Calcium in PDB 7x87: The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophotetraose Observed As Sophorose

The structure of The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophotetraose Observed As Sophorose, PDB code: 7x87 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)	47.91 / 1.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	165.135, 71.615, 130.308, 90, 104.89, 90
R / Rfree (%)	16.6 / 20.1

The binding sites of Calcium atom in the The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophotetraose Observed As Sophorose (pdb code 7x87). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophotetraose Observed As Sophorose, PDB code: 7x87:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophotetraose Observed As 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 Sophotetraose Observed As Sophorose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:22.6 occ:1.00 OD2 A:ASP64 2.1 25.7 1.0 O A:HOH1304 2.3 31.6 1.0 OD1 A:ASP64 2.4 30.2 1.0 CG A:ASP64 2.6 23.9 1.0 CB A:ASP64 4.0 20.5 1.0 CD1 A:ILE60 4.4 19.0 1.0 CA A:ASP64 4.9 19.1 1.0

Calcium binding site 2 out of 4 in the The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophotetraose Observed As 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 Sophotetraose Observed As Sophorose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:14.3 occ:1.00 O B:GLY565 2.3 12.6 1.0 O B:HOH1212 2.3 15.8 1.0 O B:HOH1141 2.4 9.8 1.0 OE2 B:GLU567 2.5 14.4 1.0 OE1 B:GLU567 2.5 11.9 1.0 O B:HOH1255 2.5 13.4 1.0 CD B:GLU567 2.8 13.0 1.0 C B:GLY565 3.4 13.4 1.0 CA B:GLY565 4.0 13.3 1.0 O B:HOH927 4.3 19.6 1.0 CG B:GLU567 4.3 13.1 1.0 N B:ILE566 4.4 13.6 1.0 OD1 B:ASN596 4.5 14.1 1.0 NZ B:LYS616 4.5 16.8 1.0 O B:HOH1146 4.6 18.0 1.0 O B:THR598 4.7 16.0 1.0 OD1 B:ASN599 4.8 31.5 1.0 CA B:ILE566 4.8 13.2 1.0 O B:HOH937 4.8 17.1 1.0 N B:GLU567 4.8 12.4 1.0 C B:ILE566 4.9 13.1 1.0 CB B:THR598 4.9 15.8 1.0

Calcium binding site 3 out of 4 in the The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophotetraose Observed As 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 Sophotetraose Observed As Sophorose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:69.1 occ:1.00 OD1 B:ASN433 2.4 28.9 1.0 O B:HOH965 2.5 14.7 1.0 O B:HOH1196 2.5 19.7 1.0 O B:HOH914 2.6 39.9 1.0 O B:HOH967 3.2 29.6 1.0 OE1 B:GLU331 3.5 23.5 1.0 CG B:ASN433 3.6 28.9 1.0 NZ B:LYS328 3.7 26.3 1.0 O B:HOH1135 4.0 22.8 1.0 ND2 B:ASN433 4.1 35.6 1.0 OE2 B:GLU331 4.1 28.3 1.0 CD B:GLU331 4.2 23.5 1.0 NH2 B:ARG666 4.2 13.0 1.0 O B:HOH912 4.2 22.6 1.0 O B:HOH969 4.3 15.7 1.0 CG2 B:VAL434 4.3 22.2 1.0 CE B:LYS328 4.5 23.5 1.0 NH1 B:ARG666 4.6 13.3 1.0 N B:VAL434 4.6 17.7 1.0 OE2 B:GLU7 4.7 20.6 1.0 OE1 B:GLU7 4.7 17.0 1.0 CB B:ASN433 4.8 23.3 1.0 CZ B:ARG666 4.9 13.1 1.0 OD1 B:ASP497 5.0 13.8 1.0 CA B:ASN433 5.0 19.9 1.0

Calcium binding site 4 out of 4 in the The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophotetraose Observed As Sophorose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Complex Structure of Beta-1,2-Glucosyltransferase From Ignavibacterium Album with Sophotetraose Observed As Sophorose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:42.9 occ:1.00 O B:HOH1257 2.4 30.2 1.0 O B:HOH1157 2.5 26.1 1.0 ND2 B:ASN218 2.5 28.7 1.0 CG B:ASN218 3.5 28.0 1.0 OD1 B:ASN218 3.7 31.9 1.0 O B:THR217 4.3 20.3 1.0 O B:SER216 4.7 24.5 1.0 CB B:ASN218 4.8 26.5 1.0 C B:THR217 4.9 23.0 1.0 C B:SER216 5.0 22.6 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