Calcium in PDB 3nae: RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite Guanidinohydantoin

All present enzymatic activity of RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite Guanidinohydantoin:
2.7.7.7;

The structure of RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite Guanidinohydantoin, PDB code: 3nae 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)	35.24 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.013, 119.783, 130.727, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23.1

The binding sites of Calcium atom in the RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite Guanidinohydantoin (pdb code 3nae). 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 Datp Opposite Guanidinohydantoin, PDB code: 3nae:
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 Datp Opposite Guanidinohydantoin


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 Datp Opposite Guanidinohydantoin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca905 b:30.8 occ:1.00 O A:LYS531 2.2 29.2 1.0 OD1 A:ASN507 2.2 34.9 1.0 O A:HOH939 2.3 32.4 1.0 O A:ASN505 2.3 32.4 1.0 O A:HOH940 2.5 31.2 1.0 O A:HOH938 2.5 24.4 1.0 O A:HOH1211 2.6 36.9 1.0 C A:LYS531 3.2 30.7 1.0 CG A:ASN507 3.4 36.2 1.0 C A:ASN505 3.6 33.3 1.0 CA A:LYS531 4.0 29.6 1.0 ND2 A:ASN507 4.0 36.4 1.0 N A:ASN507 4.2 36.0 1.0 N A:LYS532 4.2 30.3 1.0 CB A:ASN505 4.2 33.2 0.5 CB A:ASN505 4.3 33.6 0.5 CA A:PRO506 4.3 34.0 1.0 C A:PRO506 4.4 34.6 1.0 CA A:LYS532 4.4 30.9 1.0 N A:PRO506 4.4 33.0 1.0 O A:HOH1056 4.5 35.4 1.0 CA A:ASN505 4.5 33.9 0.5 CA A:ASN505 4.5 34.1 0.5 O A:LEU533 4.5 27.7 1.0 CB A:ASN507 4.6 36.8 1.0 O A:ALA502 4.6 30.8 1.0 CB A:LYS531 4.7 31.6 1.0 C A:LYS532 4.8 30.8 1.0 CA A:ASN507 4.8 36.8 1.0 N A:LEU533 4.9 30.1 1.0 O A:ILE530 4.9 25.6 1.0

Calcium binding site 2 out of 4 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite Guanidinohydantoin


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 Datp Opposite Guanidinohydantoin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca906 b:20.5 occ:1.00 O1B A:DTP904 2.2 15.9 1.0 O1G A:DTP904 2.2 20.7 1.0 OD1 A:ASP623 2.3 31.0 1.0 O A:LEU412 2.3 16.9 1.0 OD2 A:ASP411 2.4 27.8 1.0 O2A A:DTP904 2.5 21.6 1.0 OD1 A:ASP411 2.7 32.3 1.0 CG A:ASP411 2.9 26.7 1.0 PB A:DTP904 3.3 16.1 1.0 CG A:ASP623 3.4 24.5 1.0 C A:LEU412 3.5 17.0 1.0 PG A:DTP904 3.5 17.7 1.0 PA A:DTP904 3.7 20.8 1.0 O3A A:DTP904 3.7 22.9 1.0 CA A:CA907 3.8 44.4 1.0 O3B A:DTP904 3.8 17.4 1.0 OD2 A:ASP623 3.9 28.9 1.0 O A:HOH1160 4.0 41.4 1.0 N A:LEU412 4.1 17.0 1.0 O2G A:DTP904 4.2 15.3 1.0 O A:HOH1162 4.3 49.3 1.0 CA A:LEU412 4.3 16.4 1.0 CB A:ASP411 4.4 21.7 1.0 C5' A:DTP904 4.4 16.1 1.0 N A:SER414 4.4 16.9 1.0 N A:THR413 4.5 16.7 1.0 O5' A:DTP904 4.6 20.5 1.0 CB A:ASP623 4.6 23.6 1.0 C A:ASP411 4.6 19.1 1.0 CA A:THR413 4.6 17.4 1.0 O2B A:DTP904 4.7 18.8 1.0 N A:LEU415 4.7 14.4 1.0 O3G A:DTP904 4.7 17.7 1.0 C A:THR413 4.7 17.3 1.0 CB A:LEU412 4.8 17.0 1.0 O1A A:DTP904 4.9 23.1 1.0 O A:ASP623 4.9 19.0 1.0 CA A:ASP411 5.0 20.3 1.0

