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Manganese in PDB 2woe: Crystal Structure of the D97N Variant of Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum in Complex with Adp-Ribose

Enzymatic activity of Crystal Structure of the D97N Variant of Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum in Complex with Adp-Ribose

All present enzymatic activity of Crystal Structure of the D97N Variant of Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum in Complex with Adp-Ribose:
3.2.2.24;

Protein crystallography data

The structure of Crystal Structure of the D97N Variant of Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum in Complex with Adp-Ribose, PDB code: 2woe was solved by C.L.Berthold, H.Wang, S.Nordlund, M.Hogbom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.110, 84.360, 146.100, 90.00, 90.00, 90.00
R / Rfree (%) 16.71 / 20.731

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the D97N Variant of Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum in Complex with Adp-Ribose (pdb code 2woe). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of the D97N Variant of Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum in Complex with Adp-Ribose, PDB code: 2woe:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 2woe

Go back to Manganese Binding Sites List in 2woe
Manganese binding site 1 out of 3 in the Crystal Structure of the D97N Variant of Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the D97N Variant of Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum in Complex with Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn400

b:33.9
occ:1.00
 OD1 A:ASP243 2.3 30.1 1.0
O3D A:AR6401 2.3 26.6 1.0
OD1 A:ASP245 2.4 33.9 1.0
OE2 A:GLU28 2.4 31.7 1.0
O2D A:AR6401 2.4 25.1 1.0
OD2 A:ASP245 2.4 30.8 1.0
OG1 A:THR246 2.5 29.3 1.0
CG A:ASP245 2.7 30.7 1.0
C3D A:AR6401 3.2 27.5 1.0
CG A:ASP243 3.3 28.4 1.0
C2D A:AR6401 3.3 28.4 1.0
CD A:GLU28 3.4 29.6 1.0
O A:HOH2226 3.4 32.0 1.0
OD2 A:ASP243 3.6 30.1 1.0
CB A:THR246 3.7 29.1 1.0
OE1 A:GLU28 4.0 31.3 1.0
O A:HOH2225 4.0 33.4 1.0
N A:THR246 4.0 28.6 1.0
O A:HOH2114 4.2 29.8 1.0
CB A:ASP245 4.2 29.4 1.0
CG A:GLU28 4.3 28.5 1.0
C1D A:AR6401 4.4 29.7 1.0
CA A:THR246 4.5 28.7 1.0
OD2 A:ASP61 4.5 37.0 1.0
O1D A:AR6401 4.5 32.8 1.0
O A:HOH2269 4.5 34.2 1.0
C4D A:AR6401 4.5 28.1 1.0
CB A:ASP243 4.6 27.8 1.0
OD1 A:ASP61 4.7 32.8 1.0
O4D A:AR6401 4.7 29.1 1.0
C A:ASP245 4.7 28.7 1.0
OD1 A:ASP60 4.7 34.2 1.0
O A:ASP243 4.8 27.5 1.0
N A:ASP245 4.8 28.5 1.0
C A:ASP243 4.8 27.9 1.0
CA A:ASP243 4.8 27.9 1.0
CA A:ASP245 4.8 29.0 1.0
CG2 A:THR246 4.8 28.3 1.0

Manganese binding site 2 out of 3 in 2woe

Go back to Manganese Binding Sites List in 2woe
Manganese binding site 2 out of 3 in the Crystal Structure of the D97N Variant of Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the D97N Variant of Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum in Complex with Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn400

