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Manganese in PDB 4ooe: M. Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase W203Y Mutant Bound to Fosmidomycin and Nadph

Enzymatic activity of M. Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase W203Y Mutant Bound to Fosmidomycin and Nadph

All present enzymatic activity of M. Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase W203Y Mutant Bound to Fosmidomycin and Nadph:
1.1.1.267;

Protein crystallography data

The structure of M. Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase W203Y Mutant Bound to Fosmidomycin and Nadph, PDB code: 4ooe was solved by C.L.Allen, S.A.Kholodar, A.S.Murkin, A.M.Gulick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.83 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 112.270, 114.240, 133.187, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21.1

Manganese Binding Sites:

The binding sites of Manganese atom in the M. Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase W203Y Mutant Bound to Fosmidomycin and Nadph (pdb code 4ooe). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the M. Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase W203Y Mutant Bound to Fosmidomycin and Nadph, PDB code: 4ooe:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4ooe

Go back to Manganese Binding Sites List in 4ooe
Manganese binding site 1 out of 4 in the M. Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase W203Y Mutant Bound to Fosmidomycin and Nadph


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of M. Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase W203Y Mutant Bound to Fosmidomycin and Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:13.3
occ:1.00
 O2 A:FOM500 1.9 14.0 1.0
OD1 A:ASP151 2.0 16.2 1.0
OE2 A:GLU222 2.1 11.9 1.0
OE1 A:GLU153 2.1 11.2 1.0
O1 A:FOM500 2.2 10.7 1.0
N1 A:FOM500 2.8 17.8 1.0
CD A:GLU153 2.9 11.0 1.0
C1 A:FOM500 2.9 14.4 1.0
OE2 A:GLU153 2.9 9.6 1.0
CD A:GLU222 3.0 10.1 1.0
CG A:ASP151 3.0 15.8 1.0
OD2 A:ASP151 3.5 15.5 1.0
OE1 A:GLU222 3.5 9.3 1.0
NZ A:LYS128 3.8 14.7 1.0
C5N A:NDP502 4.0 13.9 1.0
N A:SER152 4.0 9.0 1.0
CG A:GLU222 4.1 8.5 1.0
ND2 A:ASN218 4.2 10.3 1.0
C2 A:FOM500 4.2 10.7 1.0
OG A:SER152 4.2 18.0 1.0
CB A:ASP151 4.2 13.2 1.0
CG A:GLU153 4.3 8.7 1.0
N A:GLU153 4.4 7.7 1.0
C3 A:FOM500 4.5 16.0 1.0
CA A:ASP151 4.5 11.2 1.0
C A:ASP151 4.6 11.7 1.0
C6N A:NDP502 4.7 16.9 1.0
C4 A:FOM500 4.7 11.5 1.0
NZ A:LYS219 4.8 7.5 1.0
C4N A:NDP502 4.8 10.2 1.0
CB A:GLU153 4.8 10.6 1.0
CA A:SER152 4.9 9.6 1.0
CE A:LYS128 5.0 12.5 1.0

Manganese binding site 2 out of 4 in 4ooe

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Manganese binding site 2 out of 4 in the M. Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase W203Y Mutant Bound to Fosmidomycin and Nadph


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of M. Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase W203Y Mutant Bound to Fosmidomycin and Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:13.8
occ:1.00
 OD2 B:ASP151 2.1 14.6 1.0
O2 B:FOM500 2.1 17.0 1.0
OE1 B:GLU153 2.1 6.5 1.0
OE2 B:GLU222 2.1 9.9 1.0
O1 B:FOM500 2.2 11.3 1.0
N1 B:FOM500 2.8 17.3 1.0
C1 B:FOM500 2.9 15.2 1.0
CD B:GLU153 2.9 12.4 1.0
CG B:ASP151 3.0 16.9 1.0
CD B:GLU222 3.0 13.9 1.0
OE2 B:GLU153 3.0 11.0 1.0
OD1 B:ASP151 3.4 15.4 1.0
OE1 B:GLU222 3.5 12.3 1.0
NZ B:LYS128 3.7 11.5 1.0
C5N B:NDP502 4.0 14.1 1.0
N B:SER152 4.1 11.2 1.0
OG B:SER152 4.1 13.9 1.0
CG B:GLU222 4.2 10.7 1.0
ND2 B:ASN218 4.2 9.3 1.0
C2 B:FOM500 4.2 12.9 1.0
CB B:ASP151 4.2 12.2 1.0
CG B:GLU153 4.3 11.9 1.0
N B:GLU153 4.4 7.7 1.0
C3 B:FOM500 4.5 16.8 1.0
CA B:ASP151 4.5 10.3 1.0
C B:ASP151 4.6 10.3 1.0
CB B:GLU153 4.8 7.8 1.0
C4N B:NDP502 4.8 13.4 1.0
C6N B:NDP502 4.8 13.4 1.0
NZ B:LYS219 4.8 11.3 1.0
C4 B:FOM500 4.8 13.0 1.0
CA B:SER152 5.0 10.2 1.0

