Calcium in PDB 2gko: S41 Psychrophilic Protease

All present enzymatic activity of S41 Psychrophilic Protease:
3.4.21.62;

The structure of S41 Psychrophilic Protease, PDB code: 2gko was solved by R.L.Walter, M.J.Mekel, R.A.Grayling, F.H.Arnold, P.L.Wintrode, O.Almog, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.70 / 1.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.000, 61.000, 174.770, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / 19.8

The structure of S41 Psychrophilic Protease also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the S41 Psychrophilic Protease (pdb code 2gko). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the S41 Psychrophilic Protease, PDB code: 2gko:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the S41 Psychrophilic Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of S41 Psychrophilic Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca610 b:9.9 occ:1.00 OD2 A:ASP97 2.2 12.1 1.0 O A:HOH1126 2.2 14.6 1.0 OD1 A:ASN29 2.2 10.4 1.0 OE1 A:GLU49 2.3 19.5 1.0 O A:HOH630 2.3 17.3 1.0 O A:HOH657 2.3 16.1 1.0 OE2 A:GLU49 2.7 23.4 1.0 CD A:GLU49 2.8 19.1 1.0 CG A:ASP97 3.2 12.8 1.0 CG A:ASN29 3.2 10.5 1.0 CB A:ASP97 3.6 11.3 1.0 ND2 A:ASN29 3.7 10.2 1.0 O A:HOH1127 3.9 24.8 1.0 O A:HOH776 4.2 23.6 1.0 OD1 A:ASP97 4.3 10.2 1.0 NE1 A:TRP99 4.3 9.9 1.0 CG A:GLU49 4.3 13.4 1.0 O A:HOH1002 4.4 45.7 1.0 O A:HOH781 4.5 25.3 1.0 O A:GLY27 4.5 13.0 1.0 CB A:ASN29 4.6 10.6 1.0 OG1 A:THR131 4.6 14.5 1.0 O A:HOH925 4.7 41.7 1.0 CZ2 A:TRP99 4.9 12.0 1.0 CE2 A:TRP99 4.9 11.2 1.0 CB A:GLU49 5.0 11.1 1.0

Calcium binding site 2 out of 4 in the S41 Psychrophilic Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of S41 Psychrophilic Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca611 b:15.3 occ:1.00 O A:THR213 2.2 14.7 1.0 OE1 A:GLN220 2.3 17.8 1.0 O A:VAL218 2.3 17.2 1.0 OD1 A:ASP223 2.3 15.6 1.0 OD1 A:ASP216 2.4 17.7 1.0 O A:HOH626 2.4 14.3 1.0 OD2 A:ASP216 3.2 20.3 1.0 CG A:ASP216 3.2 18.9 1.0 CG A:ASP223 3.3 15.4 1.0 CD A:GLN220 3.3 16.9 1.0 C A:THR213 3.4 16.1 1.0 C A:VAL218 3.5 16.9 1.0 OD2 A:ASP223 3.6 16.4 1.0 NE2 A:GLN220 3.8 18.5 1.0 N A:GLN220 4.1 15.1 1.0 CB A:THR213 4.1 15.4 1.0 N A:VAL218 4.3 16.8 1.0 CA A:THR213 4.3 15.2 1.0 CA A:ILE219 4.3 16.1 1.0 N A:ALA214 4.4 16.3 1.0 O A:HOH702 4.4 28.6 1.0 N A:ILE219 4.4 16.5 1.0 CA A:ALA214 4.4 18.0 1.0 CA A:VAL218 4.4 17.0 1.0 CB A:ASP223 4.5 12.6 1.0 OD1 A:ASP297 4.5 16.8 1.0 CG A:GLN220 4.5 16.4 1.0 OG1 A:THR213 4.6 14.6 1.0 CB A:ASP216 4.6 18.7 1.0 C A:ILE219 4.6 16.0 1.0 CB A:GLN220 4.7 15.0 1.0 CB A:VAL218 4.8 17.4 1.0 N A:ASP216 4.8 19.3 1.0 C A:ALA214 4.8 18.6 1.0 O A:HOH651 4.9 12.8 1.0

Calcium binding site 3 out of 4 in the S41 Psychrophilic Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of S41 Psychrophilic Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca612 b:15.1 occ:1.00 O A:GLY294 2.3 16.0 1.0 OD1 A:ASP286 2.3 18.8 1.0 OD2 A:ASP298 2.3 13.2 1.0 O A:GLY296 2.3 17.9 1.0 O A:ILE287 2.3 15.4 1.0 O A:HOH642 2.4 13.8 1.0 CG A:ASP298 3.5 14.8 1.0 C A:GLY294 3.5 17.3 1.0 C A:GLY296 3.5 16.4 1.0 C A:ILE287 3.5 15.9 1.0 CG A:ASP286 3.5 20.1 1.0 N A:GLY296 3.7 16.2 1.0 OG A:SER301 3.8 12.8 1.0 N A:ILE287 3.8 16.3 1.0 C A:SER295 4.0 17.1 1.0 OD2 A:ASP286 4.0 18.3 1.0 N A:GLY294 4.1 16.6 1.0 CA A:GLY296 4.1 16.7 1.0 CA A:ILE287 4.2 15.6 1.0 OD1 A:ASP298 4.3 12.8 1.0 CB A:ASP298 4.3 13.3 1.0 N A:SER295 4.4 17.2 1.0 CA A:SER295 4.4 18.0 1.0 CA A:GLY294 4.4 16.9 1.0 C A:ASP286 4.4 17.0 1.0 CD2 A:LEU288 4.5 16.8 1.0 O A:GLY302 4.5 12.9 1.0 N A:LEU288 4.5 16.3 1.0 O A:SER295 4.5 17.3 1.0 N A:ASP298 4.6 14.3 1.0 N A:ASP297 4.6 16.3 1.0 CA A:ASP286 4.7 17.8 1.0 CB A:ASP286 4.7 17.8 1.0 CB A:ILE287 4.7 15.3 1.0 CA A:LEU288 4.7 16.9 1.0 CA A:ASP297 4.9 15.7 1.0 C A:ASP297 5.0 15.7 1.0

Calcium binding site 4 out of 4 in the S41 Psychrophilic Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of S41 Psychrophilic Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca613 b:48.8 occ:1.00 O A:HOH892 2.3 29.3 1.0 O A:HOH1029 2.4 41.3 1.0 OD1 A:ASP114 2.4 17.3 1.0 O A:HOH893 2.6 47.0 1.0 O A:HOH829 3.0 30.1 1.0 O A:HOH775 3.0 38.0 1.0 CG A:ASP114 3.5 17.4 1.0 OD2 A:ASP114 3.7 16.6 1.0 O A:GLY57 3.9 36.4 1.0 OD1 A:ASP113 4.1 30.8 1.0 O A:PHE54 4.2 14.0 1.0 O A:HOH732 4.5 19.0 1.0 O A:HOH1118 4.7 63.5 1.0 CG A:ASP113 4.8 26.4 1.0 CB A:ASP114 4.8 16.2 1.0 CG2 A:THR58 4.8 38.1 1.0 C A:GLY57 4.9 35.1 1.0

O.Almog, A.Gonzalez, N.Godin, M.De Leeuw, M.J.Mekel, D.Klein, S.Braun, G.Shoham, R.L.Walter. The Crystal Structures of the Psychrophilic Subtilisin S41 and the Mesophilic Subtilisin Sph Reveal the Same Calcium-Loaded State. Proteins V. 74 489 2009.
ISSN: ISSN 0887-3585
PubMed: 18655058
DOI: 10.1002/PROT.22175