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

The structure of The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with 1-Deoxynojirimycin, PDB code: 7vkz 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)	43.11 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	162.658, 71.646, 129.52, 90, 106.34, 90
R / Rfree (%)	17.1 / 20.8

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

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


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 1-Deoxynojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:20.8 occ:1.00 O B:HOH1098 2.3 16.3 1.0 O B:GLY565 2.3 17.4 1.0 O B:HOH1135 2.4 19.2 1.0 OE2 B:GLU567 2.5 19.1 1.0 OE1 B:GLU567 2.6 24.1 1.0 O B:HOH1116 2.6 23.4 1.0 CD B:GLU567 2.9 21.6 1.0 C B:GLY565 3.4 19.2 1.0 CA B:GLY565 3.9 19.7 1.0 CG B:GLU567 4.4 20.8 1.0 N B:ILE566 4.4 18.3 1.0 NZ B:LYS616 4.4 25.5 1.0 O B:HOH927 4.5 24.9 1.0 O B:HOH1022 4.6 23.6 1.0 OD1 B:ASN596 4.6 19.9 1.0 O B:THR598 4.6 20.8 1.0 O B:HOH918 4.6 19.2 1.0 CA B:ILE566 4.8 17.7 1.0 N B:GLU567 4.8 19.0 1.0 CB B:THR598 4.9 20.6 1.0 C B:ILE566 4.9 16.7 1.0

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


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 1-Deoxynojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:47.1 occ:1.00 O B:HOH1035 2.4 28.4 1.0 O B:HOH931 2.5 29.1 1.0 OD1 B:ASN433 2.5 36.7 1.0 O B:HOH1067 2.9 26.3 1.0 OE1 B:GLU331 3.3 33.1 1.0 CG B:ASN433 3.4 32.4 1.0 NZ B:LYS328 3.7 35.5 1.0 ND2 B:ASN433 3.8 36.0 1.0 OE2 B:GLU331 3.9 38.6 1.0 CD B:GLU331 4.0 32.9 1.0 O B:HOH942 4.3 20.9 1.0 NH2 B:ARG666 4.3 23.7 1.0 O B:HOH1094 4.3 29.9 1.0 OE2 B:GLU7 4.4 33.3 1.0 O B:HOH928 4.5 30.0 1.0 OE1 B:GLU7 4.5 27.1 1.0 CE B:LYS328 4.6 31.5 1.0 CB B:ASN433 4.7 28.3 1.0 CG2 B:VAL434 4.8 24.4 1.0 CD B:GLU7 4.8 29.8 1.0 N B:VAL434 4.9 23.0 1.0 OD1 B:ASP497 5.0 19.4 1.0 NH1 B:ARG666 5.0 22.2 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