Calcium in PDB 3d4d: Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs Y91E at Cryogenic Temperature

All present enzymatic activity of Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs Y91E at Cryogenic Temperature:
3.1.31.1;

The structure of Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs Y91E at Cryogenic Temperature, PDB code: 3d4d was solved by V.S.Khangulov, J.L.Schlessman, E.B.Garcia-Moreno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.38 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	31.022, 81.293, 60.385, 90.00, 90.05, 90.00
R / Rfree (%)	23.3 / 29

The binding sites of Calcium atom in the Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs Y91E at Cryogenic Temperature (pdb code 3d4d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs Y91E at Cryogenic Temperature, PDB code: 3d4d:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs Y91E at Cryogenic Temperature


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 Staphylococcal Nuclease Variant Delta+Phs Y91E at Cryogenic Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca150 b:14.8 occ:1.00 O A:HOH222 2.4 7.7 1.0 O A:HOH218 2.5 6.2 1.0 O A:THR41 2.8 6.5 1.0 OD2 A:ASP21 2.8 4.2 1.0 OD1 A:ASP40 2.8 9.1 1.0 OE2 A:GLU43 3.1 11.5 1.0 O4P A:THP151 3.2 4.2 1.0 OD1 A:ASP21 3.5 5.7 1.0 CG A:ASP21 3.5 5.0 1.0 O A:HOH219 3.7 13.1 1.0 C A:THR41 3.9 7.2 1.0 CG A:ASP40 4.0 6.9 1.0 OG1 A:THR41 4.0 7.4 1.0 N A:THR41 4.0 6.2 1.0 O A:HOH176 4.0 12.0 1.0 P2 A:THP151 4.0 6.7 1.0 CD A:GLU43 4.1 12.1 1.0 O5P A:THP151 4.1 7.2 1.0 O A:HOH201 4.1 16.0 1.0 NH2 A:ARG35 4.2 2.0 1.0 CA A:THR41 4.5 6.8 1.0 OD2 A:ASP40 4.7 8.5 1.0 CZ A:ARG35 4.7 3.0 1.0 O6P A:THP151 4.7 7.2 1.0 CA A:ASP40 4.7 5.6 1.0 C A:ASP40 4.7 6.1 1.0 C A:PRO42 4.7 9.0 1.0 O A:HOH223 4.7 16.0 1.0 O A:PRO42 4.8 9.4 1.0 CG A:GLU43 4.8 10.9 1.0 N A:GLU43 4.8 9.6 1.0 OE1 A:GLU43 4.8 12.1 1.0 NE A:ARG35 4.8 3.5 1.0 CB A:THR41 4.9 6.4 1.0 CB A:ASP40 5.0 6.1 1.0 O A:HOH224 5.0 21.3 1.0 CB A:ASP21 5.0 4.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs Y91E at Cryogenic Temperature


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 Staphylococcal Nuclease Variant Delta+Phs Y91E at Cryogenic Temperature within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca150 b:16.8 occ:1.00 OD1 B:ASP40 2.6 9.0 1.0 O B:THR41 2.9 7.8 1.0 OD2 B:ASP21 2.9 3.6 1.0 O B:HOH237 3.0 3.7 1.0 O B:HOH238 3.1 5.5 1.0 OE2 B:GLU43 3.1 15.8 1.0 O6P B:THP151 3.2 8.7 1.0 O B:HOH198 3.6 30.1 1.0 CG B:ASP21 3.8 6.0 1.0 CG B:ASP40 3.8 6.7 1.0 OD1 B:ASP21 3.8 7.1 1.0 N B:THR41 4.0 6.4 1.0 C B:THR41 4.0 7.7 1.0 O B:HOH204 4.0 22.1 1.0 OG1 B:THR41 4.1 7.9 1.0 P2 B:THP151 4.1 8.9 1.0 NH2 B:ARG35 4.1 2.0 1.0 O B:HOH175 4.1 11.7 1.0 CD B:GLU43 4.2 15.2 1.0 O4P B:THP151 4.3 8.2 1.0 OD2 B:ASP40 4.5 6.5 1.0 CA B:THR41 4.5 7.1 1.0 CA B:ASP40 4.5 5.5 1.0 C B:ASP40 4.6 5.5 1.0 CZ B:ARG35 4.7 2.0 1.0 O5P B:THP151 4.7 8.4 1.0 CB B:ASP40 4.8 5.3 1.0 O B:PRO42 4.9 9.4 1.0 C B:PRO42 5.0 9.1 1.0 NE B:ARG35 5.0 2.0 1.0 CB B:THR41 5.0 7.2 1.0 OE1 B:GLU43 5.0 16.1 1.0

V.S.Khangulov, J.L.Schlessman, E.B.Garcia-Moreno. Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs Y91E at Cryogenic Temperature. To Be Published.