Calcium in PDB 2pfj: Crystal Structure of T7 Endo I Resolvase in Complex with A Holliday Junction

All present enzymatic activity of Crystal Structure of T7 Endo I Resolvase in Complex with A Holliday Junction:
3.1.21.2;

The structure of Crystal Structure of T7 Endo I Resolvase in Complex with A Holliday Junction, PDB code: 2pfj was solved by J.M.Hadden, A.C.Declais, S.B.Carr, D.M.Lilley, S.E.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	11.93 / 3.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.977, 92.977, 124.265, 90.00, 90.00, 120.00
R / Rfree (%)	26.7 / 29.8

The binding sites of Calcium atom in the Crystal Structure of T7 Endo I Resolvase in Complex with A Holliday Junction (pdb code 2pfj). 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 T7 Endo I Resolvase in Complex with A Holliday Junction, PDB code: 2pfj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of T7 Endo I Resolvase in Complex with A Holliday Junction


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 T7 Endo I Resolvase in Complex with A Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca150 b:89.4 occ:1.00 OD2 A:ASP55 2.2 88.6 1.0 OE2 A:GLU65 2.2 89.1 1.0 O A:THR66 2.2 85.9 1.0 OP1 Y:DT8 2.4 98.3 1.0 CG A:ASP55 3.0 85.5 1.0 CD A:GLU65 3.1 87.4 1.0 OD1 A:ASP55 3.2 93.7 1.0 CA Y:CA30 3.2 96.4 0.8 OG1 A:THR66 3.4 83.7 1.0 P Y:DT8 3.4 98.3 1.0 C A:THR66 3.4 83.6 1.0 OE1 A:GLU65 3.5 89.3 1.0 OP2 Y:DT8 3.5 96.8 1.0 N A:THR66 4.0 83.5 1.0 CA A:THR66 4.2 83.6 1.0 OE2 B:GLU20 4.2 0.3 1.0 CG A:GLU65 4.3 84.8 1.0 CB A:THR66 4.4 83.3 1.0 CB A:ASP55 4.4 82.5 1.0 N A:ALA67 4.5 82.8 1.0 O5' Y:DT8 4.5 0.7 1.0 C5' Y:DT8 4.6 0.1 1.0 OP2 Y:DC9 4.6 0.6 1.0 O3' Y:DG7 4.6 94.1 1.0 CA A:ALA67 4.7 81.8 1.0 C A:GLU65 4.8 83.3 1.0 OP1 Y:DC9 4.8 0.8 1.0 CD B:GLU20 5.0 0.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of T7 Endo I Resolvase in Complex with A Holliday Junction


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 T7 Endo I Resolvase in Complex with A Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ Y:Ca30 b:96.4 occ:0.75 OP1 Y:DT8 2.1 98.3 1.0 OD1 A:ASP55 2.2 93.7 1.0 O3' Y:DG7 2.9 94.1 1.0 P Y:DT8 2.9 98.3 1.0 CG A:ASP55 3.1 85.5 1.0 CA A:CA150 3.2 89.4 1.0 OD2 A:ASP55 3.5 88.6 1.0 C3' Y:DG7 3.6 89.5 1.0 O A:THR53 3.6 77.8 1.0 OP2 Y:DT8 3.8 96.8 1.0 OE1 A:GLU65 3.8 89.3 1.0 OE2 B:GLU37 3.9 86.9 1.0 OE2 B:GLU20 4.0 0.3 1.0 N A:ASP55 4.2 80.5 1.0 OE2 A:GLU65 4.2 89.1 1.0 O5' Y:DT8 4.2 0.7 1.0 CB A:ASP55 4.3 82.5 1.0 C4' Y:DG7 4.3 86.1 1.0 CA A:ASP55 4.3 81.6 1.0 CD A:GLU65 4.5 87.4 1.0 C5' Y:DG7 4.6 80.1 1.0 CD B:GLU37 4.7 86.2 1.0 CG B:GLU37 4.8 86.1 1.0 C A:PRO54 4.8 79.5 1.0 C A:THR53 4.8 77.2 1.0 C2' Y:DG7 4.9 87.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of T7 Endo I Resolvase in Complex with A Holliday Junction