b:35.5
occ:1.00
 OD2 B:ASP245 2.4 30.9 1.0
OD1 B:ASP245 2.5 31.4 1.0
OD1 B:ASP243 2.5 31.1 1.0
O1D B:AR6401 2.5 36.0 1.0
OG1 B:THR246 2.6 28.3 1.0
O3D B:AR6401 2.6 31.4 1.0
OD2 B:ASP243 2.7 28.7 1.0
O2D B:AR6401 2.7 31.8 1.0
CG B:ASP245 2.8 28.7 1.0
CG B:ASP243 2.9 28.7 1.0
OE2 B:GLU28 3.0 35.7 1.0
C2D B:AR6401 3.3 33.1 1.0
C3D B:AR6401 3.4 32.8 1.0
C1D B:AR6401 3.5 33.5 1.0
C4D B:AR6401 3.8 32.7 1.0
CB B:THR246 3.8 28.4 1.0
CD B:GLU28 4.0 30.8 1.0
O4D B:AR6401 4.1 33.6 1.0
N B:THR246 4.2 28.2 1.0
CB B:ASP245 4.3 28.4 1.0
CB B:ASP243 4.4 27.6 1.0
O B:HOH2070 4.4 26.5 1.0
OD1 B:ASP61 4.6 31.3 1.0
OE1 B:GLU28 4.6 33.3 1.0
CA B:THR246 4.6 28.1 1.0
OD2 B:ASP61 4.6 33.1 1.0
O B:ASP243 4.7 26.6 1.0
OD1 B:ASN126 4.7 25.6 1.0
CG B:GLU28 4.8 29.8 1.0
CG2 B:THR246 4.9 27.8 1.0
CA B:ASP243 4.9 27.5 1.0
C B:ASP243 4.9 27.5 1.0
ND2 B:ASN97 4.9 34.9 1.0
ND2 B:ASN126 4.9 26.3 1.0
C B:ASP245 5.0 28.4 1.0

Manganese binding site 3 out of 3 in 2woe

Go back to Manganese Binding Sites List in 2woe
Manganese binding site 3 out of 3 in the Crystal Structure of the D97N Variant of Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the D97N Variant of Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum in Complex with Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn400

b:40.0
occ:1.00
 OD2 C:ASP245 2.2 31.7 1.0
O2D C:AR6401 2.3 30.4 1.0
O3D C:AR6401 2.4 34.2 1.0
OD1 C:ASP243 2.4 30.7 1.0
OD1 C:ASP245 2.4 35.2 1.0
OG1 C:THR246 2.6 30.2 1.0
CG C:ASP245 2.6 29.8 1.0
OE2 C:GLU28 2.7 34.7 1.0
C3D C:AR6401 3.2 31.7 1.0
CG C:ASP243 3.3 28.8 1.0
C2D C:AR6401 3.3 32.5 1.0
OD2 C:ASP243 3.4 32.5 1.0
CD C:GLU28 3.5 30.7 1.0
O1D C:AR6401 3.8 36.9 1.0
CB C:THR246 3.9 29.1 1.0
OE1 C:GLU28 4.0 31.6 1.0
N C:THR246 4.1 28.9 1.0
C1D C:AR6401 4.1 33.1 1.0
CB C:ASP245 4.1 29.0 1.0
CG C:GLU28 4.4 29.1 1.0
O C:HOH2167 4.5 42.0 1.0
C4D C:AR6401 4.5 32.5 1.0
OD1 C:ASP61 4.5 30.4 1.0
O C:HOH2205 4.6 35.1 1.0
CA C:THR246 4.6 29.1 1.0
OD2 C:ASP61 4.6 35.3 1.0
CB C:ASP243 4.6 27.7 1.0
O4D C:AR6401 4.7 33.3 1.0
OD1 C:ASP60 4.8 33.9 1.0
O C:ASP243 4.8 26.8 1.0
C C:ASP245 4.8 28.5 1.0
CA C:ASP245 4.8 28.3 1.0
N C:ASP245 4.9 28.2 1.0
ND2 C:ASN97 4.9 35.4 1.0
C C:ASP243 4.9 27.1 1.0
CG2 C:THR246 4.9 28.6 1.0
CA C:ASP243 5.0 27.7 1.0

Reference:

C.L.Berthold, H.Wang, S.Nordlund, M.Hogbom. Mechanism of Adp-Ribosylation Removal Revealed By the Structure and Ligand Complexes of the Dimanganese Mono-Adp-Ribosylhydrolase Drag. Proc.Natl.Acad.Sci.Usa V. 106 14247 2009.
ISSN: ISSN 0027-8424
PubMed: 19706507
DOI: 10.1073/PNAS.0905906106
Page generated: Sat Oct 5 15:23:53 2024

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