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Manganese in PDB 2jd1: X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with Manganese and Nadph

Enzymatic activity of X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with Manganese and Nadph

All present enzymatic activity of X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with Manganese and Nadph:
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 Manganese and Nadph, PDB code: 2jd1 was solved by L.M.Henriksson, T.Unge, T.A.Jones, S.L.Mowbray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 2.0
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.332, 64.888, 86.059, 90.00, 101.72, 90.00
R / Rfree (%) 17.4 / 22.1

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 Manganese and Nadph (pdb code 2jd1). 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 Manganese and Nadph, PDB code: 2jd1:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 2jd1

Go back to Manganese Binding Sites List in 2jd1
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 Manganese and Nadph


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 Manganese and Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1391

b:16.0
occ:1.00
 OD2 A:ASP151 2.2 15.8 1.0
OE2 A:GLU222 2.2 12.1 1.0
OE1 A:GLU153 2.2 10.8 1.0
O A:HOH2217 2.2 16.3 1.0
O A:HOH2216 2.2 15.5 1.0
O A:HOH2218 2.2 15.7 1.0
CD A:GLU153 3.1 7.9 1.0
CD A:GLU222 3.1 10.5 1.0
CG A:ASP151 3.2 15.0 1.0
OE2 A:GLU153 3.3 9.2 1.0
OE1 A:GLU222 3.6 8.1 1.0
OD1 A:ASP151 3.6 17.3 1.0
NZ A:LYS128 3.7 15.4 1.0
OG A:SER152 3.8 13.6 1.0
ND2 A:ASN218 3.9 10.8 1.0
N A:SER152 4.2 10.6 1.0
CG A:GLU222 4.3 8.8 1.0
C5N A:NDP1390 4.3 37.4 1.0
CG A:GLU153 4.4 9.6 1.0
CB A:ASP151 4.5 13.0 1.0
N A:GLU153 4.5 9.0 1.0
CA A:ASP151 4.8 12.3 1.0
CB A:GLU153 4.8 8.5 1.0
NZ A:LYS219 4.8 10.5 1.0
C A:ASP151 4.8 11.7 1.0
O4 A:SO41392 4.9 17.8 1.0
C4N A:NDP1390 4.9 37.4 1.0
CG A:ASN218 4.9 10.3 1.0
CB A:SER152 4.9 9.9 1.0
OD1 A:ASN218 5.0 11.3 1.0

Manganese binding site 2 out of 2 in 2jd1

Go back to Manganese Binding Sites List in 2jd1
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 Manganese and Nadph


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 Manganese and Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1390

b:9.4
occ:1.00
 OE1 B:GLU222 2.2 5.5 1.0
OD2 B:ASP151 2.2 8.9 1.0
O B:HOH2283 2.2 10.3 1.0
O B:HOH2281 2.2 8.6 1.0
OE2 B:GLU153 2.2 6.9 1.0
O B:HOH2282 2.2 10.8 1.0
CG B:ASP151 3.1 9.1 1.0
CD B:GLU153 3.2 5.2 1.0
CD B:GLU222 3.2 5.4 1.0
OD1 B:ASP151 3.4 10.7 1.0
OE1 B:GLU153 3.5 6.5 1.0
OE2 B:GLU222 3.6 4.0 1.0
O B:HOH2170 3.6 15.4 1.0
O B:HOH2124 4.0 19.6 1.0
OG B:SER152 4.0 8.2 1.0
ND2 B:ASN218 4.1 7.6 1.0
CG B:GLU222 4.4 4.0 1.0
CB B:ASP151 4.5 7.6 1.0
CG B:GLU153 4.5 3.8 1.0
O B:HOH2285 4.6 20.0 1.0
O B:HOH2122 4.6 29.7 1.0
N B:GLU153 4.6 4.3 1.0
NZ B:LYS219 4.7 6.2 1.0
N B:SER152 4.7 6.4 1.0
O4 B:SO41391 4.8 10.5 1.0
CB B:GLU153 4.8 3.6 1.0

Reference:

L.M.Henriksson, T.Unge, J.Carlsson, J.Aqvist, S.L.Mowbray, T.A.Jones. Structures of Mycobacterium Tuberculosis 1-Deoxy-D- Xylulose-5-Phosphate Reductoisomerase Provide New Insights Into Catalysis. J.Biol.Chem. V. 282 19905 2007.
ISSN: ISSN 0021-9258
PubMed: 17491006
DOI: 10.1074/JBC.M701935200
Page generated: Sat Oct 5 14:33:52 2024

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