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 T7 Endo I Resolvase in Complex with A Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca150 b:89.7 occ:1.00 OD2 B:ASP55 2.2 88.7 1.0 OE2 B:GLU65 2.2 89.1 1.0 O B:THR66 2.2 85.7 1.0 OP1 Z:DC8 2.4 0.8 1.0 CD B:GLU65 3.0 87.7 1.0 CG B:ASP55 3.1 85.5 1.0 CA Z:CA30 3.3 96.5 0.8 OD1 B:ASP55 3.3 93.6 1.0 OE1 B:GLU65 3.3 89.3 1.0 O5' Z:DC8 3.4 0.6 1.0 OG1 B:THR66 3.4 83.7 1.0 C B:THR66 3.4 83.5 1.0 P Z:DC8 3.4 1.0 1.0 N B:THR66 3.9 83.3 1.0 OP2 Z:DT9 4.0 0.2 1.0 CA B:THR66 4.1 83.5 1.0 OP1 Z:DT9 4.2 0.2 1.0 CG B:GLU65 4.2 84.7 1.0 CB B:THR66 4.4 83.4 1.0 OP2 Z:DC8 4.4 0.6 1.0 N B:ALA67 4.5 82.7 1.0 CB B:ASP55 4.5 82.5 1.0 P Z:DT9 4.5 0.7 1.0 O3' Z:DC7 4.6 0.7 1.0 OE2 A:GLU20 4.6 0.4 1.0 CA B:ALA67 4.7 81.7 1.0 C B:GLU65 4.7 83.2 1.0 C5' Z:DC8 4.7 0.1 1.0 O3' Z:DC8 4.9 0.1 1.0 CA B:GLU65 5.0 83.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of T7 Endo I Resolvase in Complex with A Holliday Junction


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 T7 Endo I Resolvase in Complex with A Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ Z:Ca30 b:96.5 occ:0.75 OD1 B:ASP55 2.2 93.6 1.0 OP1 Z:DC8 2.7 0.8 1.0 CG B:ASP55 3.1 85.5 1.0 O3' Z:DC7 3.3 0.7 1.0 CA B:CA150 3.3 89.7 1.0 P Z:DC8 3.4 1.0 1.0 OD2 B:ASP55 3.4 88.7 1.0 O B:THR53 3.5 77.2 1.0 O5' Z:DC8 3.6 0.6 1.0 OE1 B:GLU65 3.8 89.3 1.0 OE2 A:GLU37 4.1 86.8 1.0 OE2 A:GLU20 4.2 0.4 1.0 N B:ASP55 4.2 80.6 1.0 CB B:ASP55 4.3 82.5 1.0 OE2 B:GLU65 4.3 89.1 1.0 CA B:ASP55 4.3 81.7 1.0 C3' Z:DC7 4.4 0.5 1.0 CD B:GLU65 4.5 87.7 1.0 C5' Z:DC8 4.6 0.1 1.0 C4' Z:DC7 4.7 0.3 1.0 C B:THR53 4.7 77.0 1.0 O5' Z:DC7 4.8 0.0 1.0 C B:PRO54 4.8 79.5 1.0 OP2 Z:DC8 4.8 0.6 1.0 CD A:GLU37 4.9 86.1 1.0 CG A:GLU37 4.9 86.1 1.0

J.M.Hadden, A.C.Declais, S.B.Carr, D.M.Lilley, S.E.Phillips. The Structural Basis of Holliday Junction Resolution By T7 Endonuclease I. Nature V. 449 621 2007.
ISSN: ISSN 0028-0836
PubMed: 17873858
DOI: 10.1038/NATURE06158