Manganese binding site 3 out of 4 in 4ooe

Go back to Manganese Binding Sites List in 4ooe
Manganese binding site 3 out of 4 in the M. Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase W203Y Mutant Bound to Fosmidomycin and Nadph


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of M. Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase W203Y Mutant Bound to Fosmidomycin and Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:13.2
occ:1.00
 OD1 C:ASP151 2.0 11.9 1.0
OE1 C:GLU153 2.1 10.0 1.0
C2 C:FOM500 2.2 7.3 1.0
OE2 C:GLU222 2.2 10.5 1.0
O2 C:FOM500 2.2 12.1 1.0
N1 C:FOM500 2.4 16.6 1.0
CD C:GLU153 2.9 9.1 1.0
OE2 C:GLU153 2.9 11.2 1.0
CG C:ASP151 3.0 14.1 1.0
CD C:GLU222 3.0 10.4 1.0
C3 C:FOM500 3.1 25.7 1.0
OD2 C:ASP151 3.4 16.8 1.0
OE1 C:GLU222 3.5 9.5 1.0
C1 C:FOM500 3.7 25.6 1.0
NZ C:LYS128 3.7 16.0 1.0
C5N C:NDP502 3.9 13.9 1.0
N C:SER152 4.0 10.8 1.0
CG C:GLU222 4.2 8.8 1.0
OG C:SER152 4.2 12.0 1.0
ND2 C:ASN218 4.2 6.3 1.0
CB C:ASP151 4.2 11.5 1.0
O1 C:FOM500 4.3 31.9 1.0
CG C:GLU153 4.3 7.7 1.0
N C:GLU153 4.4 6.9 1.0
CA C:ASP151 4.5 9.3 1.0
C4 C:FOM500 4.6 9.7 1.0
C C:ASP151 4.6 10.4 1.0
C6N C:NDP502 4.7 16.7 1.0
NZ C:LYS219 4.7 6.5 1.0
C4N C:NDP502 4.7 10.7 1.0
CB C:GLU153 4.8 7.8 1.0
CA C:SER152 4.9 9.9 1.0
CB C:SER152 5.0 7.3 1.0
CE C:LYS128 5.0 9.2 1.0

Manganese binding site 4 out of 4 in 4ooe

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Manganese binding site 4 out of 4 in the M. Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase W203Y Mutant Bound to Fosmidomycin and Nadph


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of M. Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase W203Y Mutant Bound to Fosmidomycin and Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:15.9
occ:1.00
 OD2 D:ASP151 1.9 18.0 1.0
O2 D:FOM500 2.0 13.9 1.0
OE2 D:GLU222 2.1 15.2 1.0
OE1 D:GLU153 2.1 13.4 1.0
O1 D:FOM500 2.2 12.7 1.0
N1 D:FOM500 2.7 14.0 1.0
C1 D:FOM500 2.8 15.5 1.0
CD D:GLU153 2.8 14.2 1.0
OE2 D:GLU153 2.9 15.1 1.0
CG D:ASP151 3.0 15.9 1.0
CD D:GLU222 3.0 14.6 1.0
OD1 D:ASP151 3.5 20.9 1.0
OE1 D:GLU222 3.5 11.6 1.0
NZ D:LYS128 3.7 13.6 1.0
N D:SER152 3.9 11.6 1.0
C5N D:NDP502 4.0 19.2 1.0
OG D:SER152 4.0 19.1 1.0
CB D:ASP151 4.1 15.6 1.0
C2 D:FOM500 4.1 16.3 1.0
ND2 D:ASN218 4.2 9.5 1.0
CG D:GLU222 4.2 11.3 1.0
CG D:GLU153 4.3 12.7 1.0
N D:GLU153 4.4 9.6 1.0
CA D:ASP151 4.4 14.9 1.0
C3 D:FOM500 4.5 16.4 1.0
C D:ASP151 4.5 15.7 1.0
C4N D:NDP502 4.8 10.8 1.0
C6N D:NDP502 4.8 21.6 1.0
CB D:GLU153 4.8 9.2 1.0
NZ D:LYS219 4.8 13.5 1.0
CA D:SER152 4.8 8.1 1.0
CB D:SER152 4.9 10.9 1.0
C4 D:FOM500 5.0 13.5 1.0

Reference:

S.A.Kholodar, G.Tombline, J.Liu, Z.Tan, C.L.Allen, A.M.Gulick, A.S.Murkin. Alteration of the Flexible Loop in 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase Boosts Enthalpy-Driven Inhibition By Fosmidomycin. Biochemistry V. 53 3423 2014.
ISSN: ISSN 0006-2960
PubMed: 24825256
DOI: 10.1021/BI5004074
Page generated: Sat Oct 5 20:42:51 2024

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