Calcium in PDB 2asj: Oxog-Modified Preinsertion Binary Complex

All present enzymatic activity of Oxog-Modified Preinsertion Binary Complex:
2.7.7.7;

The structure of Oxog-Modified Preinsertion Binary Complex, PDB code: 2asj was solved by O.Rechkoblit, L.Malinina, Y.Cheng, V.Kuryavyi, S.Broyde, N.E.Geacintov, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.219, 182.958, 52.209, 90.00, 107.68, 90.00
R / Rfree (%)	24.6 / 31.8

The binding sites of Calcium atom in the Oxog-Modified Preinsertion Binary Complex (pdb code 2asj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Oxog-Modified Preinsertion Binary Complex, PDB code: 2asj:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Oxog-Modified Preinsertion Binary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Oxog-Modified Preinsertion Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca416 b:75.2 occ:1.00 O E:HOH507 2.1 43.3 1.0 O D:HOH503 2.7 59.4 1.0 N6 E:DA916 4.4 55.0 1.0 O E:HOH505 4.7 65.4 1.0 C5 E:DC914 4.7 62.4 1.0 O D:HOH506 4.7 61.8 1.0 N4 E:DC914 4.8 62.2 1.0 C5 E:DC915 4.9 62.5 1.0 C4 E:DC914 4.9 62.2 1.0 N4 E:DC915 5.0 62.4 1.0

Calcium binding site 2 out of 3 in the Oxog-Modified Preinsertion Binary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Oxog-Modified Preinsertion Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca415 b:32.7 occ:1.00 OP1 D:DDG813 2.3 32.5 1.0 OE2 A:GLU106 2.5 58.5 1.0 OD2 A:ASP7 2.5 47.4 1.0 O A:HOH501 2.8 42.9 1.0 OD1 A:ASP105 2.8 54.8 1.0 O D:HOH502 2.8 72.7 1.0 CD A:GLU106 3.2 55.8 1.0 CG A:GLU106 3.2 53.6 1.0 P D:DDG813 3.5 33.3 1.0 CG A:ASP7 3.6 50.2 1.0 CG A:ASP105 3.8 54.2 1.0 OP2 D:DDG813 4.0 32.6 1.0 OD1 A:ASP7 4.3 55.0 1.0 O5' D:DDG813 4.3 34.3 1.0 OE1 A:GLU106 4.3 55.9 1.0 OD2 A:ASP105 4.4 57.9 1.0 O A:HOH502 4.4 48.0 1.0 O A:ASP105 4.5 53.1 1.0 CB A:ASP7 4.6 48.7 1.0 CB A:GLU106 4.7 53.1 1.0 O3' D:DA812 4.7 32.9 1.0 C A:ASP105 4.9 53.4 1.0 C5' D:DDG813 4.9 35.9 1.0 CB A:ASP105 5.0 53.8 1.0

Calcium binding site 3 out of 3 in the Oxog-Modified Preinsertion Binary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Oxog-Modified Preinsertion Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1415 b:52.4 occ:1.00 O B:HOH1501 2.2 51.2 1.0 OP1 H:DDG1813 2.3 48.2 1.0 OE2 B:GLU1106 2.6 50.4 1.0 OD2 B:ASP1007 2.6 49.8 1.0 OD1 B:ASP1105 2.7 53.2 1.0 CD B:GLU1106 3.4 51.7 1.0 CG B:GLU1106 3.5 51.3 1.0 CG B:ASP1105 3.6 53.1 1.0 CG B:ASP1007 3.7 50.8 1.0 P H:DDG1813 3.8 41.4 1.0 O H:HOH1502 3.8 56.6 1.0 OD2 B:ASP1105 3.9 54.5 1.0 O B:ASP1105 3.9 51.4 1.0 OD1 B:ASP1007 4.3 54.2 1.0 O B:HOH40 4.4 43.6 1.0 O5' H:DDG1813 4.4 42.2 1.0 C5' H:DDG1813 4.5 40.1 1.0 C B:ASP1105 4.5 51.4 1.0 OP2 H:DDG1813 4.6 40.7 1.0 CB B:GLU1106 4.6 50.0 1.0 OG B:SER1103 4.6 53.8 1.0 OE1 B:GLU1106 4.6 52.4 1.0 CB B:ASP1105 4.8 51.8 1.0 O3' H:DA1812 4.8 41.0 1.0 CB B:ASP1007 4.9 49.5 1.0

O.Rechkoblit, L.Malinina, Y.Cheng, V.Kuryavyi, S.Broyde, N.E.Geacintov, D.J.Patel. Stepwise Translocation of DPO4 Polymerase During Error-Free Bypass of An Oxog Lesion Plos Biol. V. 4 1 2006.
ISSN: ISSN 1544-9173
PubMed: 16379496
DOI: 10.1371/JOURNAL.PBIO.0040011