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Manganese in PDB 4umb: 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: 4umb 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) 98.99 / 2.17
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.439, 133.733, 147.237, 90.00, 90.00, 90.00
R / Rfree (%) 20.075 / 22.673

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

Manganese binding site 1 out of 4 in 4umb

Go back to Manganese Binding Sites List in 4umb
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:Mn1351

b:18.0
occ:1.00
 OD2 A:ASP324 1.8 16.3 1.0
OE2 A:GLU304 2.0 19.9 1.0
O1 A:0V51353 2.0 22.6 1.0
NE2 A:HIS270 2.3 19.1 1.0
SG A:CYS63 2.6 18.8 1.0
CG A:ASP324 2.9 17.1 1.0
CD A:GLU304 2.9 19.3 1.0
C1 A:0V51353 3.0 20.7 1.0
OE1 A:GLU304 3.1 19.3 1.0
CD2 A:HIS270 3.2 19.5 1.0
CE1 A:HIS270 3.4 19.1 1.0
CB A:ASP324 3.5 17.4 1.0
CB A:CYS63 3.6 18.8 1.0
O2' A:0V51353 3.7 21.6 1.0
C2 A:0V51353 3.8 20.7 1.0
OD1 A:ASP324 3.9 17.4 1.0
NH2 A:ARG94 4.1 17.1 1.0
NZ A:LYS99 4.1 17.8 1.0
CA A:CYS63 4.2 18.1 1.0
CG A:GLU304 4.3 19.3 1.0
O A:HOH2170 4.4 15.2 1.0
CG A:HIS270 4.4 19.4 1.0
ND1 A:HIS270 4.5 19.3 1.0
O A:HOH2186 4.7 25.2 1.0
C3 A:0V51353 4.7 20.8 1.0
CA A:ASP324 4.7 17.9 1.0
N A:ASP324 4.8 18.0 1.0
O A:CYS63 4.8 17.4 1.0
CZ A:ARG94 4.9 17.2 1.0
O2 A:0V51353 4.9 21.2 1.0
C A:CYS63 4.9 18.1 1.0
CE A:LYS99 4.9 18.1 1.0

Manganese binding site 2 out of 4 in 4umb

Go back to Manganese Binding Sites List in 4umb
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:20.0
occ:1.00
 OD2 B:ASP324 1.9 19.0 1.0
OE2 B:GLU304 2.0 19.6 1.0
O2' B:0V51351 2.1 21.1 1.0
NE2 B:HIS270 2.3 22.9 1.0
SG B:CYS63 2.6 19.6 1.0
O B:HOH2012 2.8 41.4 1.0
CD B:GLU304 2.9 19.4 1.0
CG B:ASP324 2.9 19.1 1.0
C1 B:0V51351 3.0 20.8 1.0
OE1 B:GLU304 3.1 19.5 1.0
CD2 B:HIS270 3.2 23.2 1.0
CE1 B:HIS270 3.3 23.4 1.0
CB B:ASP324 3.5 19.5 1.0
CB B:CYS63 3.6 19.4 1.0
O1 B:0V51351 3.7 21.0 1.0
C2 B:0V51351 3.8 21.0 1.0
OD1 B:ASP324 4.0 18.9 1.0
NH2 B:ARG94 4.1 18.2 1.0
NZ B:LYS99 4.1 19.4 1.0
CA B:CYS63 4.2 19.0 1.0
CG B:GLU304 4.3 19.7 1.0
CG B:HIS270 4.4 23.1 1.0
O B:HOH2113 4.4 17.2 1.0
ND1 B:HIS270 4.4 23.8 1.0
O B:HOH2132 4.4 31.8 1.0
CA B:ASP324 4.7 19.5 1.0
C3 B:0V51351 4.8 19.9 1.0
O B:CYS63 4.8 18.6 1.0
N B:ASP324 4.8 19.4 1.0
O2 B:0V51351 4.9 21.4 1.0
CZ B:ARG94 4.9 18.4 1.0
C B:CYS63 4.9 18.9 1.0
CE B:LYS99 4.9 19.3 1.0

