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Manganese in PDB 2y1d: X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue and Manganese.

Enzymatic activity of X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue and Manganese.

All present enzymatic activity of X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue and Manganese.:
1.1.1.267;

Protein crystallography data

The structure of X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue and Manganese., PDB code: 2y1d was solved by L.M.Henriksson, A.M.S.Larsson, T.Bergfors, C.Bjorkelid, T.Unge, S.L.Mowbray, T.A.Jones, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.622, 67.318, 84.301, 90.00, 107.38, 90.00
R / Rfree (%) 20.9 / 26.1

Other elements in 2y1d:

The structure of X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue and Manganese. also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue and Manganese. (pdb code 2y1d). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue and Manganese., PDB code: 2y1d:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 2y1d

Go back to Manganese Binding Sites List in 2y1d
Manganese binding site 1 out of 2 in the X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue and Manganese.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue and Manganese. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1391

b:30.9
occ:1.00
 OE2 A:GLU222 2.2 28.9 1.0
OE1 A:GLU153 2.2 28.1 1.0
OD1 A:ASP151 2.2 33.4 1.0
O2 A:34F1390 2.2 35.4 1.0
O1 A:34F1390 2.2 35.9 1.0
C1 A:34F1390 2.8 37.5 1.0
N1 A:34F1390 2.8 38.1 1.0
CG A:ASP151 2.9 33.3 1.0
CD A:GLU153 3.0 28.0 1.0
CD A:GLU222 3.0 28.2 1.0
OD2 A:ASP151 3.2 36.9 1.0
OE2 A:GLU153 3.2 26.2 1.0
OE1 A:GLU222 3.5 27.7 1.0
CG A:GLU222 4.1 26.5 1.0
ND2 A:ASN218 4.1 29.8 1.0
OG A:SER152 4.2 31.1 1.0
C2 A:34F1390 4.2 39.6 1.0
CB A:ASP151 4.2 31.7 1.0
N A:SER152 4.3 29.8 1.0
O A:HOH2033 4.3 47.0 1.0
CG A:GLU153 4.4 26.8 1.0
NZ A:LYS128 4.4 46.8 1.0
CE A:LYS128 4.5 46.0 1.0
N A:GLU153 4.5 27.5 1.0
C3 A:34F1390 4.5 41.8 1.0
C4 A:34F1390 4.6 44.1 1.0
CA A:ASP151 4.7 31.3 1.0
CB A:GLU153 4.8 27.0 1.0
C A:ASP151 4.8 30.9 1.0
NZ A:LYS219 4.9 23.5 1.0

Manganese binding site 2 out of 2 in 2y1d

Go back to Manganese Binding Sites List in 2y1d
Manganese binding site 2 out of 2 in the X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue and Manganese.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue and Manganese. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1390

b:30.9
occ:1.00
 OE2 B:GLU222 2.2 24.5 1.0
OD2 B:ASP151 2.2 32.3 1.0
OE1 B:GLU153 2.2 28.3 1.0
O B:HOH2228 2.2 31.3 1.0
O B:HOH2229 2.2 32.4 1.0
O B:HOH2227 2.2 31.2 1.0
OD1 B:ASP151 2.7 31.8 1.0
CG B:ASP151 2.8 27.3 1.0
CD B:GLU153 3.1 26.9 1.0
CD B:GLU222 3.1 20.2 1.0
OE2 B:GLU153 3.4 31.1 1.0
OE1 B:GLU222 3.6 19.5 1.0
CG B:GLU222 4.2 18.8 1.0
CB B:ASP151 4.3 25.1 1.0
ND2 B:ASN218 4.3 28.7 1.0
CG B:GLU153 4.4 24.4 1.0
N B:GLU153 4.7 22.1 1.0
N B:SER152 4.7 23.6 1.0
CB B:GLU153 4.8 22.4 1.0
NZ B:LYS128 4.8 32.8 1.0
NZ B:LYS219 4.8 21.6 1.0
CE B:LYS128 4.9 30.9 1.0

Reference:

M.Andaloussi, L.M.Henriksson, A.Wieckowska, M.Lindh, C.Bjorkelid, A.M.S.Larsson, H.Iyer, B.R.Srinivasa, T.Bergfors, T.Unge, S.L.Mowbray, M.Larhed, T.A.Jones, A.Karlen. Design, Synthesis and X-Ray Crystallographic Studies of Alpha-Aryl Substituted Fosmidomycin Analogues As Inhibitors of Mycobacterium Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase J.Med.Chem V. 54 4964 2011.
ISSN: ISSN 0022-2623
PubMed: 21678907
DOI: 10.1021/JM2000085
Page generated: Sat Aug 16 11:10:33 2025

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