Atomistry » Calcium » PDB 6kzk-6ljd » 6lgg
Atomistry »
  Calcium »
    PDB 6kzk-6ljd »
      6lgg »

Calcium in PDB 6lgg: Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Complexed with Sucrose

Protein crystallography data

The structure of Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Complexed with Sucrose, PDB code: 6lgg was solved by T.Miyazaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.28 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.700, 127.900, 154.300, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.1

Other elements in 6lgg:

The structure of Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Complexed with Sucrose 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 Mutant E322Q Complexed with Sucrose (pdb code 6lgg). 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 Mutant E322Q Complexed with Sucrose, PDB code: 6lgg:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6lgg

Go back to Calcium Binding Sites List in 6lgg
Calcium binding site 1 out of 2 in the Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Complexed with Sucrose


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 Mutant E322Q Complexed with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:25.2
occ:1.00
O A:HOH930 2.3 22.6 1.0
OD2 A:ASP217 2.4 22.7 1.0
O A:TYR251 2.4 22.2 1.0
O A:LEU252 2.4 26.4 1.0
OE2 A:GLU254 2.5 24.6 1.0
O A:HOH857 2.5 23.1 1.0
OD1 A:ASN144 2.5 22.2 1.0
C A:LEU252 3.1 23.8 1.0
CD A:GLU254 3.4 27.0 1.0
CG A:ASP217 3.4 26.2 1.0
C A:TYR251 3.5 22.2 1.0
CG A:ASN144 3.5 23.8 1.0
CA A:LEU252 3.6 25.0 1.0
OE1 A:GLU254 3.7 27.3 1.0
CB A:ASP217 3.8 28.2 1.0
ND2 A:ASN144 3.9 21.1 1.0
N A:LEU252 4.0 24.1 1.0
N A:ILE253 4.1 23.7 1.0
O A:PHE218 4.3 31.1 1.0
O A:HOH1004 4.3 27.4 1.0
NE2 A:GLN210 4.4 19.4 1.0
O A:ASN144 4.4 24.5 1.0
OD1 A:ASP217 4.6 25.3 1.0
CA A:TYR251 4.7 20.9 1.0
CA A:ASP217 4.7 27.6 1.0
CA A:ILE253 4.8 23.6 1.0
CD2 A:LEU208 4.8 24.4 1.0
CG A:GLU254 4.8 25.5 1.0
CB A:TYR251 4.8 21.0 1.0
CB A:ASN144 4.8 24.8 1.0
CG A:GLN210 4.9 21.4 1.0

Calcium binding site 2 out of 2 in 6lgg

Go back to Calcium Binding Sites List in 6lgg
Calcium binding site 2 out of 2 in the Bombyx Mori GH13 Sucrose Hydrolase Mutant E322Q Complexed with Sucrose


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 Mutant E322Q Complexed with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:18.8
occ:1.00
O B:TYR251 2.3 17.6 1.0
OD2 B:ASP217 2.4 17.4 1.0
O B:HOH874 2.4 19.4 1.0
O B:HOH917 2.4 17.7 1.0
O B:LEU252 2.4 19.7 1.0
OE2 B:GLU254 2.4 20.5 1.0
OD1 B:ASN144 2.5 19.6 1.0
C B:LEU252 3.1 18.9 1.0
CG B:ASP217 3.4 17.9 1.0
C B:TYR251 3.4 18.1 1.0
CD B:GLU254 3.5 21.6 1.0
CA B:LEU252 3.5 18.4 1.0
CG B:ASN144 3.5 20.3 1.0
CB B:ASP217 3.8 18.4 1.0
OE1 B:GLU254 3.8 18.7 1.0
ND2 B:ASN144 3.9 18.6 1.0
N B:LEU252 3.9 17.5 1.0
N B:ILE253 4.1 18.0 1.0
O B:PHE218 4.2 19.8 1.0
O B:ASN144 4.3 17.9 1.0
NE2 B:GLN210 4.4 17.0 1.0
O B:HOH1034 4.4 20.9 1.0
OD1 B:ASP217 4.5 19.3 1.0
CA B:TYR251 4.6 16.9 1.0
CA B:ASP217 4.7 17.8 1.0
CA B:ILE253 4.7 19.8 1.0
CB B:TYR251 4.8 16.6 1.0
CG B:GLU254 4.8 20.6 1.0
CD2 B:LEU208 4.8 20.1 1.0
CB B:ASN144 4.8 19.8 1.0
CB B:LEU252 4.9 19.2 1.0
CG B:GLN210 4.9 17.6 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 10:55:48 2024

Last articles

Zn in 1MC5
Zn in 1MFM
Zn in 1MA0
Zn in 1MED
Zn in 1MEA
Zn in 1MBX
Zn in 1MA3
Zn in 1M9O
Zn in 1M9R
Zn in 1M9Q
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy