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
|