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Manganese in PDB 2woc: Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum

Enzymatic activity of Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum

All present enzymatic activity of Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum:
3.2.2.24;

Protein crystallography data

The structure of Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum, PDB code: 2woc 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) 40.00 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.771, 47.537, 95.212, 80.84, 86.56, 85.83
R / Rfree (%) 17.425 / 24.016

Other elements in 2woc:

The structure of Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum (pdb code 2woc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum, PDB code: 2woc:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 2woc

Go back to Manganese Binding Sites List in 2woc
Manganese binding site 1 out of 6 in the Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum


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 Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn400

b:31.4
occ:1.00
 OG1 A:THR246 2.4 24.6 1.0
OD1 A:ASP245 2.5 28.2 1.0
OD1 A:ASP243 2.5 25.6 1.0
O A:HOH2012 2.6 15.2 1.0
OD2 A:ASP245 2.6 29.0 1.0
OD2 A:ASP243 2.6 27.9 1.0
O1 A:FMT402 2.7 27.0 1.0
O2 A:FMT402 2.8 28.3 1.0
CG A:ASP243 2.9 25.7 1.0
CG A:ASP245 2.9 26.9 1.0
C A:FMT402 3.1 29.2 1.0
CB A:THR246 3.6 24.4 1.0
N A:THR246 4.1 24.8 1.0
OD1 A:ASN126 4.2 24.0 1.0
CB A:ASP243 4.4 24.8 1.0
CB A:ASP245 4.4 25.4 1.0
CA A:THR246 4.4 24.5 1.0
OD2 A:ASP61 4.4 27.6 1.0
MN A:MN401 4.4 32.5 0.5
OE2 A:GLU28 4.5 29.4 1.0
OD1 A:ASP61 4.5 26.8 1.0
O A:ASP243 4.6 25.0 1.0
ND2 A:ASN126 4.6 20.3 1.0
CG2 A:THR246 4.6 23.8 1.0
CD A:GLU28 4.7 28.0 1.0
CG A:ASN126 4.8 22.8 1.0
OD1 A:ASP60 4.9 24.6 1.0
C A:ASP245 4.9 24.9 1.0
CG A:ASP61 4.9 26.0 1.0
C A:ASP243 4.9 25.0 1.0
CA A:ASP243 4.9 24.9 1.0

Manganese binding site 2 out of 6 in 2woc

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Manganese binding site 2 out of 6 in the Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum


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 Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:32.5
occ:0.50
 OD2 A:ASP97 2.6 25.9 1.0
OD2 A:ASP245 2.9 29.0 1.0
OG1 A:THR59 3.0 25.4 1.0
OD1 A:ASP60 3.0 24.6 1.0
OE1 A:GLU28 3.0 30.4 1.0
O A:HOH2012 3.2 15.2 1.0
CB A:THR59 3.4 25.4 1.0
CG A:ASP245 3.5 26.9 1.0
OE2 A:GLU28 3.6 29.4 1.0
CD A:GLU28 3.7 28.0 1.0
CG A:ASP97 3.7 25.9 1.0
CG2 A:THR59 3.9 25.1 1.0
CB A:ASP97 4.0 26.0 1.0
CB A:ASP245 4.1 25.4 1.0
CG A:ASP60 4.1 24.9 1.0
OD2 A:ASP61 4.1 27.6 1.0
OD1 A:ASP245 4.2 28.2 1.0
CD1 A:LEU51 4.2 25.9 1.0
O1 A:FMT402 4.3 27.0 1.0
N A:ASP60 4.3 24.9 1.0
MN A:MN400 4.4 31.4 1.0
OD2 A:ASP60 4.7 25.6 1.0
OD1 A:ASP97 4.8 26.8 1.0
CA A:THR59 4.8 25.0 1.0

Manganese binding site 3 out of 6 in 2woc

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Manganese binding site 3 out of 6 in the Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum


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 Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn400

b:30.6
occ:1.00
 OD1 B:ASP243 2.5 23.3 1.0
OG1 B:THR246 2.5 23.1 1.0
OD1 B:ASP245 2.5 26.9 1.0
OD2 B:ASP243 2.6 26.6 1.0
O1 B:FMT402 2.7 20.4 1.0
OD2 B:ASP245 2.7 30.5 1.0
O2 B:FMT402 2.7 19.6 1.0
O B:HOH2013 2.7 18.9 1.0
CG B:ASP243 2.9 25.2 1.0
CG B:ASP245 3.0 26.8 1.0
C B:FMT402 3.0 22.9 1.0
CB B:THR246 3.7 24.4 1.0
N B:THR246 4.2 24.6 1.0
OD1 B:ASN126 4.4 23.3 1.0
CB B:ASP243 4.4 25.0 1.0
MN B:MN401 4.4 43.8 0.5
CB B:ASP245 4.5 25.0 1.0
O B:HOH2014 4.5 39.6 1.0
OD2 B:ASP61 4.5 27.0 1.0
CA B:THR246 4.5 24.4 1.0
OD1 B:ASP61 4.6 25.8 1.0
O B:HOH2125 4.6 20.4 1.0
O B:HOH2052 4.6 29.0 1.0
OE2 B:GLU28 4.7 31.1 1.0
CD B:GLU28 4.7 27.9 1.0
O B:ASP243 4.7 25.1 1.0
CG2 B:THR246 4.8 24.2 1.0
ND2 B:ASN126 4.8 22.2 1.0
OE1 B:GLU28 4.8 28.6 1.0
OD1 B:ASP60 4.8 29.2 1.0
C B:ASP245 4.9 24.8 1.0
CA B:ASP243 5.0 24.9 1.0
CG B:ASN126 5.0 23.6 1.0
CG B:ASP61 5.0 26.2 1.0

