Atomistry » Magnesium » PDB 3g8d-3gn6 » 3g9d
Atomistry »
  Magnesium »
    PDB 3g8d-3gn6 »
      3g9d »

Magnesium in PDB 3g9d: Crystal Structure Glycohydrolase

Enzymatic activity of Crystal Structure Glycohydrolase

All present enzymatic activity of Crystal Structure Glycohydrolase:
3.2.2.24;

Protein crystallography data

The structure of Crystal Structure Glycohydrolase, PDB code: 3g9d was solved by X.-D.Li, F.K.Winkler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.50
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 163.866, 163.866, 46.274, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 26.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure Glycohydrolase (pdb code 3g9d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure Glycohydrolase, PDB code: 3g9d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3g9d

Go back to Magnesium Binding Sites List in 3g9d
Magnesium binding site 1 out of 4 in the Crystal Structure Glycohydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure Glycohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg298

b:41.6
occ:1.00
OD2 A:ASP245 1.9 44.8 1.0
OD1 A:ASP60 1.9 49.3 1.0
O A:HOH335 2.0 39.9 1.0
O A:HOH333 2.0 19.3 1.0
OD1 A:ASP61 2.5 42.3 1.0
OG1 A:THR59 2.5 22.9 1.0
CG A:ASP245 2.9 36.3 1.0
CG A:ASP60 3.1 40.9 1.0
OD1 A:ASP245 3.3 27.4 1.0
CB A:THR59 3.3 31.2 1.0
MG A:MG299 3.5 26.5 1.0
OE2 A:GLU28 3.5 50.3 1.0
OD2 A:ASP60 3.6 48.3 1.0
CG A:ASP61 3.7 35.6 1.0
OD2 A:ASP97 3.7 44.1 1.0
N A:ASP60 3.9 34.3 1.0
O A:HOH336 4.0 35.1 1.0
CG2 A:THR59 4.1 25.8 1.0
OE1 A:GLU28 4.2 52.9 1.0
N A:ASP61 4.2 33.6 1.0
CD A:GLU28 4.2 41.8 1.0
CB A:ASP245 4.2 30.0 1.0
CB A:ASP60 4.3 34.4 1.0
OD2 A:ASP61 4.3 43.4 1.0
OD1 A:ASP21 4.3 36.1 1.0
OG1 A:THR246 4.4 29.4 1.0
CA A:ASP60 4.5 35.0 1.0
CA A:THR59 4.6 31.5 1.0
CG A:ASP97 4.6 42.8 1.0
C A:THR59 4.7 32.2 1.0
O A:HOH334 4.7 34.0 1.0
CB A:ASP97 4.7 37.2 1.0
CB A:ASP61 4.8 34.1 1.0
C A:ASP60 4.9 34.2 1.0

Magnesium binding site 2 out of 4 in 3g9d

Go back to Magnesium Binding Sites List in 3g9d
Magnesium binding site 2 out of 4 in the Crystal Structure Glycohydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure Glycohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg299

b:26.5
occ:1.00
O A:HOH333 2.0 19.3 1.0
OD1 A:ASP243 2.2 38.3 1.0
OD1 A:ASP245 2.2 27.4 1.0
O A:HOH334 2.3 34.0 1.0
O A:HOH338 2.4 49.9 1.0
OE2 A:GLU28 2.4 50.3 1.0
OG1 A:THR246 2.7 29.4 1.0
CG A:ASP245 3.2 36.3 1.0
CG A:ASP243 3.2 38.3 1.0
CD A:GLU28 3.5 41.8 1.0
OD2 A:ASP245 3.5 44.8 1.0
MG A:MG298 3.5 41.6 1.0
OD2 A:ASP243 3.7 39.4 1.0
O A:HOH336 3.7 35.1 1.0
CB A:THR246 3.9 29.1 1.0
O A:HOH335 4.1 39.9 1.0
CG A:GLU28 4.1 41.4 1.0
N A:THR246 4.2 28.0 1.0
OE1 A:GLU28 4.4 52.9 1.0
CB A:ASP243 4.4 34.3 1.0
CA A:ASP243 4.5 34.8 1.0
OD1 A:ASP61 4.6 42.3 1.0
CB A:ASP245 4.6 30.0 1.0
O A:ASP243 4.6 37.7 1.0
CA A:THR246 4.6 27.8 1.0
C A:ASP243 4.7 35.8 1.0
OD1 A:ASP60 4.9 49.3 1.0
C A:ASP245 4.9 30.8 1.0
OD2 A:ASP97 4.9 44.1 1.0
OD2 A:ASP61 4.9 43.4 1.0
N A:ASP245 4.9 31.2 1.0

