Calcium in PDB 3lzj: RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 7,8- Dihydro-8-Oxoguanine

All present enzymatic activity of RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 7,8- Dihydro-8-Oxoguanine:
2.7.7.7;

The structure of RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 7,8- Dihydro-8-Oxoguanine, PDB code: 3lzj was solved by M.Wang, J.Beckman, G.Blaha, J.Wang, W.H.Konigsberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.81 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.394, 121.089, 122.857, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 25.1

The binding sites of Calcium atom in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 7,8- Dihydro-8-Oxoguanine (pdb code 3lzj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 7,8- Dihydro-8-Oxoguanine, PDB code: 3lzj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 7,8- Dihydro-8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 7,8- Dihydro-8-Oxoguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca905 b:31.4 occ:1.00 OD1 A:ASP623 2.2 9.2 1.0 O A:LEU412 2.2 2.5 1.0 O1G A:CTP904 2.3 2.0 1.0 O2A A:CTP904 2.4 2.0 1.0 O2B A:CTP904 2.5 2.0 1.0 OD2 A:ASP411 2.6 10.0 1.0 OD1 A:ASP411 3.1 19.0 1.0 CG A:ASP411 3.1 11.6 1.0 CG A:ASP623 3.3 6.9 1.0 PB A:CTP904 3.4 2.0 1.0 C A:LEU412 3.5 2.4 1.0 PG A:CTP904 3.5 2.0 1.0 OD2 A:ASP623 3.7 8.8 1.0 PA A:CTP904 3.7 2.0 1.0 O A:HOH1046 3.7 4.6 1.0 CA A:CA907 3.8 69.7 1.0 O3A A:CTP904 3.8 4.0 1.0 O3B A:CTP904 3.8 2.0 1.0 N A:LEU412 4.0 3.2 1.0 O2G A:CTP904 4.1 3.0 1.0 O A:HOH1537 4.3 13.9 1.0 C5' A:CTP904 4.3 2.0 1.0 CA A:LEU412 4.3 5.2 1.0 N A:SER414 4.4 2.0 1.0 CB A:ASP411 4.4 9.6 1.0 N A:THR413 4.5 2.0 1.0 O5' A:CTP904 4.5 2.0 1.0 C A:ASP411 4.6 5.8 1.0 CB A:ASP623 4.6 7.0 1.0 CA A:THR413 4.6 2.0 1.0 C A:THR413 4.7 2.0 1.0 O3G A:CTP904 4.7 2.0 1.0 O1B A:CTP904 4.8 2.0 1.0 N A:LEU415 4.8 2.0 1.0 O1A A:CTP904 4.8 2.0 1.0 CB A:LEU412 4.8 3.9 1.0 CA A:ASP411 5.0 8.0 1.0

Calcium binding site 2 out of 4 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 7,8- Dihydro-8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 7,8- Dihydro-8-Oxoguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca906 b:54.7 occ:1.00 O A:ASN505 2.3 2.0 1.0 O A:LYS531 2.4 2.0 1.0 O A:HOH1183 2.5 2.0 1.0 OD1 A:ASN507 2.6 2.0 1.0 O A:HOH1314 2.8 2.0 1.0 O A:HOH1116 2.8 2.0 1.0 C A:LYS531 3.4 3.5 1.0 C A:ASN505 3.5 2.0 1.0 CG A:ASN507 3.6 6.7 1.0 ND2 A:ASN507 4.0 2.0 1.0 CA A:LYS531 4.1 3.2 1.0 CB A:ASN505 4.1 6.6 1.0 O A:HOH1525 4.3 10.8 1.0 N A:LYS532 4.3 3.7 1.0 CA A:ASN505 4.4 4.7 1.0 C A:PRO506 4.4 2.4 1.0 N A:PRO506 4.4 2.0 1.0 O A:ALA502 4.4 4.4 1.0 CA A:PRO506 4.4 2.0 1.0 N A:ASN507 4.5 4.3 1.0 CA A:LYS532 4.6 2.0 1.0 CB A:LYS531 4.6 6.7 1.0 O A:LEU533 4.7 2.0 1.0 CB A:ASN507 4.8 5.7 1.0 O A:PRO506 4.8 2.0 1.0 C A:LYS532 5.0 2.0 1.0

Calcium binding site 3 out of 4 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 7,8- Dihydro-8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 7,8- Dihydro-8-Oxoguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca907 b:69.7 occ:1.00 OD2 A:ASP623 2.4 8.8 1.0 O A:HOH1537 2.6 13.9 1.0 O2A A:CTP904 2.8 2.0 1.0 OD2 A:ASP411 2.9 10.0 1.0 O A:HOH1156 2.9 12.4 1.0 O A:HOH1150 3.1 12.9 1.0 CG A:ASP623 3.4 6.9 1.0 C3' P:DOC115 3.7 2.0 1.0 OD1 A:ASP623 3.7 9.2 1.0 CA A:CA905 3.8 31.4 1.0 CB A:SER624 3.8 4.4 1.0 CG A:ASP411 3.9 11.6 1.0 PA A:CTP904 3.9 2.0 1.0 O A:HOH1046 4.0 4.6 1.0 O A:HOH1027 4.2 15.8 1.0 CB A:ASP411 4.3 9.6 1.0 O1A A:CTP904 4.3 2.0 1.0 C5' P:DOC115 4.4 8.0 1.0 OG A:SER624 4.4 12.0 1.0 O5' A:CTP904 4.5 2.0 1.0 C4' P:DOC115 4.6 2.0 1.0 C5' A:CTP904 4.6 2.0 1.0 N A:SER624 4.7 4.7 1.0 O5' P:DOC115 4.7 7.5 1.0 O A:ASP621 4.7 2.0 1.0 C A:ASP623 4.7 6.9 1.0 CA A:SER624 4.7 5.6 1.0 CB A:ASP623 4.8 7.0 1.0 OD1 A:ASP411 4.9 19.0 1.0 C2' P:DOC115 5.0 2.0 1.0 OE1 A:GLU686 5.0 25.9 1.0 OE2 A:GLU686 5.0 31.7 1.0 O A:ASP623 5.0 6.4 1.0 O1G A:CTP904 5.0 2.0 1.0

Calcium binding site 4 out of 4 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 7,8- Dihydro-8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 7,8- Dihydro-8-Oxoguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca908 b:59.6 occ:1.00 O A:HOH1566 2.4 24.5 1.0 OD2 A:ASP515 2.5 14.8 1.0 O A:HOH1369 2.6 19.1 1.0 O A:HOH1357 2.8 38.5 1.0 O A:HOH1565 2.8 16.9 1.0 OD1 A:ASP515 2.9 9.7 1.0 CG A:ASP515 3.0 8.0 1.0 O A:HOH1101 3.9 12.3 1.0 CB A:ASP515 4.5 2.0 1.0

J.Beckman, M.Wang, G.Blaha, J.Wang, W.H.Konigsberg. Substitution of Ala For TYR567 in RB69 Dna Polymerase Allows Damp to Be Inserted Opposite 7,8-Dihydro-8-Oxoguanine . Biochemistry V. 49 4116 2010.
ISSN: ISSN 0006-2960
PubMed: 20411947
DOI: 10.1021/BI100102S