Magnesium in PDB 5ddy: Binary Complex of Human Polymerase Lambda with Dctp

All present enzymatic activity of Binary Complex of Human Polymerase Lambda with Dctp:
2.7.7.7;

The structure of Binary Complex of Human Polymerase Lambda with Dctp, PDB code: 5ddy was solved by M.S.Liu, M.D.Tsai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.66 / 3.36
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	206.015, 206.015, 114.266, 90.00, 90.00, 90.00
R / Rfree (%)	26.2 / 29.7

The structure of Binary Complex of Human Polymerase Lambda with Dctp also contains other interesting chemical elements:

Manganese

(Mn)

8 atoms

The binding sites of Magnesium atom in the Binary Complex of Human Polymerase Lambda with Dctp (pdb code 5ddy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Binary Complex of Human Polymerase Lambda with Dctp, PDB code: 5ddy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Binary Complex of Human Polymerase Lambda with Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Binary Complex of Human Polymerase Lambda with Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:0.0 occ:1.00 O2B A:DCP603 2.2 0.2 1.0 OD1 A:ASP427 2.3 0.1 1.0 OD2 A:ASP429 2.3 0.9 1.0 O2A A:DCP603 2.6 0.2 1.0 O2G A:DCP603 2.8 0.5 1.0 O A:ASP427 3.1 0.9 1.0 CA A:GLY416 3.3 0.5 1.0 CG A:ASP427 3.4 0.7 1.0 CG A:ASP429 3.5 0.9 1.0 N A:SER417 3.6 0.0 1.0 PB A:DCP603 3.6 97.1 1.0 C A:ASP427 3.7 0.2 1.0 OG A:SER417 3.9 0.5 1.0 PA A:DCP603 3.9 0.2 1.0 C A:GLY416 3.9 0.2 1.0 PG A:DCP603 4.0 0.2 1.0 N A:ASP429 4.1 0.1 1.0 OD2 A:ASP427 4.1 0.0 1.0 O3A A:DCP603 4.3 0.1 1.0 O3B A:DCP603 4.3 96.0 1.0 N A:VAL428 4.3 0.8 1.0 N A:ASP427 4.4 0.6 1.0 CB A:ASP429 4.4 0.3 1.0 CA A:VAL428 4.4 0.0 1.0 O3G A:DCP603 4.4 0.6 1.0 CA A:ASP427 4.4 0.6 1.0 OD1 A:ASP429 4.4 0.4 1.0 C5' A:DCP603 4.5 0.1 1.0 N A:GLY416 4.5 1.0 1.0 CB A:ASP427 4.5 1.0 1.0 C A:VAL428 4.6 0.4 1.0 O1B A:DCP603 4.6 0.8 1.0 MN A:MN602 4.6 0.5 1.0 O5' A:DCP603 4.7 0.5 1.0 CA A:SER417 4.8 0.4 1.0 CB A:SER417 4.9 0.2 1.0 CA A:ASP429 4.9 0.6 1.0

Magnesium binding site 2 out of 4 in the Binary Complex of Human Polymerase Lambda with Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Binary Complex of Human Polymerase Lambda with Dctp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:0.1 occ:1.00 OD1 C:ASP427 2.2 0.0 1.0 O2B C:DCP603 2.2 0.0 1.0 OD1 C:ASP429 2.4 0.6 1.0 O2G C:DCP603 2.4 0.9 1.0 O C:ASP427 2.7 0.1 1.0 O2A C:DCP603 2.7 0.7 1.0 CG C:ASP427 3.4 1.0 1.0 N C:SER417 3.5 0.3 1.0 C C:ASP427 3.5 0.3 1.0 CA C:GLY416 3.5 0.4 1.0 PB C:DCP603 3.6 97.9 1.0 PG C:DCP603 3.6 0.9 1.0 CG C:ASP429 3.6 0.8 1.0 N C:ASP427 3.9 0.7 1.0 OG C:SER417 3.9 94.7 1.0 O3G C:DCP603 4.0 0.8 1.0 PA C:DCP603 4.0 0.2 1.0 C C:GLY416 4.0 0.5 1.0 O3B C:DCP603 4.1 0.3 1.0 CA C:ASP427 4.1 0.8 1.0 OD2 C:ASP427 4.2 0.5 1.0 O3A C:DCP603 4.3 0.8 1.0 MN C:MN602 4.3 0.9 1.0 OD2 C:ASP429 4.4 0.6 1.0 N C:ASP429 4.4 0.5 1.0 CB C:ASP427 4.4 0.4 1.0 N C:VAL428 4.4 0.0 1.0 CB C:SER417 4.6 0.7 1.0 CB C:ASP429 4.6 1.0 1.0 CA C:SER417 4.6 0.7 1.0 O1B C:DCP603 4.6 0.5 1.0 CA C:VAL428 4.7 0.6 1.0 C5' C:DCP603 4.8 0.3 1.0 N C:GLY416 4.8 0.7 1.0 O1G C:DCP603 4.9 0.2 1.0 C C:VAL428 4.9 0.1 1.0 N C:GLY426 4.9 0.9 1.0 O5' C:DCP603 4.9 0.5 1.0