Manganese binding site 4 out of 6 in 2woc

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Manganese binding site 4 out of 6 in the Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:43.8
occ:0.50
 OD2 B:ASP97 2.7 29.6 1.0
OG1 B:THR59 2.8 24.8 1.0
OD1 B:ASP60 2.8 29.2 1.0
OD2 B:ASP245 2.8 30.5 1.0
OE1 B:GLU28 3.0 28.6 1.0
CG B:ASP245 3.4 26.8 1.0
O B:HOH2013 3.4 18.9 1.0
CB B:THR59 3.4 24.9 1.0
O B:HOH2052 3.8 29.0 1.0
CG B:ASP97 3.8 26.9 1.0
CD B:GLU28 3.8 27.9 1.0
OE2 B:GLU28 3.8 31.1 1.0
CG B:ASP60 3.9 26.2 1.0
OD2 B:ASP61 3.9 27.0 1.0
CB B:ASP245 4.0 25.0 1.0
CG2 B:THR59 4.0 24.9 1.0
OD1 B:ASP245 4.0 26.9 1.0
CB B:ASP97 4.2 26.3 1.0
N B:ASP60 4.3 24.9 1.0
CD1 B:LEU51 4.3 27.2 1.0
MN B:MN400 4.4 30.6 1.0
OD2 B:ASP60 4.5 27.7 1.0
O1 B:FMT402 4.7 20.4 1.0
CA B:THR59 4.8 24.9 1.0
OD1 B:ASP21 4.8 28.4 1.0
OD1 B:ASP97 4.9 25.8 1.0
CB B:ASP60 5.0 25.5 1.0
CB B:ALA25 5.0 24.5 1.0

Manganese binding site 5 out of 6 in 2woc

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Manganese binding site 5 out of 6 in the Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn400

b:28.1
occ:1.00
 OG1 C:THR246 2.5 22.3 1.0
OD2 C:ASP245 2.5 26.6 1.0
OD1 C:ASP245 2.5 26.3 1.0
OD2 C:ASP243 2.5 25.8 1.0
OD1 C:ASP243 2.5 26.1 1.0
O C:HOH2101 2.6 22.0 1.0
O1 C:FMT402 2.7 24.8 1.0
CG C:ASP245 2.8 25.9 1.0
CG C:ASP243 2.8 25.4 1.0
O2 C:FMT402 2.9 26.0 1.0
C C:FMT402 3.1 26.9 1.0
CB C:THR246 3.7 24.1 1.0
N C:THR246 4.1 24.6 1.0
CB C:ASP243 4.3 25.0 1.0
OD1 C:ASN126 4.3 21.3 1.0
CB C:ASP245 4.3 25.1 1.0
OE2 C:GLU28 4.4 29.7 1.0
CA C:THR246 4.4 24.4 1.0
MN C:MN401 4.4 36.5 0.5
OD2 C:ASP61 4.5 25.5 1.0
CD C:GLU28 4.5 27.3 1.0
O C:ASP243 4.6 25.0 1.0
OD1 C:ASP61 4.6 24.4 1.0
OE1 C:GLU28 4.6 28.4 1.0
ND2 C:ASN126 4.7 22.9 1.0
CG2 C:THR246 4.7 23.3 1.0
CA C:ASP243 4.9 25.0 1.0
C C:ASP245 4.9 24.9 1.0
C C:ASP243 4.9 24.9 1.0
OD1 C:ASP60 4.9 25.9 1.0
CG C:ASN126 4.9 23.2 1.0
CG C:ASP61 5.0 25.1 1.0

Manganese binding site 6 out of 6 in 2woc

Go back to Manganese Binding Sites List in 2woc
Manganese binding site 6 out of 6 in the Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:36.5
occ:0.50
 OG1 C:THR59 2.7 24.0 1.0
OD2 C:ASP97 2.8 26.7 1.0
OD1 C:ASP60 2.9 25.9 1.0
OD2 C:ASP245 2.9 26.6 1.0
OE1 C:GLU28 3.0 28.4 1.0
O C:HOH2101 3.2 22.0 1.0
CB C:THR59 3.4 24.6 1.0
CG C:ASP245 3.4 25.9 1.0
CD C:GLU28 3.8 27.3 1.0
CG C:ASP97 3.8 26.1 1.0
CG C:ASP60 3.8 25.8 1.0
CG2 C:THR59 3.9 23.9 1.0
OD2 C:ASP61 3.9 25.5 1.0
OE2 C:GLU28 3.9 29.7 1.0
CB C:ASP245 3.9 25.1 1.0
CB C:ASP97 4.1 25.7 1.0
OD1 C:ASP245 4.1 26.3 1.0
OD2 C:ASP60 4.3 25.5 1.0
CD1 C:LEU51 4.3 27.3 1.0
N C:ASP60 4.3 24.9 1.0
MN C:MN400 4.4 28.1 1.0
O2 C:FMT402 4.6 26.0 1.0
OD1 C:ASP21 4.8 28.2 1.0
CA C:THR59 4.8 24.8 1.0
OD1 C:ASP97 5.0 26.0 1.0
CB C:ASP60 5.0 25.1 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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