Calcium in PDB 7vky: The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophorose

The structure of The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophorose, PDB code: 7vky was solved by K.Kobayashi, H.Shimizu, N.Tanaka, K.Kuramochi, H.Nakai, M.Nakajima, H.Taguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.31 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	163.53, 71.66, 129.82, 90, 106.02, 90
R / Rfree (%)	16.6 / 20.4

The binding sites of Calcium atom in the The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophorose (pdb code 7vky). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophorose, PDB code: 7vky:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophorose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophorose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:33.0 occ:1.00 OD1 A:ASN433 2.3 23.1 1.0 O A:HOH936 2.4 13.9 1.0 O A:HOH1162 2.7 17.9 1.0 CG A:ASN433 3.4 22.4 1.0 NZ A:LYS328 3.9 12.2 1.0 ND2 A:ASN433 3.9 24.5 1.0 NH2 A:ARG666 4.2 11.4 1.0 OE1 A:GLU7 4.2 22.4 1.0 OE2 A:GLU7 4.2 21.9 1.0 OE1 A:GLU331 4.3 19.9 1.0 O A:HOH942 4.5 10.0 1.0 OE2 A:GLU331 4.6 22.0 1.0 CG2 A:VAL434 4.6 19.4 1.0 CD A:GLU7 4.6 23.1 1.0 N A:VAL434 4.7 15.8 1.0 CB A:ASN433 4.7 19.6 1.0 O A:HOH903 4.8 21.1 1.0 OD1 A:ASP497 4.9 9.7 1.0 CD A:GLU331 4.9 15.9 1.0 NH1 A:ARG666 4.9 12.3 1.0 CA A:ASN433 4.9 16.2 1.0 CE A:LYS328 4.9 11.0 1.0 CZ A:ARG666 5.0 12.0 1.0

Calcium binding site 2 out of 3 in the The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophorose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophorose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:12.0 occ:1.00 O B:HOH1112 2.3 9.0 1.0 O B:GLY565 2.3 11.2 1.0 OE1 B:GLU567 2.4 11.2 1.0 O B:HOH1146 2.4 9.7 1.0 OE2 B:GLU567 2.5 11.5 1.0 O B:HOH1076 2.5 16.0 1.0 CD B:GLU567 2.8 11.1 1.0 C B:GLY565 3.4 11.5 1.0 CA B:GLY565 4.0 11.6 1.0 NZ B:LYS616 4.2 15.3 1.0 CG B:GLU567 4.3 11.3 1.0 O B:HOH910 4.3 14.1 1.0 N B:ILE566 4.4 11.1 1.0 OD1 B:ASN596 4.5 11.6 1.0 O B:HOH1018 4.5 16.7 1.0 O B:HOH903 4.5 14.6 1.0 O B:THR598 4.7 13.1 1.0 CA B:ILE566 4.7 10.7 1.0 N B:GLU567 4.8 10.5 1.0 C B:ILE566 4.8 10.7 1.0 CB B:THR598 4.9 13.1 1.0

Calcium binding site 3 out of 3 in the The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophorose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophorose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:26.4 occ:1.00 O B:HOH1003 2.4 11.8 1.0 OD1 B:ASN433 2.4 19.3 1.0 O B:HOH976 2.5 17.8 1.0 O B:HOH971 2.5 16.6 1.0 O B:HOH1132 2.7 12.7 1.0 OE1 B:GLU331 3.1 28.0 1.0 CG B:ASN433 3.4 19.7 1.0 OE2 B:GLU331 3.6 33.3 1.0 CD B:GLU331 3.8 26.3 1.0 ND2 B:ASN433 3.9 21.4 1.0 O B:HOH963 4.1 13.7 1.0 NZ B:LYS328 4.2 19.7 1.0 OE2 B:GLU7 4.3 16.0 1.0 NH2 B:ARG666 4.4 13.2 1.0 OE1 B:GLU7 4.5 14.0 1.0 O B:HOH1074 4.5 25.2 1.0 CB B:ASN433 4.6 17.1 1.0 CG2 B:VAL434 4.8 15.8 1.0 CD B:GLU7 4.8 16.5 1.0 N B:VAL434 4.9 15.7 1.0 OD1 B:ASP497 4.9 8.4 1.0 CE B:LYS328 5.0 17.4 1.0

K.Kobayashi, H.Shimizu, N.Tanaka, K.Kuramochi, H.Nakai, M.Nakajima, H.Taguchi. Characterization and Structural Analyses of A Novel Glycosyltransferase Acting on the Beta-1,2-Glucosidic Linkages. J.Biol.Chem. V. 298 01606 2022.
ISSN: ESSN 1083-351X
PubMed: 35065074
DOI: 10.1016/J.JBC.2022.101606