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Calcium in PDB 6lgd: Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol

Protein crystallography data

The structure of Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol, PDB code: 6lgd was solved by T.Miyazaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.29 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.054, 146.444, 153.291, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 18.4

Other elements in 6lgd:

The structure of Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol (pdb code 6lgd). 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 Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol, PDB code: 6lgd:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6lgd

Go back to Calcium Binding Sites List in 6lgd
Calcium binding site 1 out of 2 in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol


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 Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:23.8
occ:1.00
OD2 A:ASP217 2.3 22.6 1.0
O A:HOH912 2.3 23.3 1.0
O A:LEU252 2.4 24.3 1.0
O A:TYR251 2.4 22.8 1.0
OE2 A:GLU254 2.4 24.6 1.0
O A:HOH820 2.5 23.7 1.0
OD1 A:ASN144 2.5 24.6 1.0
C A:LEU252 3.1 26.0 1.0
CG A:ASP217 3.4 23.9 1.0
CD A:GLU254 3.4 25.6 1.0
C A:TYR251 3.5 23.1 1.0
CG A:ASN144 3.5 24.2 1.0
CA A:LEU252 3.6 25.4 1.0
OE1 A:GLU254 3.8 24.9 1.0
CB A:ASP217 3.8 23.6 1.0
ND2 A:ASN144 3.9 22.2 1.0
N A:LEU252 4.0 23.6 1.0
N A:ILE253 4.1 23.9 1.0
O A:PHE218 4.3 26.4 1.0
O A:ASN144 4.3 22.9 1.0
NE2 A:GLN210 4.5 21.8 1.0
O A:HOH1110 4.5 27.9 1.0
OD1 A:ASP217 4.5 23.8 1.0
CA A:ILE253 4.7 24.2 1.0
CA A:ASP217 4.7 24.1 1.0
CA A:TYR251 4.7 22.5 1.0
CG A:GLU254 4.8 24.4 1.0
CB A:ASN144 4.8 23.2 1.0
CG A:GLN210 4.9 23.1 1.0
CD2 A:LEU208 4.9 26.2 1.0
CB A:TYR251 4.9 22.2 1.0

Calcium binding site 2 out of 2 in 6lgd

Go back to Calcium Binding Sites List in 6lgd
Calcium binding site 2 out of 2 in the Bombyx Mori GH13 Sucrose Hydrolase Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol


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 Complexed with 1,4-Dideoxy-1,4- Imino-D-Arabinitol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:25.0
occ:1.00
OD2 B:ASP217 2.4 25.8 1.0
O B:TYR251 2.4 23.9 1.0
O B:HOH872 2.4 23.4 1.0
OE2 B:GLU254 2.4 26.8 1.0
O B:HOH817 2.4 22.2 1.0
OD1 B:ASN144 2.4 22.5 1.0
O B:LEU252 2.5 23.1 1.0
C B:LEU252 3.1 22.0 1.0
CG B:ASP217 3.4 26.1 1.0
CD B:GLU254 3.4 26.3 1.0
CG B:ASN144 3.5 25.2 1.0
C B:TYR251 3.5 23.5 1.0
CA B:LEU252 3.6 23.3 1.0
OE1 B:GLU254 3.8 25.8 1.0
CB B:ASP217 3.8 25.7 1.0
ND2 B:ASN144 3.9 24.1 1.0
N B:LEU252 4.0 23.2 1.0
N B:ILE253 4.1 23.4 1.0
O B:ASN144 4.3 23.8 1.0
O B:PHE218 4.3 23.6 1.0
NE2 B:GLN210 4.5 26.3 1.0
O B:HOH1126 4.5 23.1 1.0
OD1 B:ASP217 4.5 25.1 1.0
CA B:TYR251 4.7 24.2 1.0
CB B:ASN144 4.7 24.5 1.0
CA B:ASP217 4.7 25.6 1.0
CA B:ILE253 4.7 26.4 1.0
CG B:GLU254 4.8 24.4 1.0
CB B:TYR251 4.9 23.6 1.0
CG B:GLN210 4.9 27.6 1.0
CD2 B:LEU208 4.9 26.3 1.0
CB B:LEU252 5.0 24.0 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: Wed Jul 9 15:51:59 2025

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