Calcium in PDB 3vyv: Crystal Structure of Subtilisin Nat at 1.36

All present enzymatic activity of Crystal Structure of Subtilisin Nat at 1.36:
3.4.21.62;

The structure of Crystal Structure of Subtilisin Nat at 1.36, PDB code: 3vyv was solved by H.Ushijima, N.Fuchita, T.Kajiwara, H.Motoshima, G.Ueno, K.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.07 / 1.36
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.682, 80.039, 87.449, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 17.6

The binding sites of Calcium atom in the Crystal Structure of Subtilisin Nat at 1.36 (pdb code 3vyv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Subtilisin Nat at 1.36, PDB code: 3vyv:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Subtilisin Nat at 1.36


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Subtilisin Nat at 1.36 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:4.3 occ:1.00 O A:LEU75 2.3 4.3 1.0 O A:ILE79 2.3 4.6 1.0 O A:VAL81 2.4 4.2 1.0 OE1 A:GLN2 2.4 5.1 1.0 OD1 A:ASN77 2.4 4.8 1.0 OD1 A:ASP41 2.4 4.6 1.0 OD2 A:ASP41 2.5 4.8 1.0 CG A:ASP41 2.8 4.2 1.0 CG A:ASN77 3.4 3.6 1.0 CD A:GLN2 3.4 4.6 1.0 C A:ILE79 3.5 4.3 1.0 C A:LEU75 3.5 4.0 1.0 C A:VAL81 3.5 3.4 1.0 N A:VAL81 3.7 3.9 1.0 ND2 A:ASN77 3.9 4.9 1.0 CG A:GLN2 3.9 5.3 1.0 N A:ASN77 4.1 5.7 1.0 C A:GLY80 4.1 4.0 1.0 CA A:VAL81 4.3 3.6 1.0 N A:LEU75 4.3 4.0 1.0 CA A:GLY80 4.3 4.3 1.0 CB A:ASP41 4.4 4.4 1.0 CA A:LEU75 4.4 3.9 1.0 N A:GLY80 4.4 5.0 1.0 N A:ILE79 4.4 5.0 1.0 CG1 A:ILE79 4.4 6.1 1.0 N A:ASN76 4.5 4.8 1.0 CA A:ILE79 4.5 4.7 1.0 CB A:GLN2 4.5 5.5 1.0 N A:LEU82 4.6 4.2 1.0 NE2 A:GLN2 4.6 6.8 1.0 CB A:ASN77 4.6 4.5 1.0 CA A:ASN76 4.6 5.2 1.0 O A:ASN77 4.6 6.2 1.0 CA A:ASN77 4.7 4.8 1.0 C A:ASN77 4.7 5.4 1.0 CB A:LEU75 4.7 4.6 1.0 C A:ASN76 4.7 5.4 1.0 C A:ALA74 4.8 3.5 1.0 CA A:LEU82 4.8 3.7 1.0 O A:GLY80 4.8 5.1 1.0 CB A:ALA74 5.0 3.9 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Subtilisin Nat at 1.36


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Subtilisin Nat at 1.36 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:34.4 occ:1.00 O A:THR174 2.7 5.3 1.0 O A:ALA169 2.8 6.7 1.0 O A:HOH470 3.0 12.5 1.0 OD2 A:ASP197 3.0 7.9 1.0 O A:TYR171 3.0 7.4 1.0 O A:HOH481 3.2 19.2 1.0 O A:GLU195 3.4 7.2 1.0 OG1 A:THR174 3.4 6.9 1.0 C A:THR174 3.7 4.4 1.0 CB A:ALA176 3.8 6.4 1.0 N A:ALA176 3.9 4.5 1.0 C A:TYR171 3.9 7.2 1.0 C A:ALA169 4.0 5.6 1.0 CG A:ASP197 4.0 8.4 1.0 CA A:PRO172 4.2 7.1 1.0 NH2 A:ARG247 4.3 9.1 1.0 O A:PRO172 4.4 7.2 1.0 OD1 A:ASP197 4.4 9.5 1.0 C A:GLU195 4.4 6.6 1.0 C A:PRO172 4.4 6.6 1.0 C A:LYS170 4.4 7.7 1.0 CA A:ALA176 4.4 4.2 1.0 N A:THR174 4.5 5.6 1.0 N A:PRO172 4.5 7.1 1.0 CA A:THR174 4.5 4.8 1.0 CB A:GLU195 4.5 7.0 1.0 O A:LYS170 4.5 8.7 1.0 CB A:THR174 4.6 6.2 1.0 C A:ILE175 4.6 4.8 1.0 N A:ILE175 4.6 4.5 1.0 N A:TYR171 4.6 6.4 1.0 CA A:ILE175 4.7 3.8 1.0 CA A:GLU195 4.8 6.7 1.0 CA A:LYS170 4.8 7.7 1.0 CA A:ALA169 4.8 5.8 1.0 N A:LYS170 4.9 6.5 1.0 CA A:TYR171 4.9 6.9 1.0 O A:HOH498 5.0 19.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Subtilisin Nat at 1.36


