Calcium in PDB 1ubn: Selenosubtilisin Bpn

All present enzymatic activity of Selenosubtilisin Bpn:
3.4.21.62;

The structure of Selenosubtilisin Bpn, PDB code: 1ubn was solved by D.E.Mcree, M.Mctigue, D.Hilvert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.880, 74.450, 42.430, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / n/a

The binding sites of Calcium atom in the Selenosubtilisin Bpn (pdb code 1ubn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Selenosubtilisin Bpn, PDB code: 1ubn:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Selenosubtilisin Bpn


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Selenosubtilisin Bpn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca276 b:16.3 occ:1.00 O A:ILE79 2.2 18.8 1.0 OD1 A:ASN77 2.2 19.9 1.0 O A:LEU75 2.2 14.4 1.0 O A:VAL81 2.3 6.3 1.0 OE1 A:GLN2 2.3 6.4 1.0 OD1 A:ASP41 2.4 10.7 1.0 OD2 A:ASP41 2.6 8.3 1.0 CG A:ASP41 2.9 7.4 1.0 CG A:ASN77 3.3 13.6 1.0 CD A:GLN2 3.4 13.5 1.0 C A:ILE79 3.5 16.5 1.0 C A:LEU75 3.5 15.2 1.0 C A:VAL81 3.5 9.0 1.0 HD21 A:ASN77 3.7 0.0 0.0 H A:ASN77 3.8 0.0 0.0 H A:ILE79 3.8 0.0 0.0 H A:VAL81 3.8 0.0 0.0 N A:VAL81 3.9 10.3 1.0 ND2 A:ASN77 3.9 5.7 1.0 CG A:GLN2 4.0 9.6 1.0 N A:ASN77 4.1 18.4 1.0 C A:GLY80 4.2 10.9 1.0 CA A:VAL81 4.3 8.1 1.0 N A:LEU75 4.3 12.5 1.0 N A:GLY80 4.4 14.8 1.0 CA A:LEU75 4.4 15.0 1.0 CB A:ASP41 4.4 6.8 1.0 N A:ASN76 4.4 17.2 1.0 CG1 A:ILE79 4.4 17.1 1.0 N A:ILE79 4.5 19.7 1.0 CA A:GLY80 4.5 11.3 1.0 CB A:ASN77 4.5 14.6 1.0 N A:LEU82 4.5 9.8 1.0 CA A:ILE79 4.5 15.6 1.0 CA A:ASN76 4.6 19.3 1.0 NE2 A:GLN2 4.6 8.6 1.0 O A:ASN77 4.6 22.1 1.0 H A:LEU75 4.6 0.0 0.0 CB A:GLN2 4.6 14.2 1.0 CA A:ASN77 4.6 19.3 1.0 C A:ASN77 4.7 17.9 1.0 C A:ASN76 4.7 20.5 1.0 HE21 A:GLN2 4.7 0.0 0.0 CA A:LEU82 4.8 6.6 1.0 C A:ALA74 4.8 10.6 1.0 HD22 A:ASN77 4.8 0.0 0.0 O A:GLY80 4.8 16.9 1.0 CB A:LEU75 4.9 12.6 1.0 CB A:ALA74 5.0 5.7 1.0

Calcium binding site 2 out of 2 in the Selenosubtilisin Bpn


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Selenosubtilisin Bpn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca277 b:44.4 occ:1.00 O A:HOH365 2.1 70.3 1.0 O A:TYR171 2.4 18.7 1.0 O A:GLY169 2.4 20.5 1.0 O A:VAL174 2.5 19.9 1.0 H1 A:HOH365 2.8 0.0 0.0 H2 A:HOH365 2.9 0.0 0.0 OD2 A:ASP197 3.2 30.2 1.0 O A:GLU195 3.3 19.8 1.0 C A:TYR171 3.4 17.7 1.0 C A:GLY169 3.7 18.4 1.0 C A:VAL174 3.7 15.7 1.0 CA A:PRO172 4.0 15.8 1.0 N A:PRO172 4.0 16.8 1.0 H A:ALA176 4.0 0.0 0.0 CB A:ALA176 4.0 8.9 1.0 H A:VAL174 4.0 0.0 0.0 HH22 A:ARG247 4.1 0.0 0.0 C A:LYS170 4.1 17.1 1.0 O A:LYS170 4.1 17.6 1.0 O A:PRO172 4.1 16.9 1.0 N A:TYR171 4.2 15.8 1.0 N A:ALA176 4.2 12.9 1.0 CG A:ASP197 4.3 31.2 1.0 C A:PRO172 4.3 18.8 1.0 HH12 A:ARG247 4.3 0.0 0.0 O A:HOH483 4.4 68.7 1.0 C A:GLU195 4.4 15.6 1.0 CA A:TYR171 4.5 15.8 1.0 CA A:LYS170 4.5 17.9 1.0 N A:LYS170 4.5 17.6 1.0 N A:VAL174 4.5 17.7 1.0 CA A:VAL174 4.5 13.9 1.0 H A:TYR171 4.5 0.0 0.0 CB A:GLU195 4.5 14.1 1.0 OD1 A:ASP197 4.6 34.8 1.0 CB A:VAL174 4.7 11.3 1.0 CA A:GLY169 4.7 19.4 1.0 N A:ILE175 4.7 14.6 1.0 CA A:ALA176 4.8 11.5 1.0 C A:ILE175 4.8 16.7 1.0 CA A:GLU195 4.8 13.2 1.0 CA A:ILE175 4.9 15.5 1.0 H2 A:HOH483 5.0 0.0 0.0

D.Dinakarpandian, B.C.Shenoy, D.Hilvert, D.E.Mcree, M.Mctigue, P.R.Carey. Electric Fields in Active Sites: Substrate Switching From Null to Strong Fields in Thiol- and Selenol-Subtilisins. Biochemistry V. 38 6659 1999.
ISSN: ISSN 0006-2960
PubMed: 10350485
DOI: 10.1021/BI9902541