Calcium in PDB 3c25: Crystal Structure of Noti Restriction Endonuclease Bound to Cognate Dna

The structure of Crystal Structure of Noti Restriction Endonuclease Bound to Cognate Dna, PDB code: 3c25 was solved by A.R.Lambert, D.Sussman, B.Shen, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.890, 81.712, 73.583, 90.00, 99.51, 90.00
R / Rfree (%)	22.3 / 27.7

The structure of Crystal Structure of Noti Restriction Endonuclease Bound to Cognate Dna also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Noti Restriction Endonuclease Bound to Cognate Dna (pdb code 3c25). 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 Noti Restriction Endonuclease Bound to Cognate Dna, PDB code: 3c25:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Noti Restriction Endonuclease Bound to Cognate Dna


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 Noti Restriction Endonuclease Bound to Cognate Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:0.7 occ:1.00 OD1 A:ASP160 2.4 69.8 1.0 O A:HOH946 2.6 66.9 1.0 OE2 A:GLU145 2.8 73.2 1.0 OE1 A:GLU145 3.2 73.3 1.0 CD A:GLU145 3.3 72.3 1.0 CG A:ASP160 3.5 68.7 1.0 O3' D:DC9 3.6 57.8 1.0 O A:HOH945 3.6 59.8 1.0 C4' D:DC9 3.7 57.5 1.0 N A:ASP160 3.8 68.3 1.0 C5' D:DC9 3.9 56.9 1.0 CA A:ASP160 3.9 68.1 1.0 C A:PHE159 3.9 68.3 1.0 O A:SER158 4.0 68.7 1.0 OP1 D:DG10 4.0 59.0 1.0 CB A:SER158 4.1 68.8 1.0 C A:SER158 4.2 68.6 1.0 O A:PHE159 4.2 68.4 1.0 C3' D:DC9 4.3 57.8 1.0 CB A:ASP160 4.4 68.2 1.0 OD2 A:ASP160 4.4 68.9 1.0 N A:PHE159 4.5 68.4 1.0 P D:DG10 4.5 58.7 1.0 CA A:PHE159 4.6 68.3 1.0 CG A:GLU145 4.6 71.9 1.0 OE2 A:GLU182 4.7 69.3 1.0 O D:HOH49 4.7 0.2 1.0 CA A:SER158 4.8 68.7 1.0 O4' D:DC9 4.9 58.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Noti Restriction Endonuclease Bound to Cognate Dna


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 Noti Restriction Endonuclease Bound to Cognate Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:97.8 occ:1.00 O A:HOH923 2.5 49.9 1.0 OP1 D:DG10 2.7 59.0 1.0 OE2 A:GLU182 2.9 69.3 1.0 OP2 D:DG10 3.1 58.3 1.0 O A:ILE183 3.3 66.4 1.0 P D:DG10 3.3 58.7 1.0 OD2 A:ASP160 3.3 68.9 1.0 O A:HOH946 3.4 66.9 1.0 OE1 A:GLN241 3.4 70.3 1.0 CB A:GLU182 4.0 66.4 1.0 CD A:GLU182 4.0 68.2 1.0 C A:ILE183 4.1 66.2 1.0 CD A:GLN241 4.1 69.2 1.0 CE1 A:PHE259 4.3 64.7 1.0 NE2 A:GLN241 4.3 69.7 1.0 CG A:ASP160 4.3 68.7 1.0 N A:ILE183 4.3 66.3 1.0 NE2 A:GLN184 4.4 66.4 1.0 O5' D:DG10 4.5 58.6 1.0 O3' D:DC9 4.5 57.8 1.0 CG A:GLU182 4.5 67.0 1.0 OD1 A:ASP160 4.6 69.8 1.0 C A:GLU182 4.6 66.3 1.0 CB A:GLN184 4.6 65.7 1.0 CA A:GLU182 4.7 66.4 1.0 N A:GLN184 4.8 65.9 1.0 CD1 A:PHE259 4.8 65.0 1.0 CA A:ILE183 4.9 66.2 1.0 CA A:GLN184 4.9 65.6 1.0 CG2 A:THR238 5.0 65.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Noti Restriction Endonuclease Bound to Cognate Dna


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 Noti Restriction Endonuclease Bound to Cognate Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:0.2 occ:1.00 OD1 B:ASP160 2.8 69.4 1.0 O3' C:DC9 2.9 61.1 1.0 OE2 B:GLU145 2.9 72.7 1.0 O B:HOH916 3.3 46.1 1.0 C4' C:DC9 3.6 60.7 1.0 OP1 C:DG10 3.7 61.1 1.0 CD B:GLU145 3.8 71.9 1.0 OE1 B:GLU145 3.8 73.1 1.0 C3' C:DC9 3.9 60.8 1.0 P C:DG10 3.9 61.9 1.0 C5' C:DG10 3.9 61.1 1.0 CG B:ASP160 4.0 68.9 1.0 O C:HOH40 4.0 56.1 1.0 O5' C:DG10 4.4 61.7 1.0 O4' C:DC9 4.5 60.8 1.0 C1' C:DC9 4.5 61.1 1.0 C5' C:DC9 4.5 60.1 1.0 C2' C:DC9 4.6 61.0 1.0 OD2 B:ASP160 4.6 69.5 1.0 O C:HOH42 4.7 47.4 1.0 O B:HOH946 4.8 47.7 1.0 O B:HOH930 5.0 58.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Noti Restriction Endonuclease Bound to Cognate Dna


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 Noti Restriction Endonuclease Bound to Cognate Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca804 b:89.0 occ:1.00 O B:HOH918 2.6 46.7 1.0 OE1 B:GLU182 2.9 69.1 1.0 O B:ILE183 3.2 65.9 1.0 OP1 C:DG10 3.2 61.1 1.0 OD2 B:ASP160 3.4 69.5 1.0 OP2 C:DG10 3.5 61.4 1.0 CB B:GLU182 3.7 66.2 1.0 OE1 B:GLN241 3.8 70.3 1.0 P C:DG10 3.8 61.9 1.0 C B:ILE183 3.8 65.8 1.0 CE1 B:PHE259 3.9 64.9 1.0 N B:ILE183 3.9 66.1 1.0 CD B:GLU182 3.9 68.5 1.0 C B:GLU182 4.2 66.0 1.0 CD1 B:PHE259 4.3 65.0 1.0 CD B:GLN241 4.3 69.2 1.0 CB B:GLN184 4.3 65.5 1.0 CG B:GLU182 4.3 66.9 1.0 CA B:GLU182 4.4 66.1 1.0 NE2 B:GLN241 4.4 69.2 1.0 NE2 B:GLN184 4.5 66.2 1.0 N B:GLN184 4.5 65.6 1.0 CG B:ASP160 4.5 68.9 1.0 CA B:ILE183 4.5 66.0 1.0 CG2 B:THR238 4.7 65.6 1.0 CA B:GLN184 4.7 65.4 1.0 CZ B:PHE259 4.8 64.9 1.0 O B:GLU182 4.9 66.0 1.0 O3' C:DC9 5.0 61.1 1.0 O5' C:DG10 5.0 61.7 1.0 OE2 B:GLU182 5.0 68.9 1.0

A.R.Lambert, D.Sussman, B.Shen, R.Maunus, J.Nix, J.Samuelson, S.Y.Xu, B.L.Stoddard. Structures of the Rare-Cutting Restriction Endonuclease Noti Reveal A Unique Metal Binding Fold Involved in Dna Binding. Structure V. 16 558 2008.
ISSN: ISSN 0969-2126
PubMed: 18400177
DOI: 10.1016/J.STR.2008.01.017