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Subtilisin Nat at 1.36 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:7.7 occ:1.00 O B:LEU75 2.3 4.9 1.0 O B:VAL81 2.3 5.0 1.0 O B:ILE79 2.3 6.3 1.0 OE1 B:GLN2 2.4 7.0 1.0 OD1 B:ASN77 2.4 6.5 1.0 OD1 B:ASP41 2.4 5.8 1.0 OD2 B:ASP41 2.5 6.1 1.0 CG B:ASP41 2.8 6.1 1.0 CG B:ASN77 3.4 5.8 1.0 CD B:GLN2 3.4 6.3 1.0 C B:VAL81 3.5 4.1 1.0 C B:LEU75 3.5 4.1 1.0 C B:ILE79 3.5 6.5 1.0 N B:VAL81 3.7 4.9 1.0 ND2 B:ASN77 3.8 7.7 1.0 CG B:GLN2 3.9 7.5 1.0 N B:ASN77 4.1 7.5 1.0 C B:GLY80 4.1 5.9 1.0 CA B:VAL81 4.3 5.5 1.0 N B:LEU75 4.3 4.8 1.0 CA B:GLY80 4.3 6.4 1.0 CB B:ASP41 4.4 5.7 1.0 CA B:LEU75 4.4 5.0 1.0 N B:GLY80 4.4 7.2 1.0 CG1 B:ILE79 4.4 7.6 1.0 N B:ILE79 4.4 8.3 1.0 N B:ASN76 4.5 4.9 1.0 CB B:GLN2 4.5 7.0 1.0 CA B:ILE79 4.5 7.3 1.0 N B:LEU82 4.6 4.9 1.0 NE2 B:GLN2 4.6 7.9 1.0 CB B:ASN77 4.6 7.8 1.0 CA B:ASN76 4.6 7.4 1.0 CA B:ASN77 4.7 7.1 1.0 C B:ASN77 4.7 8.8 1.0 O B:ASN77 4.7 9.9 1.0 C B:ALA74 4.8 4.4 1.0 CB B:LEU75 4.8 5.2 1.0 C B:ASN76 4.8 7.0 1.0 CA B:LEU82 4.8 4.3 1.0 O B:GLY80 4.8 6.5 1.0 CB B:ALA74 4.9 4.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Subtilisin Nat at 1.36


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Subtilisin Nat at 1.36 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:32.7 occ:1.00 O B:ALA169 2.8 7.1 1.0 O B:THR174 2.8 5.1 1.0 O B:HOH481 2.9 14.6 1.0 OD2 B:ASP197 2.9 8.5 1.0 O B:TYR171 3.1 8.2 1.0 O B:HOH491 3.1 22.2 1.0 O B:GLU195 3.3 8.1 1.0 OG1 B:THR174 3.6 6.8 1.0 CB B:ALA176 3.7 6.3 1.0 C B:THR174 3.9 4.6 1.0 C B:TYR171 3.9 7.1 1.0 N B:ALA176 3.9 4.3 1.0 CG B:ASP197 4.0 8.5 1.0 C B:ALA169 4.0 6.3 1.0 CA B:PRO172 4.3 7.0 1.0 NH2 B:ARG247 4.3 8.1 1.0 C B:GLU195 4.3 7.5 1.0 OD1 B:ASP197 4.3 9.1 1.0 C B:LYS170 4.4 9.1 1.0 O B:LYS170 4.4 9.9 1.0 O B:PRO172 4.4 6.4 1.0 CB B:GLU195 4.4 8.2 1.0 CA B:ALA176 4.5 4.2 1.0 C B:PRO172 4.5 5.9 1.0 N B:PRO172 4.5 6.8 1.0 N B:THR174 4.6 4.9 1.0 N B:TYR171 4.6 6.9 1.0 CA B:THR174 4.6 4.7 1.0 CA B:GLU195 4.6 7.4 1.0 C B:ILE175 4.7 4.5 1.0 CB B:THR174 4.7 6.0 1.0 N B:ILE175 4.7 4.8 1.0 CA B:LYS170 4.8 9.1 1.0 CA B:ILE175 4.8 3.5 1.0 N B:LYS170 4.9 7.1 1.0 CA B:ALA169 4.9 5.4 1.0 CA B:TYR171 4.9 7.4 1.0 O B:HOH508 5.0 20.4 1.0

K.Watanabe, H.Ushijima, N.Fuchita, T.Kajiwara, H.Motoshima, G.Ueno, K.Watanabe. N/A N/A.