Calcium in PDB 6lga: Bombyx Mori GH13 Sucrose Hydrolase

Protein crystallography data

The structure of Bombyx Mori GH13 Sucrose Hydrolase, PDB code: 6lga was solved by T.Miyazaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.91 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.880, 145.684, 153.796, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 18.6

Other elements in 6lga:

The structure of Bombyx Mori GH13 Sucrose Hydrolase also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Bombyx Mori GH13 Sucrose Hydrolase (pdb code 6lga). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Bombyx Mori GH13 Sucrose Hydrolase, PDB code: 6lga:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6lga

Go back to Calcium Binding Sites List in 6lga
Calcium binding site 1 out of 2 in the Bombyx Mori GH13 Sucrose Hydrolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bombyx Mori GH13 Sucrose Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:16.9
occ:1.00
OD2 A:ASP217 2.4 18.0 1.0
OE2 A:GLU254 2.4 17.4 1.0
O A:TYR251 2.4 16.3 1.0
O A:LEU252 2.4 19.0 1.0
O A:HOH914 2.4 16.4 1.0
O A:HOH872 2.4 14.0 1.0
OD1 A:ASN144 2.5 15.7 1.0
C A:LEU252 3.1 17.6 1.0
CD A:GLU254 3.4 17.8 1.0
CG A:ASP217 3.4 16.3 1.0
C A:TYR251 3.5 17.1 1.0
CG A:ASN144 3.5 16.2 1.0
CA A:LEU252 3.5 17.9 1.0
OE1 A:GLU254 3.8 17.9 1.0
CB A:ASP217 3.8 16.4 1.0
ND2 A:ASN144 3.9 14.4 1.0
N A:LEU252 4.0 17.0 1.0
N A:ILE253 4.1 17.6 1.0
O A:PHE218 4.3 16.6 1.0
O A:ASN144 4.3 17.3 1.0
NE2 A:GLN210 4.4 15.8 1.0
O A:HOH1150 4.5 16.9 1.0
OD1 A:ASP217 4.6 18.0 1.0
CA A:TYR251 4.7 16.3 1.0
CA A:ILE253 4.7 18.4 1.0
CA A:ASP217 4.7 16.5 1.0
CG A:GLU254 4.8 17.5 1.0
CB A:TYR251 4.8 17.2 1.0
CB A:ASN144 4.8 16.1 1.0
CG A:GLN210 4.8 17.0 1.0
CD2 A:LEU208 4.9 18.9 1.0
CB A:LEU252 5.0 18.4 1.0

Calcium binding site 2 out of 2 in 6lga

Go back to Calcium Binding Sites List in 6lga
Calcium binding site 2 out of 2 in the Bombyx Mori GH13 Sucrose Hydrolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bombyx Mori GH13 Sucrose Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:17.7
occ:1.00
OD2 B:ASP217 2.3 17.5 1.0
O B:TYR251 2.4 18.2 1.0
OE2 B:GLU254 2.4 19.4 1.0
O B:HOH891 2.4 16.2 1.0
O B:HOH927 2.4 15.8 1.0
OD1 B:ASN144 2.5 16.5 1.0
O B:LEU252 2.5 17.0 1.0
C B:LEU252 3.2 17.6 1.0
CG B:ASP217 3.4 16.9 1.0
CD B:GLU254 3.4 20.1 1.0
C B:TYR251 3.5 17.6 1.0
CG B:ASN144 3.5 16.6 1.0
CA B:LEU252 3.6 17.6 1.0
CB B:ASP217 3.8 17.2 1.0
OE1 B:GLU254 3.8 20.0 1.0
ND2 B:ASN144 3.9 15.0 1.0
N B:LEU252 4.0 17.4 1.0
N B:ILE253 4.2 18.4 1.0
O B:PHE218 4.2 17.0 1.0
O B:ASN144 4.3 17.9 1.0
NE2 B:GLN210 4.4 17.4 1.0
O B:HOH1171 4.4 19.2 1.0
OD1 B:ASP217 4.5 19.4 1.0
CA B:TYR251 4.7 17.1 1.0
CA B:ASP217 4.7 17.7 1.0
CG B:GLU254 4.7 18.6 1.0
CB B:TYR251 4.8 17.6 1.0
CB B:ASN144 4.8 16.9 1.0
CA B:ILE253 4.8 19.5 1.0
CD2 B:LEU208 4.8 20.1 1.0
CG B:GLN210 4.9 18.4 1.0

Reference:

T.Miyazaki, E.Y.Park. Structure-Function Analysis of Silkworm Sucrose Hydrolase Uncovers the Mechanism of Substrate Specificity in GH13 Subfamily 17EXO-Alpha-Glucosidases. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32381508
DOI: 10.1074/JBC.RA120.013595
Page generated: Sat Dec 12 06:22:17 2020

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