Magnesium binding site 3 out of 4 in 3g9d

Go back to Magnesium Binding Sites List in 3g9d
Magnesium binding site 3 out of 4 in the Crystal Structure Glycohydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure Glycohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg298

b:37.0
occ:1.00
OD1 B:ASP243 2.2 43.3 1.0
O B:HOH327 2.2 21.2 1.0
O B:HOH330 2.4 46.8 1.0
OD1 B:ASP245 2.6 29.7 1.0
OE2 B:GLU28 2.6 41.0 1.0
OG1 B:THR246 2.7 31.0 1.0
OD2 B:ASP245 3.0 50.8 1.0
CG B:ASP243 3.1 38.1 1.0
CG B:ASP245 3.2 36.9 1.0
O B:HOH329 3.4 53.2 1.0
OD2 B:ASP243 3.4 46.7 1.0
MG B:MG299 3.4 55.4 1.0
CD B:GLU28 3.6 36.4 1.0
CB B:THR246 4.0 29.0 1.0
OE1 B:GLU28 4.1 41.4 1.0
OD1 B:ASP61 4.2 40.1 1.0
OD2 B:ASP61 4.4 42.6 1.0
N B:THR246 4.4 30.6 1.0
CB B:ASP243 4.5 33.4 1.0
CG B:GLU28 4.5 35.0 1.0
CB B:ASP245 4.7 34.5 1.0
CG B:ASP61 4.8 42.2 1.0
CA B:THR246 4.8 29.0 1.0
CA B:ASP243 4.9 33.6 1.0
CG2 B:THR246 5.0 23.8 1.0

Magnesium binding site 4 out of 4 in 3g9d

Go back to Magnesium Binding Sites List in 3g9d
Magnesium binding site 4 out of 4 in the Crystal Structure Glycohydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure Glycohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg299

b:55.4
occ:1.00
OD2 B:ASP245 2.1 50.8 1.0
OD1 B:ASP60 2.1 41.2 1.0
OD1 B:ASP61 2.3 40.1 1.0
OG1 B:THR59 2.6 37.3 1.0
O B:HOH330 3.0 46.8 1.0
CG B:ASP60 3.2 37.2 1.0
CG B:ASP245 3.3 36.9 1.0
MG B:MG298 3.4 37.0 1.0
CB B:THR59 3.5 40.4 1.0
CG B:ASP61 3.5 42.2 1.0
OD2 B:ASP60 3.5 48.2 1.0
OD1 B:ASP97 3.6 59.3 1.0
OD1 B:ASP245 4.0 29.7 1.0
N B:ASP60 4.1 38.4 1.0
OD2 B:ASP61 4.1 42.6 1.0
OD2 B:ASP97 4.2 50.4 1.0
OE1 B:GLU28 4.3 41.4 1.0
N B:ASP61 4.3 34.6 1.0
CG2 B:THR59 4.3 40.4 1.0
CG B:ASP97 4.3 52.5 1.0
CB B:ASP245 4.4 34.5 1.0
OE2 B:GLU28 4.4 41.0 1.0
OD1 B:ASP21 4.4 49.6 1.0
CB B:ASP60 4.5 38.3 1.0
OG1 B:THR246 4.6 31.0 1.0
CB B:ASP61 4.7 35.5 1.0
CD B:GLU28 4.7 36.4 1.0
CA B:ASP60 4.7 37.6 1.0
CA B:THR59 4.8 40.5 1.0
C B:THR59 4.8 39.9 1.0
O B:HOH329 4.8 53.2 1.0

Reference:

X.-D.Li, L.F.Huergo, A.Gasperina, F.O.Pedrosa, M.Merrick, F.K.Winkler. Crystal Structure of Dinitrogenase Reductase-Activating Glycohydrolase (Drag) Reveals Conservation in the Adp-Ribosylhydrolase Fold and Specific Features in the Adp-Ribose-Binding Pocket J.Mol.Biol. V. 390 737 2009.
ISSN: ISSN 0022-2836
PubMed: 19477184
DOI: 10.1016/J.JMB.2009.05.031
Page generated: Mon Dec 14 08:11:09 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy