Calcium in PDB 2vs7: The Crystal Structure of I-Dmoi in Complex with Dna and Ca

The structure of The Crystal Structure of I-Dmoi in Complex with Dna and Ca, PDB code: 2vs7 was solved by M.J.Marcaida, J.Prieto, P.Redondo, A.D.Nadra, A.Alibes, L.Serrano, S.Grizot, P.Duchateau, F.Paques, F.J.Blanco, G.Montoya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.76 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	106.988, 70.587, 106.848, 90.00, 119.75, 90.00
R / Rfree (%)	18.7 / 22.8

The binding sites of Calcium atom in the The Crystal Structure of I-Dmoi in Complex with Dna and Ca (pdb code 2vs7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The Crystal Structure of I-Dmoi in Complex with Dna and Ca, PDB code: 2vs7:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the The Crystal Structure of I-Dmoi in Complex with Dna and Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of I-Dmoi in Complex with Dna and Ca within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1183 b:35.0 occ:1.00 OP1 B:DA14 2.2 37.5 1.0 O A:ALA116 2.3 31.3 1.0 OP2 C:DC16 2.4 33.8 1.0 O B:HOH2029 2.4 44.4 1.0 O A:HOH2022 2.4 33.7 1.0 OD2 A:ASP21 2.4 33.9 1.0 OD1 A:ASP21 2.6 31.7 1.0 CG A:ASP21 2.8 32.2 1.0 C A:ALA116 3.4 31.7 1.0 O B:HOH2031 3.6 24.4 1.0 P C:DC16 3.6 34.7 1.0 P B:DA14 3.7 39.1 1.0 CA A:ALA116 3.9 31.6 1.0 O C:HOH2035 4.0 45.3 1.0 O5' C:DC16 4.1 34.8 1.0 NE2 A:GLN42 4.3 45.6 1.0 CB A:ASP21 4.4 31.5 1.0 O A:HOH2076 4.4 54.0 1.0 C5' B:DA14 4.4 37.7 1.0 O3' B:DA13 4.4 41.3 1.0 C4' B:DA14 4.4 36.9 1.0 O A:VAL115 4.4 32.7 1.0 OP1 C:DC16 4.5 36.5 1.0 N A:GLU117 4.5 31.6 1.0 OE1 A:GLN42 4.5 46.1 1.0 O5' B:DA14 4.6 38.3 1.0 OP2 B:DA14 4.6 36.3 1.0 C5' C:DC16 4.6 34.1 1.0 CB A:ALA116 4.7 31.1 1.0 O3' C:DC15 4.8 35.1 1.0 CD A:GLN42 4.8 45.7 1.0 OE1 A:GLU117 4.8 35.7 1.0 CA A:GLU117 4.9 31.8 1.0 O3' B:DA14 5.0 34.5 1.0 N A:ALA116 5.0 31.4 1.0

Calcium binding site 2 out of 3 in the The Crystal Structure of I-Dmoi in Complex with Dna and Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of I-Dmoi in Complex with Dna and Ca within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1196 b:34.1 occ:1.00 OP1 E:DA14 2.2 32.6 1.0 OD2 D:ASP21 2.3 23.9 1.0 OP2 F:DC16 2.3 34.5 1.0 O D:ALA116 2.4 29.3 1.0 O D:HOH2085 2.4 29.7 1.0 O D:HOH2089 2.5 37.5 1.0 OD1 D:ASP21 2.7 26.1 1.0 CG D:ASP21 2.8 27.8 1.0 C D:ALA116 3.4 30.0 1.0 P F:DC16 3.6 34.8 1.0 P E:DA14 3.7 34.4 1.0 O D:HOH2006 3.7 23.1 1.0 OE1 D:GLN42 3.8 36.0 1.0 CA D:ALA116 3.8 29.9 1.0 O5' F:DC16 4.2 34.0 1.0 O D:VAL115 4.3 30.6 1.0 C5' E:DA14 4.3 31.8 1.0 CB D:ASP21 4.3 27.4 1.0 NZ D:LYS120 4.3 42.6 1.0 O D:HOH2007 4.4 50.9 1.0 OP1 F:DC16 4.4 35.1 1.0 C4' E:DA14 4.4 33.0 1.0 O3' E:DA13 4.4 35.7 1.0 O5' E:DA14 4.5 32.9 1.0 OP2 E:DA14 4.6 34.9 1.0 C5' F:DC16 4.6 36.6 1.0 N D:GLU117 4.6 31.2 1.0 CD D:GLN42 4.7 35.2 1.0 NE2 D:GLN42 4.7 34.2 1.0 CB D:ALA116 4.7 29.8 1.0 O3' F:DC15 4.7 34.4 1.0 OE1 D:GLU117 4.8 41.8 1.0 N D:ALA116 5.0 30.0 1.0

Calcium binding site 3 out of 3 in the The Crystal Structure of I-Dmoi in Complex with Dna and Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of I-Dmoi in Complex with Dna and Ca within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca1182 b:35.7 occ:1.00 OP1 H:DA14 2.2 36.7 1.0 OP2 I:DC16 2.3 34.4 1.0 O G:ALA116 2.3 32.6 1.0 O I:HOH2020 2.4 37.2 1.0 O G:HOH2020 2.5 36.5 1.0 OD2 G:ASP21 2.5 32.4 1.0 OD1 G:ASP21 2.7 30.9 1.0 CG G:ASP21 2.9 31.6 1.0 C G:ALA116 3.4 33.0 1.0 O G:HOH2004 3.6 26.3 1.0 P I:DC16 3.6 34.1 1.0 P H:DA14 3.7 37.0 1.0 CA G:ALA116 3.9 32.9 1.0 O I:HOH2022 3.9 45.9 1.0 O5' I:DC16 4.2 35.1 1.0 OE1 G:GLN42 4.3 48.1 1.0 C5' H:DA14 4.3 35.9 1.0 O3' H:DA13 4.3 39.9 1.0 OP1 I:DC16 4.4 37.3 1.0 C4' H:DA14 4.4 35.9 1.0 NE2 G:GLN42 4.4 46.2 1.0 CB G:ASP21 4.5 30.8 1.0 O G:VAL115 4.5 34.0 1.0 O5' H:DA14 4.5 37.9 1.0 O G:HOH2062 4.5 57.1 1.0 N G:GLU117 4.6 32.6 1.0 OP2 H:DA14 4.6 37.5 1.0 CD G:GLN42 4.6 45.7 1.0 CB G:ALA116 4.6 32.7 1.0 C5' I:DC16 4.7 34.0 1.0 O3' I:DC15 4.8 35.8 1.0 OE2 G:GLU117 4.9 39.3 1.0 CA G:GLU117 5.0 33.5 1.0

M.J.Marcaida, J.Prieto, P.Redondo, A.D.Nadra, A.Alibes, L.Serrano, S.Grizot, P.Duchateau, F.Paques, F.J.Blanco, G.Montoya. Crystal Structure of I-Dmoi in Complex with Its Target Dna Provides New Insights Into Meganuclease Engineering. Proc.Nat.Acad.Sci.Usa V. 105 16888 2008.
ISSN: ISSN 0027-8424
PubMed: 18974222
DOI: 10.1073/PNAS.0804795105