Magnesium binding site 3 out of 4 in the Binary Complex of Human Polymerase Lambda with Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Binary Complex of Human Polymerase Lambda with Dctp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg601 b:0.3 occ:1.00 OD1 E:ASP427 2.0 0.4 1.0 O2B E:DCP603 2.1 0.7 1.0 OD2 E:ASP429 2.2 0.7 1.0 O2G E:DCP603 2.6 0.1 1.0 O2A E:DCP603 2.6 0.7 1.0 CG E:ASP427 3.2 0.0 1.0 CA E:GLY416 3.4 0.3 1.0 O E:ASP427 3.4 1.0 1.0 CG E:ASP429 3.4 0.3 1.0 PB E:DCP603 3.5 0.9 1.0 N E:SER417 3.7 1.0 1.0 C E:ASP427 3.7 0.9 1.0 PG E:DCP603 3.7 0.6 1.0 PA E:DCP603 3.9 0.9 1.0 OD2 E:ASP427 4.0 0.4 1.0 N E:ASP429 4.0 0.4 1.0 C E:GLY416 4.1 0.7 1.0 O3B E:DCP603 4.1 0.1 1.0 N E:VAL428 4.1 0.8 1.0 OD1 E:ASP429 4.1 0.0 1.0 O3A E:DCP603 4.2 0.5 1.0 CA E:VAL428 4.2 0.7 1.0 CB E:ASP427 4.3 0.3 1.0 CA E:ASP427 4.3 0.0 1.0 O3G E:DCP603 4.4 0.1 1.0 N E:ASP427 4.4 0.5 1.0 OG E:SER417 4.4 0.4 1.0 C E:VAL428 4.4 0.7 1.0 CB E:ASP429 4.4 0.3 1.0 O1B E:DCP603 4.5 0.6 1.0 C5' E:DCP603 4.6 0.9 1.0 N E:GLY416 4.6 0.3 1.0 O5' E:DCP603 4.8 0.1 1.0 CA E:ASP429 4.9 0.0 1.0 MN E:MN602 4.9 0.8 1.0 CA E:SER417 4.9 0.5 1.0 O1A E:DCP603 5.0 0.4 1.0 CB E:SER417 5.0 0.5 1.0

Magnesium binding site 4 out of 4 in the Binary Complex of Human Polymerase Lambda with Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Binary Complex of Human Polymerase Lambda with Dctp within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg601 b:1.0 occ:1.00 O2B G:DCP603 2.2 1.0 1.0 OD1 G:ASP427 2.3 0.0 1.0 O2G G:DCP603 2.4 0.1 1.0 OD2 G:ASP429 2.6 0.3 1.0 O G:ASP427 2.7 0.6 1.0 O2A G:DCP603 3.1 0.4 1.0 N G:SER417 3.3 0.6 1.0 CG G:ASP427 3.3 0.8 1.0 CA G:GLY416 3.4 0.4 1.0 CG G:ASP429 3.5 0.8 1.0 PB G:DCP603 3.6 0.8 1.0 PG G:DCP603 3.6 0.4 1.0 C G:ASP427 3.6 0.8 1.0 OD1 G:ASP429 3.8 0.0 1.0 OG G:SER417 3.8 0.6 1.0 C G:GLY416 3.9 0.4 1.0 N G:ASP427 3.9 0.7 1.0 O3B G:DCP603 4.0 0.7 1.0 OD2 G:ASP427 4.0 0.2 1.0 O3G G:DCP603 4.1 0.6 1.0 CA G:ASP427 4.1 0.2 1.0 CB G:ASP427 4.3 0.8 1.0 CB G:SER417 4.3 0.2 1.0 PA G:DCP603 4.4 0.4 1.0 CA G:SER417 4.4 0.5 1.0 O3A G:DCP603 4.5 0.0 1.0 O1B G:DCP603 4.5 0.7 1.0 N G:VAL428 4.6 0.3 1.0 N G:GLY416 4.8 0.2 1.0 N G:GLY426 4.8 0.8 1.0 N G:ASP429 4.8 0.6 1.0 CB G:ASP429 4.8 0.2 1.0 O1G G:DCP603 4.8 0.6 1.0 CA G:VAL428 4.9 0.5 1.0

M.S.Liu, H.Y.Tsai, X.X.Liu, M.C.Ho, W.J.Wu, M.D.Tsai. Structural Mechanism For the Fidelity Modulation of Dna Polymerase Lambda J.Am.Chem.Soc. V. 138 2389 2016.
ISSN: ESSN 1520-5126
PubMed: 26836966
DOI: 10.1021/JACS.5B13368