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Calcium 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:

Magnesium (Mg) 2 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 3k8k

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Susg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca710

b:31.0
occ:1.00
OD1 A:ASN153 2.2 29.8 1.0
O A:ILE393 2.3 29.4 1.0
O A:HIS392 2.4 30.6 1.0
O A:HOH838 2.5 30.3 1.0
OD2 A:ASP352 2.5 32.6 1.0
O A:HOH709 2.5 25.2 1.0
O A:HOH837 2.6 23.6 1.0
C A:ILE393 3.2 30.9 1.0
CG A:ASN153 3.4 28.1 1.0
CA A:ILE393 3.5 30.6 1.0
C A:HIS392 3.5 30.5 1.0
CG A:ASP352 3.5 29.2 1.0
N A:ILE393 4.0 29.4 1.0
CB A:ASP352 4.0 25.9 1.0
ND2 A:ASN153 4.0 24.6 1.0
O A:ASN153 4.2 28.6 1.0
N A:TYR394 4.4 29.7 1.0
ND1 A:HIS344 4.5 34.6 1.0
CB A:ASN153 4.6 28.1 1.0
OD1 A:ASP352 4.6 29.2 1.0
CB A:HIS344 4.7 32.9 1.0
O A:HOH740 4.8 27.7 1.0
CA A:HIS392 4.8 28.4 1.0
C A:TYR394 4.9 30.1 1.0
CB A:ILE393 4.9 30.7 1.0
N A:HIS395 4.9 30.6 1.0
CB A:HIS392 4.9 30.1 1.0
CA A:TYR394 4.9 30.0 1.0
CD2 A:HIS342 4.9 28.1 1.0
NE2 A:HIS342 4.9 28.9 1.0
CA A:ASN153 4.9 27.6 1.0
C A:ASN153 5.0 26.9 1.0

Calcium binding site 2 out of 2 in 3k8k

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Susg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca810

b:39.0
occ:1.00
O B:ILE393 2.3 40.0 1.0
OD1 B:ASN153 2.4 33.5 1.0
O B:HOH749 2.4 48.3 1.0
O B:HIS392 2.4 41.0 1.0
OD2 B:ASP352 2.4 46.1 1.0
O B:HOH746 2.5 36.2 1.0
O B:HOH748 2.5 41.1 1.0
C B:ILE393 3.2 38.5 1.0
CA B:ILE393 3.5 38.3 1.0
C B:HIS392 3.5 40.2 1.0
CG B:ASN153 3.5 34.9 1.0
CG B:ASP352 3.5 40.9 1.0
N B:ILE393 4.0 39.4 1.0
CB B:ASP352 4.1 40.6 1.0
ND2 B:ASN153 4.1 33.8 1.0
O B:ASN153 4.3 36.2 1.0
N B:TYR394 4.4 38.7 1.0
OD1 B:ASP352 4.6 41.7 1.0
ND1 B:HIS344 4.6 45.4 1.0
NE2 B:HIS342 4.7 45.0 1.0
CB B:ASN153 4.7 36.1 1.0
CB B:HIS344 4.7 43.0 1.0
CD2 B:HIS342 4.7 44.5 1.0
CA B:HIS392 4.8 40.1 1.0
C B:TYR394 4.8 37.8 1.0
CB B:ILE393 4.9 37.9 1.0
CA B:TYR394 4.9 38.7 1.0
N B:HIS395 4.9 40.6 1.0
CB B:HIS392 4.9 38.0 1.0
O B:LEU353 5.0 42.1 1.0
O B:HOH772 5.0 36.7 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: Sat Dec 12 04:17:19 2020

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