Calcium in PDB 2asl: Oxog-Modified Postinsertion Binary Complex

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

The structure of Oxog-Modified Postinsertion Binary Complex, PDB code: 2asl 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 / 2.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.218, 101.024, 84.925, 90.00, 97.16, 90.00
R / Rfree (%)	23.2 / 28.7

The binding sites of Calcium atom in the Oxog-Modified Postinsertion Binary Complex (pdb code 2asl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Oxog-Modified Postinsertion Binary Complex, PDB code: 2asl:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Oxog-Modified Postinsertion 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 Postinsertion Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca416 b:36.5 occ:1.00 O D:HOH509 2.3 43.5 1.0 O D:HOH506 2.4 30.4 1.0 O E:HOH504 2.6 40.4 1.0 O E:HOH507 2.7 27.2 1.0 O E:HOH508 2.7 45.7 1.0 O D:HOH505 2.9 34.2 1.0 N2 D:DG806 4.2 10.3 1.0 O2 E:DC915 4.4 14.6 1.0 N2 D:DG805 4.5 10.3 1.0 O4' E:DA916 4.6 14.7 1.0 C4' E:DA916 4.8 15.0 1.0 N3 D:DG806 4.8 11.7 1.0 C5' E:DA916 4.8 15.2 1.0 C2 D:DG806 5.0 10.9 1.0

Calcium binding site 2 out of 4 in the Oxog-Modified Postinsertion 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 Postinsertion Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca1416 b:30.8 occ:1.00 O H:HOH1504 2.3 50.8 1.0 O H:HOH1509 2.3 48.5 1.0 O H:HOH1508 2.5 29.8 1.0 O J:HOH1507 3.0 36.4 1.0 O H:HOH1506 3.2 43.1 1.0 C5' J:DA1916 4.6 14.3 1.0 O J:HOH1505 4.6 46.3 1.0 C4' J:DA1916 4.6 13.8 1.0 C5' H:DA1807 4.8 15.1 1.0 C4' H:DA1807 4.8 14.4 1.0 O4' J:DA1916 4.8 13.8 1.0

Calcium binding site 3 out of 4 in the Oxog-Modified Postinsertion 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 Postinsertion Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca415 b:25.0 occ:1.00 O A:HOH502 1.7 48.6 1.0 O A:HOH503 1.9 18.1 1.0 O A:HOH537 2.4 32.2 1.0 OD2 A:ASP7 2.6 16.8 1.0 O A:HOH501 2.7 23.5 1.0 OD2 A:ASP105 2.7 17.4 1.0 O A:HOH547 2.9 12.4 1.0 OP1 D:DOC814 2.9 32.4 1.0 CG A:ASP7 3.4 15.0 1.0 OD1 A:ASP7 3.4 15.9 1.0 OD1 A:ASP105 3.5 14.1 1.0 CG A:ASP105 3.5 15.4 1.0 OE1 A:GLU106 3.8 17.6 1.0 CG A:GLU106 3.8 15.5 1.0 CD A:GLU106 4.0 17.5 1.0 P D:DOC814 4.0 32.7 1.0 O5' D:DOC814 4.0 30.4 1.0 C5' D:DOC814 4.1 32.1 1.0 O A:HOH534 4.4 31.6 1.0 CB A:ASP7 4.8 13.4 1.0 OE2 A:GLU106 4.9 18.9 1.0 OP2 D:DOC814 4.9 29.1 1.0 CB A:ASP105 4.9 15.3 1.0 O A:PHE8 5.0 13.5 1.0 O A:ASP105 5.0 15.3 1.0

Calcium binding site 4 out of 4 in the Oxog-Modified Postinsertion Binary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Oxog-Modified Postinsertion Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1415 b:14.0 occ:1.00 OD2 B:ASP1105 2.3 14.1 1.0 OD2 B:ASP1007 2.3 15.3 1.0 OP1 H:DOC1814 2.6 35.6 1.0 O B:HOH1501 2.6 20.4 1.0 OD1 B:ASP1105 2.9 16.2 1.0 O B:HOH1503 2.9 12.8 1.0 CG B:ASP1105 3.0 13.8 1.0 OE1 B:GLU1106 3.0 20.5 1.0 CG B:GLU1106 3.3 15.4 1.0 CD B:GLU1106 3.3 18.7 1.0 CG B:ASP1007 3.5 14.3 1.0 P H:DOC1814 3.8 33.5 1.0 C5' H:DOC1814 3.9 35.8 1.0 O5' H:DOC1814 3.9 34.3 1.0 OD1 B:ASP1007 4.0 16.3 1.0 O B:HOH1502 4.2 35.9 1.0 OE2 B:GLU1106 4.2 20.5 1.0 CB B:ASP1105 4.4 13.7 1.0 O B:ASP1105 4.5 13.7 1.0 OP2 H:DOC1814 4.6 32.3 1.0 CB B:ASP1007 4.7 13.6 1.0 CB B:GLU1106 4.8 13.9 1.0 C B:ASP1105 4.8 13.6 1.0 OG B:SER1103 4.8 13.3 1.0 O B:HOH131 4.8 38.9 1.0 NZ B:LYS1152 4.9 13.8 1.0 C4' H:DOC1814 4.9 36.8 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