Calcium in PDB 3spz: Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da (CA2+)

All present enzymatic activity of Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da (CA2+):
2.7.7.7;

The structure of Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da (CA2+), PDB code: 3spz was solved by S.Xia, W.H.Konigsberg, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.87 / 2.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.168, 119.064, 130.208, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25.7

The binding sites of Calcium atom in the Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da (CA2+) (pdb code 3spz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da (CA2+), PDB code: 3spz:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da (CA2+)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da (CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca905 b:22.2 occ:1.00 O1G A:UPC904 2.2 30.0 1.0 OD1 A:ASP623 2.3 20.9 1.0 OD2 A:ASP411 2.4 41.1 1.0 O2B A:UPC904 2.4 26.9 1.0 O A:LEU412 2.5 30.7 1.0 O2A A:UPC904 2.6 27.2 1.0 CG A:ASP411 3.0 27.8 1.0 OD1 A:ASP411 3.1 35.7 1.0 C3A A:UPC904 3.1 26.8 1.0 PB A:UPC904 3.3 27.3 1.0 CG A:ASP623 3.4 20.1 1.0 PG A:UPC904 3.4 24.5 1.0 PA A:UPC904 3.5 24.5 1.0 C A:LEU412 3.6 25.9 1.0 OD2 A:ASP623 3.8 21.5 1.0 O3B A:UPC904 3.8 28.2 1.0 C5' A:UPC904 4.0 21.3 1.0 N A:LEU412 4.1 25.1 1.0 O2G A:UPC904 4.2 28.5 1.0 O5' A:UPC904 4.3 25.8 1.0 CB A:ASP411 4.4 22.8 1.0 CA A:LEU412 4.4 25.4 1.0 CA A:CA906 4.4 70.8 1.0 N A:SER414 4.4 25.8 1.0 C A:ASP411 4.5 24.1 1.0 N A:ALA415 4.6 21.3 1.0 N A:THR413 4.7 24.5 1.0 CB A:ASP623 4.7 22.4 1.0 CB A:ALA415 4.7 16.7 1.0 O1B A:UPC904 4.7 25.2 1.0 O1A A:UPC904 4.8 30.7 1.0 CA A:THR413 4.8 26.3 1.0 C A:THR413 4.9 27.0 1.0 CB A:LEU412 4.9 24.9 1.0 CA A:ASP411 4.9 23.5 1.0

Calcium binding site 2 out of 4 in the Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da (CA2+)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da (CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca906 b:70.8 occ:1.00 OD2 A:ASP411 2.8 41.1 1.0 O2A A:UPC904 2.8 27.2 1.0 O3' P:DC115 3.0 23.7 1.0 OD2 A:ASP623 3.2 21.5 1.0 O A:HOH1029 3.4 17.9 1.0 C3' P:DC115 3.7 23.4 1.0 CG A:ASP411 3.7 27.8 1.0 CB A:SER624 3.8 24.4 1.0 OG A:SER624 4.0 24.4 1.0 PA A:UPC904 4.0 24.5 1.0 CB A:ASP411 4.1 22.8 1.0 CG A:ASP623 4.2 20.1 1.0 O5' P:DC115 4.3 26.2 1.0 CA A:CA905 4.4 22.2 1.0 C5' P:DC115 4.4 24.2 1.0 O1A A:UPC904 4.4 30.7 1.0 OD1 A:ASP623 4.5 20.9 1.0 C4' P:DC115 4.6 22.2 1.0 OE1 A:GLU686 4.6 52.7 1.0 O5' A:UPC904 4.7 25.8 1.0 OD1 A:ASP411 4.7 35.7 1.0 O A:ASP621 4.9 27.8 1.0 CA A:SER624 4.9 25.8 1.0

Calcium binding site 3 out of 4 in the Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da (CA2+)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da (CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca907 b:56.3 occ:1.00 O A:HOH922 2.0 23.9 1.0 O A:LYS531 2.2 41.9 1.0 OD1 A:ASN507 2.2 60.2 1.0 O A:HOH920 2.3 22.8 1.0 O A:ASN505 2.4 58.4 1.0 C A:LYS531 3.2 43.8 1.0 CG A:ASN507 3.4 58.8 1.0 C A:ASN505 3.6 57.7 1.0 CA A:LYS531 4.0 42.4 1.0 N A:ASN507 4.0 59.1 1.0 N A:LYS532 4.1 45.4 1.0 ND2 A:ASN507 4.2 58.4 1.0 CB A:ASN505 4.3 59.7 1.0 CA A:LYS532 4.3 46.9 1.0 CA A:PRO506 4.4 57.1 1.0 C A:PRO506 4.4 58.5 1.0 CB A:ASN507 4.4 59.0 1.0 O A:ALA502 4.5 51.3 1.0 O A:LEU533 4.5 44.3 1.0 N A:PRO506 4.5 57.2 1.0 CA A:ASN505 4.6 59.0 1.0 C A:LYS532 4.7 46.1 1.0 CA A:ASN507 4.7 60.1 1.0 O A:ILE530 4.7 38.5 1.0 CB A:LYS531 4.8 42.4 1.0 N A:LEU533 4.9 44.6 1.0

Calcium binding site 4 out of 4 in the Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da (CA2+)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Dna Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with Dupcpp Opposite Da (CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca908 b:69.5 occ:1.00 OE2 A:GLU116 2.7 51.9 1.0 OE1 A:GLU116 2.8 50.4 1.0 CD A:GLU116 3.1 45.6 1.0 OD2 A:ASP114 3.6 53.8 1.0 O A:ILE115 4.5 34.2 1.0 CG A:GLU116 4.6 41.2 1.0 CG A:ASP114 4.8 48.3 1.0

S.Xia, M.Wang, G.Blaha, W.H.Konigsberg, J.Wang. Structural Insights Into Complete Metal Ion Coordination From Ternary Complexes of B Family RB69 Dna Polymerase. Biochemistry V. 50 9114 2011.
ISSN: ISSN 0006-2960
PubMed: 21923197
DOI: 10.1021/BI201260H