23.7 1.0
CAA A:GZ31351 4.5 30.5 1.0
CA A:ASP324 4.7 22.9 1.0
CAG A:GZ31351 4.8 21.9 1.0
N A:ASP324 4.8 22.7 1.0
O A:CYS63 4.8 20.7 1.0
C A:CYS63 4.9 20.1 1.0
CZ A:ARG94 4.9 22.1 1.0
CE A:LYS99 4.9 20.0 1.0

Manganese binding site 2 out of 4 in 4uma

Go back to Manganese Binding Sites List in 4uma
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:Mn1350

b:21.2
occ:1.00
OE2 B:GLU304 2.0 22.9 1.0
OD2 B:ASP324 2.0 27.2 1.0
NE2 B:HIS270 2.4 26.0 1.0
OAD B:GZ31351 2.4 27.9 1.0
SG B:CYS63 2.5 23.7 1.0
CD B:GLU304 2.8 21.8 1.0
CG B:ASP324 3.0 26.1 1.0
CAI B:GZ31351 3.0 24.3 1.0
OE1 B:GLU304 3.1 22.0 1.0
CD2 B:HIS270 3.3 24.7 1.0
CE1 B:HIS270 3.3 24.9 1.0
OAB B:GZ31351 3.4 24.6 1.0
CB B:ASP324 3.4 25.3 1.0
CB B:CYS63 3.6 23.7 1.0
O B:HOH2203 4.0 28.6 1.0
CAH B:GZ31351 4.0 23.5 1.0
NH2 B:ARG94 4.1 22.5 1.0
OD1 B:ASP324 4.1 26.1 1.0
CA B:CYS63 4.1 23.2 1.0
NZ B:LYS99 4.2 22.0 1.0
CG B:GLU304 4.2 22.6 1.0
O B:HOH2178 4.3 25.6 1.0
ND1 B:HIS270 4.4 22.6 1.0
CG B:HIS270 4.4 23.7 1.0
CAA B:GZ31351 4.5 24.8 1.0
CA B:ASP324 4.7 24.9 1.0
N B:ASP324 4.8 23.9 1.0
O B:CYS63 4.8 23.3 1.0
CAG B:GZ31351 4.8 20.7 1.0
C B:CYS63 4.9 23.1 1.0
CZ B:ARG94 4.9 22.2 1.0
CE B:LYS99 4.9 22.3 1.0

Manganese binding site 3 out of 4 in 4uma

Go back to Manganese Binding Sites List in 4uma
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:24.1
occ:1.00
OE2 C:GLU304 2.0 25.6 1.0
OD2 C:ASP324 2.0 28.6 1.0
NE2 C:HIS270 2.3 25.9 1.0
OAD C:GZ31351 2.4 23.8 1.0
SG C:CYS63 2.5 28.2 1.0
CD C:GLU304 2.9 26.8 1.0
CAI C:GZ31351 2.9 22.6 1.0
CG C:ASP324 3.0 29.5 1.0
OE1 C:GLU304 3.1 27.5 1.0
CD2 C:HIS270 3.2 26.6 1.0
OAB C:GZ31351 3.2 25.2 1.0
CE1 C:HIS270 3.4 26.1 1.0
CB C:ASP324 3.4 29.4 1.0
CB C:CYS63 3.6 27.2 1.0
CAH C:GZ31351 3.9 26.4 1.0
O C:HOH2182 4.0 31.9 1.0
NH2 C:ARG94 4.1 23.7 1.0
OD1 C:ASP324 4.1 30.5 1.0
NZ C:LYS99 4.1 21.8 1.0
CA C:CYS63 4.2 26.7 1.0
O C:HOH2164 4.2 25.3 1.0
CG C:GLU304 4.3 26.0 1.0
CG C:HIS270 4.4 26.8 1.0
ND1 C:HIS270 4.4 25.5 1.0
CAA C:GZ31351 4.5 30.1 1.0
CA C:ASP324 4.7 30.4 1.0
CAG C:GZ31351 4.7 23.9 1.0
N C:ASP324 4.8 30.4 1.0
O C:CYS63 4.8 25.0 1.0
CZ C:ARG94 4.9 24.3 1.0
C C:CYS63 4.9 26.1 1.0
CE C:LYS99 4.9 22.5 1.0

Manganese binding site 4 out of 4 in 4uma

Go back to Manganese Binding Sites List in 4uma
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:28.4
occ:1.00
OE2 D:GLU304 2.0 29.2 1.0
OD2 D:ASP324 2.0 32.2 1.0
OAD D:GZ31351 2.3 25.2 1.0
NE2 D:HIS270 2.4 32.4 1.0
SG D:CYS63 2.6 29.5 1.0
CD D:GLU304 2.9 29.2 1.0
CAI D:GZ31351 2.9 24.6 1.0
CG D:ASP324 3.0 32.5 1.0
OE1 D:GLU304 3.1 29.0 1.0
CD2 D:HIS270 3.3 30.5 1.0
OAB D:GZ31351 3.3 25.6 1.0
CE1 D:HIS270 3.4 32.9 1.0
CB D:ASP324 3.4 31.4 1.0
CB D:CYS63 3.6 30.4 1.0
O D:HOH2142 3.9 36.8 1.0
CAH D:GZ31351 3.9 28.4 1.0
NH2 D:ARG94 4.1 32.0 1.0
OD1 D:ASP324 4.1 32.5 1.0
NZ D:LYS99 4.2 27.7 1.0
CA D:CYS63 4.2 30.2 1.0
CG D:GLU304 4.2 29.6 1.0
O D:HOH2126 4.3 29.4 1.0
CAA D:GZ31351 4.4 33.3 1.0
CG D:HIS270 4.5 31.1 1.0
ND1 D:HIS270 4.5 31.8 1.0
CA D:ASP324 4.7 32.3 1.0
CAG D:GZ31351 4.8 25.2 1.0
O D:CYS63 4.8 31.5 1.0
N D:ASP324 4.8 32.2 1.0
CZ D:ARG94 4.9 32.1 1.0
C D:CYS63 4.9 30.3 1.0
CE D:LYS99 4.9 27.7 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 21:20:49 2024

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