Manganese binding site 3 out of 4 in 4umb

Go back to Manganese Binding Sites List in 4umb
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:21.3
occ:1.00
 OD2 C:ASP324 1.8 22.6 1.0
OE2 C:GLU304 2.1 19.7 1.0
O2' C:0V51351 2.1 27.3 1.0
NE2 C:HIS270 2.3 23.7 1.0
SG C:CYS63 2.6 21.0 1.0
CG C:ASP324 2.9 22.8 1.0
CD C:GLU304 3.0 19.4 1.0
C1 C:0V51351 3.0 25.5 1.0
OE1 C:GLU304 3.2 19.4 1.0
CD2 C:HIS270 3.2 24.2 1.0
CE1 C:HIS270 3.4 24.0 1.0
CB C:ASP324 3.4 23.0 1.0
CB C:CYS63 3.6 20.9 1.0
C2 C:0V51351 3.8 26.2 1.0
O1 C:0V51351 3.9 25.8 1.0
OD1 C:ASP324 3.9 22.6 1.0
NH2 C:ARG94 4.1 20.0 1.0
NZ C:LYS99 4.1 19.8 1.0
CA C:CYS63 4.2 20.3 1.0
O C:HOH2139 4.3 16.4 1.0
CG C:GLU304 4.3 19.7 1.0
CG C:HIS270 4.4 24.2 1.0
ND1 C:HIS270 4.5 23.8 1.0
CA C:ASP324 4.7 23.1 1.0
N C:ASP324 4.7 22.8 1.0
C3 C:0V51351 4.7 25.7 1.0
O2 C:0V51351 4.8 25.3 1.0
O C:CYS63 4.8 19.5 1.0
C C:CYS63 4.9 19.8 1.0
CZ C:ARG94 4.9 19.5 1.0
CE C:LYS99 4.9 20.0 1.0

Manganese binding site 4 out of 4 in 4umb

Go back to Manganese Binding Sites List in 4umb
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:20.2
occ:1.00
 OD2 D:ASP324 1.9 21.1 1.0
OE2 D:GLU304 2.0 23.7 1.0
O2' D:0V51351 2.3 22.9 1.0
NE2 D:HIS270 2.4 26.2 1.0
SG D:CYS63 2.6 19.8 1.0
CD D:GLU304 2.9 22.9 1.0
CG D:ASP324 2.9 21.8 1.0
C1 D:0V51351 3.0 24.0 1.0
OE1 D:GLU304 3.2 23.3 1.0
CD2 D:HIS270 3.3 26.7 1.0
CE1 D:HIS270 3.4 26.4 1.0
CB D:ASP324 3.5 22.2 1.0
CB D:CYS63 3.5 20.4 1.0
O1 D:0V51351 3.7 23.3 1.0
C2 D:0V51351 3.8 24.5 1.0
OD1 D:ASP324 4.0 21.9 1.0
NH2 D:ARG94 4.0 20.3 1.0
NZ D:LYS99 4.1 19.4 1.0
CA D:CYS63 4.2 19.9 1.0
CG D:GLU304 4.3 22.6 1.0
O D:HOH2116 4.4 18.2 1.0
CG D:HIS270 4.4 27.0 1.0
ND1 D:HIS270 4.5 26.5 1.0
CA D:ASP324 4.7 22.7 1.0
O D:CYS63 4.8 18.8 1.0
C3 D:0V51351 4.8 23.7 1.0
N D:ASP324 4.8 22.2 1.0
CZ D:ARG94 4.8 20.1 1.0
O2 D:0V51351 4.8 25.7 1.0
C D:CYS63 4.9 19.5 1.0
CE D:LYS99 4.9 19.8 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 21:20:53 2024

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