Atomistry » Manganese » PDB 2jck-2nym » 2jd1
Atomistry »
  Manganese »
    PDB 2jck-2nym »
      2jd1 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy