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Magnesium in PDB 3k8k: Crystal Structure of Susg

Protein crystallography data

The structure of Crystal Structure of Susg, PDB code: 3k8k was solved by N.M.Koropatkin, T.J.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 128.038, 128.038, 129.774, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 23

Other elements in 3k8k:

The structure of Crystal Structure of Susg also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Susg (pdb code 3k8k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Susg, PDB code: 3k8k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3k8k

Go back to Magnesium Binding Sites List in 3k8k
Magnesium binding site 1 out of 2 in the Crystal Structure of Susg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Susg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg700

b:36.1
occ:1.00
O A:HOH1013 2.0 44.7 1.0
OD1 A:ASP75 2.0 44.5 1.0
OD1 A:ASP73 2.1 38.0 1.0
OD1 A:ASP77 2.2 44.0 1.0
OD1 A:ASP81 2.2 35.7 1.0
O A:TYR79 2.2 37.0 1.0
CG A:ASP77 3.0 43.8 1.0
CG A:ASP75 3.1 43.5 1.0
OD2 A:ASP77 3.2 44.2 1.0
CG A:ASP73 3.2 37.4 1.0
C A:TYR79 3.4 35.3 1.0
CG A:ASP81 3.4 33.0 1.0
OD2 A:ASP75 3.4 45.9 1.0
N A:TYR79 3.9 38.9 1.0
N A:ASP77 4.0 43.0 1.0
OD2 A:ASP73 4.1 33.1 1.0
CB A:ASP73 4.1 34.8 1.0
CB A:ASP81 4.1 31.6 1.0
CA A:TYR79 4.1 36.7 1.0
N A:ASP75 4.1 42.3 1.0
CA A:ASP73 4.2 34.7 1.0
CB A:TYR79 4.2 37.3 1.0
CB A:ASP77 4.3 42.2 1.0
N A:SER74 4.3 36.2 1.0
CB A:ASP75 4.4 43.7 1.0
C A:GLY80 4.4 33.3 1.0
OD2 A:ASP81 4.4 37.3 1.0
N A:GLY80 4.4 34.5 1.0
N A:GLY76 4.5 44.4 1.0
N A:ASP81 4.5 32.9 1.0
O A:GLY80 4.6 34.6 1.0
CA A:ASP75 4.6 43.4 1.0
CA A:ASP77 4.6 42.2 1.0
C A:ASP73 4.6 36.1 1.0
CA A:GLY80 4.6 32.9 1.0
C A:ASP75 4.6 44.3 1.0
N A:GLY78 4.6 41.2 1.0
C A:ASP77 4.8 41.8 1.0
CA A:ASP81 5.0 33.4 1.0

Magnesium binding site 2 out of 2 in 3k8k

Go back to Magnesium Binding Sites List in 3k8k
Magnesium binding site 2 out of 2 in the Crystal Structure of Susg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Susg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg800

b:53.6
occ:1.00
O B:HOH805 2.0 49.7 1.0
OD1 B:ASP73 2.0 55.3 1.0
OD1 B:ASP77 2.1 55.8 1.0
OD1 B:ASP81 2.2 52.9 1.0
OD1 B:ASP75 2.2 60.3 1.0
O B:TYR79 2.3 52.2 1.0
CG B:ASP75 2.9 57.4 1.0
OD2 B:ASP75 3.0 57.9 1.0
CG B:ASP77 3.1 54.1 1.0
CG B:ASP73 3.2 56.1 1.0
CG B:ASP81 3.3 53.0 1.0
C B:TYR79 3.5 50.2 1.0
OD2 B:ASP77 3.7 54.3 1.0
N B:ASP75 3.8 54.5 1.0
CB B:ASP81 4.0 51.0 1.0
N B:SER74 4.0 53.0 1.0
N B:TYR79 4.0 48.4 1.0
N B:ASP77 4.0 51.6 1.0
CB B:ASP73 4.0 54.3 1.0
CA B:ASP73 4.0 54.4 1.0
CB B:ASP75 4.1 55.1 1.0
CA B:TYR79 4.2 47.9 1.0
OD2 B:ASP73 4.2 54.6 1.0
OD2 B:ASP81 4.2 52.1 1.0
CB B:ASP77 4.2 52.2 1.0
CA B:ASP75 4.3 55.0 1.0
N B:GLY76 4.3 54.1 1.0
C B:ASP73 4.4 53.9 1.0
C B:GLY80 4.4 48.7 1.0
CB B:TYR79 4.4 46.2 1.0
C B:ASP75 4.5 54.5 1.0
N B:GLY80 4.5 49.3 1.0
N B:ASP81 4.5 49.1 1.0
CA B:ASP77 4.6 51.2 1.0
O B:GLY80 4.6 49.2 1.0
CA B:GLY80 4.7 48.3 1.0
N B:GLY78 4.7 51.8 1.0
C B:ASP77 4.7 52.0 1.0
C B:SER74 4.8 53.6 1.0
CA B:ASP81 4.9 49.5 1.0
CA B:SER74 4.9 52.6 1.0

Reference:

N.M.Koropatkin, T.J.Smith. Susg: A Unique Cell-Membrane-Associated Alpha-Amylase From A Prominent Human Gut Symbiont Targets Complex Starch Molecules. Structure V. 18 200 2010.
ISSN: ISSN 0969-2126
PubMed: 20159465
DOI: 10.1016/J.STR.2009.12.010
Page generated: Mon Dec 14 08:21:40 2020

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