Calcium in PDB 6bs6: Susg with Mixed Linkage Amylosaccharide

Enzymatic activity of Susg with Mixed Linkage Amylosaccharide

All present enzymatic activity of Susg with Mixed Linkage Amylosaccharide:
3.2.1.1;

Protein crystallography data

The structure of Susg with Mixed Linkage Amylosaccharide, PDB code: 6bs6 was solved by N.M.Koropatkin, D.W.Cockburn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.40 / 2.17
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 127.439, 127.439, 129.410, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 23.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Susg with Mixed Linkage Amylosaccharide (pdb code 6bs6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Susg with Mixed Linkage Amylosaccharide, PDB code: 6bs6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6bs6

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Calcium binding site 1 out of 4 in the Susg with Mixed Linkage Amylosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Susg with Mixed Linkage Amylosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca719

b:24.1
occ:1.00
OD2 A:ASP352 2.4 21.8 1.0
O A:HOH974 2.4 21.8 1.0
O A:HIS392 2.4 22.2 1.0
OD1 A:ASN153 2.4 29.1 1.0
O A:HOH1165 2.5 25.1 1.0
O A:ILE393 2.5 29.4 1.0
C A:ILE393 3.3 30.9 1.0
CG A:ASP352 3.4 26.3 1.0
CG A:ASN153 3.5 22.1 1.0
C A:HIS392 3.5 24.1 1.0
CA A:ILE393 3.6 23.1 1.0
CB A:ASP352 3.9 22.5 1.0
ND2 A:ASN153 3.9 18.5 1.0
N A:ILE393 4.0 20.9 1.0
CD2 A:HIS344 4.2 26.1 1.0
O A:ASN153 4.2 24.1 1.0
O A:HOH1047 4.5 22.6 1.0
OD1 A:ASP352 4.5 28.2 1.0
N A:TYR394 4.5 23.4 1.0
CB A:HIS344 4.6 31.1 1.0
NE2 A:HIS342 4.6 21.5 1.0
CB A:ASN153 4.7 19.2 1.0
CD2 A:HIS342 4.7 21.6 1.0
CA A:HIS392 4.8 21.2 1.0
CG A:HIS344 4.8 38.8 1.0
C A:TYR394 4.8 26.1 1.0
O A:LEU353 4.9 20.7 1.0
N A:HIS395 4.9 24.4 1.0
CB A:HIS392 4.9 20.3 1.0
CB A:ILE393 4.9 22.5 1.0
CA A:TYR394 4.9 26.4 1.0
CA A:ASN153 5.0 26.9 1.0
CE A:MET194 5.0 25.0 1.0

Calcium binding site 2 out of 4 in 6bs6

Go back to Calcium Binding Sites List in 6bs6
Calcium binding site 2 out of 4 in the Susg with Mixed Linkage Amylosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Susg with Mixed Linkage Amylosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca720

b:89.0
occ:1.00
OD2 A:ASP81 2.4 30.0 1.0
OD1 A:ASP77 2.4 44.3 1.0
OD1 A:ASP75 2.4 41.5 1.0
O A:TYR79 2.4 41.1 1.0
O A:HOH890 2.6 27.0 1.0
OD1 A:ASP73 2.6 47.0 1.0
CG A:ASP77 3.0 46.2 1.0
OD2 A:ASP77 3.0 54.5 1.0
CG A:ASP75 3.5 47.7 1.0
CG A:ASP81 3.5 33.6 1.0
C A:TYR79 3.6 36.4 1.0
CG A:ASP73 3.6 38.5 1.0
OD2 A:ASP75 3.8 55.1 1.0
CB A:ASP81 3.8 31.3 1.0
N A:TYR79 4.2 34.9 1.0
CA A:TYR79 4.3 35.2 1.0
OD2 A:ASP73 4.4 42.3 1.0
CB A:TYR79 4.4 31.3 1.0
O A:GLY80 4.4 27.9 1.0
N A:SER74 4.4 37.0 1.0
C A:GLY80 4.4 30.1 1.0
CB A:ASP73 4.4 31.3 1.0
N A:ASP75 4.4 44.8 1.0
CB A:ASP77 4.4 47.1 1.0
CA A:ASP73 4.5 39.4 1.0
N A:ASP77 4.5 38.2 1.0
OD1 A:ASP81 4.6 38.2 1.0
N A:GLY80 4.6 38.7 1.0
N A:ASP81 4.7 27.8 1.0
CB A:ASP75 4.8 42.8 1.0
C A:ASP73 4.8 45.4 1.0
CA A:GLY80 4.9 35.6 1.0
CA A:ASP81 4.9 24.1 1.0
O A:HOH1176 4.9 56.2 1.0
CA A:ASP77 4.9 37.6 1.0
CA A:ASP75 5.0 40.9 1.0

