Calcium in PDB 7un7: Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate

All present enzymatic activity of Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate:
2.7.7.7;

The structure of Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate, PDB code: 7un7 was solved by J.A.Jamsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.76 / 2.04
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.135, 62.774, 140.193, 90, 90, 90
R / Rfree (%)	22 / 24.7

The structure of Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate (pdb code 7un7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate, PDB code: 7un7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:23.9 occ:1.00 OD2 A:ASP429 2.2 22.3 1.0 OD1 A:ASP427 2.2 29.8 1.0 O1B A:TTP601 2.2 23.4 1.0 O1A A:TTP601 2.2 23.1 1.0 O1G A:TTP601 2.2 27.6 1.0 O A:HOH711 2.3 29.9 1.0 O A:ASP427 2.8 34.3 1.0 CG A:ASP429 3.1 28.5 1.0 OD1 A:ASP429 3.3 30.9 1.0 CG A:ASP427 3.5 37.0 1.0 PB A:TTP601 3.5 26.3 1.0 PG A:TTP601 3.5 30.5 1.0 PA A:TTP601 3.6 29.5 1.0 CA A:CA606 3.7 44.8 1.0 C A:ASP427 3.7 28.8 1.0 N A:ASP427 3.9 31.3 1.0 O3B A:TTP601 4.0 28.2 1.0 O3A A:TTP601 4.0 28.7 1.0 O2G A:TTP601 4.1 31.8 1.0 O A:HOH703 4.1 28.1 1.0 O A:HOH724 4.1 25.6 1.0 OD2 A:ASP427 4.2 33.6 1.0 CA A:ASP427 4.2 30.9 1.0 CB A:ASP427 4.4 27.9 1.0 C5' A:TTP601 4.5 27.7 1.0 N A:SER417 4.5 29.4 1.0 CB A:ASP429 4.5 27.5 1.0 O5' A:TTP601 4.5 27.0 1.0 OG A:SER417 4.5 29.2 1.0 O2A A:TTP601 4.6 26.7 1.0 N A:VAL428 4.7 25.7 1.0 O2B A:TTP601 4.7 27.9 1.0 O3G A:TTP601 4.7 30.9 1.0 O A:HOH714 4.7 33.0 1.0 CA A:GLY416 4.7 25.8 1.0 N A:ASP429 4.8 26.4 1.0 N A:GLY426 4.9 28.5 1.0 C A:GLY426 5.0 30.2 1.0 C A:VAL428 5.0 26.6 1.0

Calcium binding site 2 out of 2 in the Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Dna Polymerase Lambda in Complex with A 1NT Microhomology Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca606 b:44.8 occ:1.00 OD1 A:ASP429 2.2 30.9 1.0 O A:HOH714 2.4 33.0 1.0 OD2 A:ASP490 2.5 33.0 1.0 O1A A:TTP601 2.7 23.1 1.0 OD1 A:ASP427 2.8 29.8 1.0 O A:HOH748 2.8 37.3 1.0 OD2 A:ASP427 3.1 33.6 1.0 CG A:ASP427 3.2 37.0 1.0 CG A:ASP429 3.3 28.5 1.0 CG A:ASP490 3.4 32.6 1.0 O3' P:DC6 3.5 37.2 1.0 PA A:TTP601 3.6 29.5 1.0 CA A:CA605 3.7 23.9 1.0 C3' P:DC6 3.7 31.1 1.0 OD2 A:ASP429 3.8 22.3 1.0 O5' A:TTP601 3.9 27.0 1.0 O2A A:TTP601 3.9 26.7 1.0 O A:HOH703 4.0 28.1 1.0 C5' A:TTP601 4.2 27.7 1.0 CB A:ASP490 4.2 25.2 1.0 OD1 A:ASP490 4.2 31.9 1.0 CB A:ASP427 4.4 27.9 1.0 CB A:ASP429 4.6 27.5 1.0 NH2 A:ARG488 4.7 29.4 1.0 C4' P:DC6 4.7 30.2 1.0 O5' P:DC6 4.7 20.1 1.0 OP1 P:DC6 4.7 21.5 1.0 C2' P:DC6 4.8 34.8 1.0 C5' P:DC6 4.9 28.3 1.0 O1G A:TTP601 4.9 27.6 1.0 O A:VAL428 4.9 26.4 1.0

G.Chandramouly, J.Jamsen, N.Borisonnik, M.Tyagi, M.L.Calbert, T.Tredinnick, A.Y.Ozdemir, T.Kent, E.V.Demidova, S.Arora, S.H.Wilson, R.T.Pomerantz. Pol Lambda Promotes Microhomology-Mediated End-Joining. Nat.Struct.Mol.Biol. V. 30 107 2023.
ISSN: ESSN 1545-9985
PubMed: 36536104
DOI: 10.1038/S41594-022-00895-4