Calcium in PDB 8d43: Cryo-Em Structure of Human Kidney Glucosidase II

All present enzymatic activity of Cryo-Em Structure of Human Kidney Glucosidase II:
3.2.1.207;

The binding sites of Calcium atom in the Cryo-Em Structure of Human Kidney Glucosidase II (pdb code 8d43). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cryo-Em Structure of Human Kidney Glucosidase II, PDB code: 8d43:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of Human Kidney Glucosidase II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Human Kidney Glucosidase II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:58.2 occ:1.00 OE2 B:GLU105 2.1 68.5 1.0 OD1 B:ASP94 2.1 76.1 1.0 O B:VAL96 2.2 78.8 1.0 O B:ARG91 2.2 66.9 1.0 OD2 B:ASP98 2.4 81.8 1.0 OD2 B:ASP104 2.4 82.9 1.0 CG B:ASP94 3.1 72.3 1.0 CD B:GLU105 3.2 78.1 1.0 C B:VAL96 3.4 72.9 1.0 C B:ARG91 3.4 69.7 1.0 CG B:ASP104 3.5 79.2 1.0 CG B:ASP98 3.6 78.8 1.0 OD2 B:ASP94 3.6 73.2 1.0 N B:ASP98 3.9 78.5 1.0 CG B:GLU105 4.0 79.6 1.0 CB B:ASP104 4.0 80.4 1.0 N B:VAL96 4.1 72.2 1.0 OE1 B:GLU105 4.1 82.7 1.0 N B:ASP94 4.1 79.7 1.0 CA B:VAL96 4.2 74.3 1.0 CA B:ARG91 4.2 71.9 1.0 CB B:ASP98 4.2 75.6 1.0 N B:CYS97 4.4 77.0 1.0 CB B:ARG91 4.4 66.8 1.0 CB B:ASP94 4.4 68.7 1.0 N B:VAL92 4.4 71.2 1.0 OD1 B:ASP104 4.4 77.5 1.0 N B:ASN93 4.4 73.7 1.0 CA B:CYS97 4.5 82.3 1.0 CA B:VAL92 4.5 68.4 1.0 CB B:VAL96 4.5 76.5 1.0 OD1 B:ASP98 4.6 80.8 1.0 CA B:ASP94 4.7 72.0 1.0 C B:CYS97 4.7 80.2 1.0 C B:VAL92 4.7 69.5 1.0 CA B:ASP98 4.7 81.1 1.0 NH1 A:ARG818 4.7 61.4 1.0 N B:GLY95 4.8 67.2 1.0 O B:ASP104 4.8 85.2 1.0 C B:ASP104 4.9 81.7 1.0 C B:ASP94 4.9 70.4 1.0 CD1 B:ILE87 5.0 67.1 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of Human Kidney Glucosidase II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Human Kidney Glucosidase II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:54.3 occ:1.00 OD2 B:ASP57 1.4 62.3 1.0 OD1 B:ASP53 2.2 53.1 1.0 O B:GLN50 2.4 79.8 1.0 OD2 B:ASP63 2.4 71.8 1.0 CG B:ASP57 2.5 66.8 1.0 O B:TYR55 2.5 59.6 1.0 OE2 B:GLU64 2.6 72.5 1.0 CG B:ASP53 3.2 58.7 1.0 CB B:ASP57 3.3 63.4 1.0 OD1 B:ASP57 3.4 65.0 1.0 CG B:ASP63 3.5 73.1 1.0 N B:ASP57 3.5 68.3 1.0 C B:GLN50 3.5 69.2 1.0 C B:TYR55 3.6 51.5 1.0 CD B:GLU64 3.6 70.3 1.0 OD2 B:ASP53 3.9 61.8 1.0 CB B:ASP63 4.0 65.9 1.0 CA B:ASP57 4.0 68.5 1.0 CB B:GLN50 4.1 66.2 1.0 CA B:GLN50 4.2 63.7 1.0 N B:TYR55 4.2 47.7 1.0 CA B:TYR55 4.2 46.0 1.0 CG B:GLU64 4.3 66.5 1.0 CB B:TYR55 4.3 53.8 1.0 CB B:ASP53 4.3 58.2 1.0 OE1 B:GLU64 4.5 69.3 1.0 N B:ASP53 4.5 57.9 1.0 N B:CYS56 4.5 65.2 1.0 C B:CYS56 4.6 63.2 1.0 N B:VAL51 4.6 71.0 1.0 OD1 B:ASP63 4.6 76.7 1.0 CD1 B:ILE46 4.7 78.1 1.0 NH2 A:ARG929 4.8 54.4 1.0 CA B:CYS56 4.8 66.2 1.0 CD2 B:TYR55 4.8 51.4 1.0 CA B:VAL51 4.9 70.9 1.0 CA B:ASP53 4.9 59.5 1.0 O B:ASP63 5.0 72.2 1.0 N B:ASN52 5.0 65.8 1.0

M.Lyu, E.W.Yu. Cryo-Em Structure of Human Kidney Glucosidase II To Be Published.