Atomistry » Calcium » PDB 6kzo-6lje » 6lge
Atomistry »
  Calcium »
    PDB 6kzo-6lje »
      6lge »

Calcium in PDB 6lge: Bombyx Mori GH13 Sucrose Hydrolase Complexed with Acarbose

Protein crystallography data

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

Resolution Low / High (Å) 48.66 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.247, 145.792, 152.857, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.9

Other elements in 6lge:

The structure of Bombyx Mori GH13 Sucrose Hydrolase Complexed with Acarbose 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 Acarbose (pdb code 6lge). 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 Acarbose, PDB code: 6lge:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6lge

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


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 Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:25.7
occ:1.00
OD2 A:ASP217 2.3 24.7 1.0
O A:HOH810 2.3 23.9 1.0
O A:HOH926 2.4 25.6 1.0
O A:LEU252 2.4 23.7 1.0
OD1 A:ASN144 2.4 22.8 1.0
O A:TYR251 2.5 25.9 1.0
OE2 A:GLU254 2.5 27.1 1.0
C A:LEU252 3.1 25.9 1.0
CG A:ASP217 3.4 23.5 1.0
CG A:ASN144 3.5 22.6 1.0
CD A:GLU254 3.5 27.5 1.0
C A:TYR251 3.6 24.1 1.0
CA A:LEU252 3.6 24.9 1.0
OE1 A:GLU254 3.7 25.8 1.0
CB A:ASP217 3.8 21.5 1.0
ND2 A:ASN144 3.9 22.6 1.0
N A:LEU252 4.0 25.0 1.0
N A:ILE253 4.1 26.6 1.0
O A:ASN144 4.3 20.9 1.0
O A:PHE218 4.3 26.8 1.0
O A:HOH970 4.4 26.3 1.0
OD1 A:ASP217 4.5 26.3 1.0
NE2 A:GLN210 4.5 22.4 1.0
CA A:ASP217 4.7 24.2 1.0
CA A:ILE253 4.8 28.7 1.0
CB A:ASN144 4.8 25.7 1.0
CA A:TYR251 4.8 23.6 1.0
CG A:GLU254 4.8 28.6 1.0
CD2 A:LEU208 4.9 27.9 1.0
CG A:GLN210 4.9 24.0 1.0
CB A:TYR251 4.9 23.6 1.0
CB A:LEU252 5.0 26.0 1.0

Calcium binding site 2 out of 2 in 6lge

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


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 Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:26.2
occ:1.00
O B:TYR251 2.3 24.2 1.0
OD2 B:ASP217 2.3 30.5 1.0
O B:HOH863 2.3 24.8 1.0
OE2 B:GLU254 2.4 31.9 1.0
OD1 B:ASN144 2.4 25.7 1.0
O B:HOH862 2.5 24.3 1.0
O B:LEU252 2.5 26.8 1.0
C B:LEU252 3.1 25.3 1.0
CG B:ASP217 3.4 25.9 1.0
CD B:GLU254 3.4 31.8 1.0
C B:TYR251 3.4 23.8 1.0
CG B:ASN144 3.5 23.4 1.0
CA B:LEU252 3.5 22.4 1.0
CB B:ASP217 3.7 22.9 1.0
OE1 B:GLU254 3.7 29.8 1.0
ND2 B:ASN144 3.9 22.7 1.0
N B:LEU252 4.0 24.4 1.0
N B:ILE253 4.0 25.2 1.0
O B:PHE218 4.3 25.3 1.0
O B:ASN144 4.3 25.4 1.0
NE2 B:GLN210 4.4 27.0 1.0
O B:HOH997 4.5 27.5 1.0
OD1 B:ASP217 4.5 29.6 1.0
CA B:TYR251 4.7 26.4 1.0
CA B:ILE253 4.7 31.7 1.0
CG B:GLU254 4.7 30.1 1.0
CA B:ASP217 4.7 23.0 1.0
CB B:ASN144 4.7 25.2 1.0
CB B:TYR251 4.8 26.0 1.0
CD2 B:LEU208 4.9 32.0 1.0
CG B:GLN210 4.9 28.2 1.0
CB B:LEU252 4.9 22.0 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: Tue Jul 16 10:54:58 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy