Calcium in PDB 2odi: Restriction Endonuclease Bcni-Cognate Dna Substrate Complex

The structure of Restriction Endonuclease Bcni-Cognate Dna Substrate Complex, PDB code: 2odi was solved by M.Sokolowska, M.Kaus-Drobek, H.Czapinska, G.Tamulaitis, R.H.Szczepanowski, C.Urbanke, V.Siksnys, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.38 / 1.45
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.553, 87.870, 79.391, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 19.9

The structure of Restriction Endonuclease Bcni-Cognate Dna Substrate Complex also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Restriction Endonuclease Bcni-Cognate Dna Substrate Complex (pdb code 2odi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Restriction Endonuclease Bcni-Cognate Dna Substrate Complex, PDB code: 2odi:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Restriction Endonuclease Bcni-Cognate Dna Substrate Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Restriction Endonuclease Bcni-Cognate Dna Substrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:8.1 occ:1.00 OD2 A:ASP55 2.1 20.5 1.0 OP1 C:DC0 2.3 9.0 1.0 OE2 A:GLU60 2.3 12.4 1.0 O A:HOH707 2.4 10.3 1.0 O A:LEU61 2.4 9.6 1.0 O C:HOH7 2.4 8.9 1.0 CG A:ASP55 3.1 17.0 1.0 CD A:GLU60 3.2 14.4 1.0 OD1 A:ASP55 3.5 22.4 1.0 P C:DC0 3.5 8.6 1.0 C A:LEU61 3.5 9.4 1.0 OE1 A:GLU60 3.7 15.0 1.0 O A:HOH749 4.0 14.5 1.0 CA A:CA703 4.1 19.2 0.5 O5' C:DC0 4.1 7.3 1.0 OP2 C:DC0 4.1 9.3 1.0 N A:LEU61 4.1 9.7 1.0 CA A:LEU61 4.3 9.6 1.0 C5' C:DC0 4.3 7.3 1.0 CG A:GLU60 4.3 11.3 1.0 NZ A:LYS62 4.4 14.8 1.0 CB A:ASP55 4.4 13.1 1.0 CD A:LYS62 4.4 15.9 1.0 CB A:LEU61 4.5 9.3 1.0 OE2 A:GLU41 4.5 17.7 1.0 O C:HOH9 4.6 9.0 1.0 N A:LYS62 4.6 9.3 1.0 O3' C:DC-1 4.7 8.0 1.0 CA A:LYS62 4.9 9.8 1.0 OP2 C:DG1 4.9 8.6 1.0 O A:HOH768 4.9 21.1 1.0 CE A:LYS62 4.9 15.1 1.0 O3' C:DC0 4.9 7.5 1.0

Calcium binding site 2 out of 3 in the Restriction Endonuclease Bcni-Cognate Dna Substrate Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Restriction Endonuclease Bcni-Cognate Dna Substrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:19.2 occ:0.50 O A:HOH749 2.2 14.5 1.0 O A:HOH768 2.2 21.1 1.0 OD1 A:ASP55 2.4 22.4 1.0 OD1 A:ASN49 2.4 20.7 1.0 OP1 C:DC0 2.6 9.0 1.0 O3' C:DC-1 2.9 8.0 1.0 P C:DC0 3.4 8.6 1.0 CG A:ASP55 3.5 17.0 1.0 CG A:ASN49 3.5 20.6 1.0 O A:HOH794 3.5 20.9 1.0 O A:HOH884 3.6 27.8 1.0 OD2 A:ASP55 3.9 20.5 1.0 CB A:ASN49 3.9 21.4 1.0 CA A:ASN49 4.0 21.6 1.0 CA A:CA701 4.1 8.1 1.0 C3' C:DC-1 4.2 7.7 1.0 NZ A:LYS152 4.2 18.2 0.5 O A:HOH747 4.3 13.7 1.0 NZ A:LYS152 4.3 13.5 0.5 O A:HOH856 4.3 28.4 1.0 OP2 C:DC0 4.3 9.3 1.0 OE2 A:GLU41 4.4 17.7 1.0 C4' C:DC-1 4.4 7.5 1.0 OE1 A:GLU60 4.5 15.0 1.0 O5' C:DC0 4.5 7.3 1.0 ND2 A:ASN49 4.6 18.6 1.0 OE2 A:GLU60 4.6 12.4 1.0 C5' C:DC-1 4.6 8.4 1.0 C5' C:DC0 4.7 7.3 1.0 CB A:ASP55 4.7 13.1 1.0 N A:ASN50 4.8 21.4 1.0 O A:HOH707 4.9 10.3 1.0 N A:ASN49 4.9 22.1 1.0 C A:ASN49 5.0 21.6 1.0

Calcium binding site 3 out of 3 in the Restriction Endonuclease Bcni-Cognate Dna Substrate Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Restriction Endonuclease Bcni-Cognate Dna Substrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:7.2 occ:1.00 OP1 E:DC0 2.3 9.4 1.0 O B:LEU61 2.3 9.5 1.0 O B:HOH736 2.3 9.5 1.0 OE2 B:GLU60 2.4 12.7 1.0 O E:HOH80 2.4 9.3 1.0 OD2 B:ASP55 2.5 22.4 1.0 OD1 B:ASP55 2.6 19.1 1.0 CG B:ASP55 2.9 17.1 1.0 CD B:GLU60 3.3 14.2 1.0 C B:LEU61 3.5 9.7 1.0 P E:DC0 3.5 7.9 1.0 OE1 B:GLU60 3.8 14.9 1.0 O B:HOH739 3.9 15.8 1.0 N B:LEU61 4.1 9.9 1.0 O5' E:DC0 4.1 7.5 1.0 OP2 E:DC0 4.1 9.5 1.0 CA B:LEU61 4.2 9.8 1.0 C5' E:DC0 4.3 6.5 1.0 CB B:ASP55 4.4 15.1 1.0 NZ B:LYS62 4.4 14.7 1.0 CG B:GLU60 4.4 12.4 1.0 CB B:LEU61 4.5 10.0 1.0 CG B:LYS62 4.5 14.7 1.0 O E:HOH75 4.5 9.0 1.0 N B:LYS62 4.5 10.0 1.0 ND2 B:ASN49 4.6 18.4 1.0 O3' E:DC-1 4.7 7.3 1.0 CA B:LYS62 4.8 10.5 1.0 OE1 B:GLU41 4.8 15.7 1.0 OP2 E:DG1 4.9 9.1 1.0 O3' E:DC0 4.9 7.1 1.0

M.Sokolowska, M.Kaus-Drobek, H.Czapinska, G.Tamulaitis, R.H.Szczepanowski, C.Urbanke, V.Siksnys, M.Bochtler. Monomeric Restriction Endonuclease Bcni in the Apo Form and in An Asymmetric Complex with Target Dna. J.Mol.Biol. V. 369 722 2007.
ISSN: ISSN 0022-2836
PubMed: 17445830
DOI: 10.1016/J.JMB.2007.03.018