Calcium binding site 3 out of 4 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite Guanidinohydantoin


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 Datp Opposite Guanidinohydantoin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca907 b:44.4 occ:1.00 O A:HOH1022 2.4 31.1 1.0 O2A A:DTP904 2.6 21.6 1.0 OD2 A:ASP411 2.7 27.8 1.0 OD2 A:ASP623 2.8 28.9 1.0 O A:HOH1212 3.0 39.8 1.0 CG A:ASP623 3.7 24.5 1.0 PA A:DTP904 3.7 20.8 1.0 CA A:CA906 3.8 20.5 1.0 OD1 A:ASP623 3.8 31.0 1.0 C3' P:DOC115 3.8 21.1 1.0 CG A:ASP411 3.8 26.7 1.0 CB A:SER624 3.9 22.9 1.0 C5' P:DOC115 4.1 25.9 1.0 O1A A:DTP904 4.1 23.1 1.0 OG A:SER624 4.4 27.6 1.0 O A:HOH1160 4.4 41.4 1.0 O A:HOH1054 4.4 22.4 1.0 C4' P:DOC115 4.5 22.1 1.0 O5' A:DTP904 4.5 20.5 1.0 OD1 A:ASP411 4.6 32.3 1.0 CB A:ASP411 4.6 21.7 1.0 O A:ASP621 4.7 18.8 1.0 C5' A:DTP904 4.7 16.1 1.0 O P:HOH359 4.7 30.1 1.0 N A:SER624 4.7 20.6 1.0 C A:ASP623 4.8 21.5 1.0 O1G A:DTP904 4.8 20.7 1.0 CA A:SER624 4.9 21.4 1.0 O A:HOH1470 5.0 38.3 1.0 O A:ASP623 5.0 19.0 1.0

Calcium binding site 4 out of 4 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite Guanidinohydantoin


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 Datp Opposite Guanidinohydantoin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca908 b:59.5 occ:1.00 O A:HOH1027 2.3 34.8 1.0 O A:HOH1144 2.4 42.6 1.0 OD1 A:ASP144 3.6 26.5 1.0 NZ A:LYS185 3.7 24.3 1.0 CD A:LYS185 4.0 20.4 1.0 CG2 A:ILE182 4.1 21.1 1.0 CE1 A:PHE146 4.1 19.5 1.0 CE2 A:TYR139 4.2 21.0 1.0 OH A:TYR139 4.2 19.8 1.0 CE1 A:TYR329 4.3 23.1 1.0 CZ A:PHE146 4.3 18.2 1.0 CE A:LYS185 4.4 23.0 1.0 CZ A:TYR139 4.5 19.2 1.0 O A:HOH1368 4.5 48.4 1.0 O A:HOH1176 4.6 38.2 1.0 CG A:ASP144 4.7 25.5 1.0 CD1 A:TYR329 4.7 20.2 1.0 CD1 A:LEU332 4.8 13.9 1.0 OD2 A:ASP144 4.9 28.4 1.0

J.Beckman, M.Wang, G.Blaha, J.Wang, W.H.Konigsberg. Substitution of Ala For TYR567 in RB69 Dna Polymerase Allows Damp and Dgmp to Be Inserted Opposite Guanidinohydantoin . Biochemistry V. 49 8554 2010.
ISSN: ISSN 0006-2960
PubMed: 20795733
DOI: 10.1021/BI100913V