Calcium binding site 3 out of 4 in 6bs6

Go back to Calcium Binding Sites List in 6bs6
Calcium binding site 3 out of 4 in the Susg with Mixed Linkage Amylosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Susg with Mixed Linkage Amylosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca715

b:41.0
occ:1.00
OD1 B:ASN153 2.3 43.0 1.0
O B:ILE393 2.4 41.2 1.0
O B:HIS392 2.5 41.4 1.0
OD2 B:ASP352 2.5 35.8 1.0
C B:ILE393 3.3 40.1 1.0
CG B:ASN153 3.4 39.6 1.0
CA B:ILE393 3.5 34.4 1.0
C B:HIS392 3.5 37.9 1.0
CG B:ASP352 3.6 34.4 1.0
CB B:ASP352 3.9 36.5 1.0
N B:ILE393 4.0 36.2 1.0
ND2 B:ASN153 4.0 40.0 1.0
O B:ASN153 4.2 30.9 1.0
N B:TYR394 4.5 31.7 1.0
CD2 B:HIS344 4.5 50.1 1.0
CB B:ASN153 4.6 32.7 1.0
CB B:HIS344 4.7 42.0 1.0
NE2 B:HIS342 4.7 29.3 1.0
OD1 B:ASP352 4.7 31.6 1.0
O B:HOH831 4.7 39.0 1.0
O B:LEU353 4.8 31.6 1.0
CD2 B:HIS342 4.8 30.5 1.0
CE B:MET194 4.8 28.9 1.0
CA B:HIS392 4.8 31.7 1.0
C B:TYR394 4.9 34.7 1.0
CB B:ILE393 4.9 37.6 1.0
CA B:TYR394 4.9 31.1 1.0
CA B:ASN153 4.9 32.2 1.0
C B:ASN153 4.9 31.5 1.0
N B:HIS395 4.9 35.7 1.0
CG B:HIS344 5.0 51.1 1.0
CB B:HIS392 5.0 35.0 1.0

Calcium binding site 4 out of 4 in 6bs6

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Calcium binding site 4 out of 4 in the Susg with Mixed Linkage Amylosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Susg with Mixed Linkage Amylosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca716

b:77.5
occ:1.00
OD1 B:ASP77 2.4 72.3 1.0
OD1 B:ASP75 2.4 80.3 1.0
O B:TYR79 2.5 76.8 1.0
OD2 B:ASP81 2.5 65.2 1.0
OD1 B:ASP73 2.8 77.0 1.0
CG B:ASP77 3.1 65.5 1.0
OD2 B:ASP77 3.2 65.9 1.0
CG B:ASP75 3.3 76.1 1.0
CG B:ASP81 3.4 63.9 1.0
OD2 B:ASP75 3.5 80.9 1.0
CB B:ASP81 3.6 55.2 1.0
C B:TYR79 3.7 64.2 1.0
CG B:ASP73 3.9 71.6 1.0
O B:GLY80 4.3 52.7 1.0
CB B:TYR79 4.3 55.3 1.0
CA B:TYR79 4.4 57.5 1.0
C B:GLY80 4.4 50.1 1.0
N B:TYR79 4.4 67.9 1.0
N B:ASP75 4.4 69.3 1.0
CB B:ASP77 4.5 64.2 1.0
N B:SER74 4.6 68.2 1.0
OD1 B:ASP81 4.6 75.2 1.0
N B:ASP81 4.6 60.1 1.0
CB B:ASP73 4.6 60.2 1.0
CB B:ASP75 4.6 71.4 1.0
CA B:ASP73 4.6 65.7 1.0
N B:ASP77 4.7 73.9 1.0
N B:GLY80 4.7 59.2 1.0
CA B:ASP81 4.7 55.3 1.0
OD2 B:ASP73 4.8 64.7 1.0
CA B:GLY80 4.9 58.1 1.0
O B:GLN125 4.9 55.6 1.0
CA B:ASP75 5.0 69.1 1.0

Reference:

G.Arnal, D.W.Cockburn, H.Brumer, N.M.Koropatkin. Structural Basis For the Flexible Recognition of Alpha-Glucan Substrates By Bacteroides Thetaiotaomicron Susg. Protein Sci. V. 27 1093 2018.
ISSN: ESSN 1469-896X
PubMed: 29603462
DOI: 10.1002/PRO.3410
Page generated: Sat Dec 12 05:59:56 2020

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