Manganese in PDB 4i29: Binary Complex of Mouse Tdt with Ssdna and Mn++

All present enzymatic activity of Binary Complex of Mouse Tdt with Ssdna and Mn++:
2.7.7.31;

The structure of Binary Complex of Mouse Tdt with Ssdna and Mn++, PDB code: 4i29 was solved by J.Gouge, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.65 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.755, 84.923, 115.141, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 22.5

The structure of Binary Complex of Mouse Tdt with Ssdna and Mn++ also contains other interesting chemical elements:

Bromine	(Br)	1 atom
Sodium	(Na)	1 atom

The binding sites of Manganese atom in the Binary Complex of Mouse Tdt with Ssdna and Mn++ (pdb code 4i29). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Binary Complex of Mouse Tdt with Ssdna and Mn++, PDB code: 4i29:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Binary Complex of Mouse Tdt with Ssdna and Mn++


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Binary Complex of Mouse Tdt with Ssdna and Mn++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:26.6 occ:1.00 OD2 A:ASP343 2.0 30.4 1.0 OD1 A:ASP345 2.1 24.9 1.0 OD2 A:ASP434 2.1 19.5 1.0 OP1 C:DA5 2.4 38.1 0.5 O C:HOH113 2.4 33.1 1.0 OP1 C:DA5 2.4 30.9 0.5 O3' C:DA4 2.5 36.4 1.0 CG A:ASP343 2.9 26.0 1.0 P C:DA5 3.0 32.0 0.5 P C:DA5 3.0 38.9 0.5 CG A:ASP345 3.0 22.7 1.0 CG A:ASP434 3.2 20.9 1.0 OD1 A:ASP343 3.2 26.2 1.0 OD2 A:ASP345 3.3 25.6 1.0 C3' C:DA4 3.6 37.7 1.0 MN A:MN603 3.6 28.5 1.0 C4' C:DA4 3.8 38.3 1.0 CB A:ASP434 3.9 21.8 1.0 C5' C:DA4 4.0 37.5 1.0 O5' C:DA5 4.0 41.8 0.5 O5' C:DA5 4.1 28.4 0.5 OP2 C:DA5 4.1 32.1 0.5 OP2 C:DA5 4.1 39.1 0.5 OD1 A:ASP434 4.1 25.1 1.0 C5' C:DA5 4.2 43.8 0.5 C5' C:DA5 4.2 23.9 0.5 CB A:ASP343 4.3 20.2 1.0 O C:HOH102 4.3 29.3 1.0 CB A:ASP345 4.4 17.8 1.0 NH2 A:ARG432 4.5 20.3 1.0 O C:HOH104 4.7 23.6 1.0 C2' C:DA4 4.7 39.0 1.0 CZ3 A:TRP450 4.7 24.2 1.0 OP1 C:DA4 4.7 36.0 1.0 O5' C:DA4 4.9 37.1 1.0

Manganese binding site 2 out of 2 in the Binary Complex of Mouse Tdt with Ssdna and Mn++


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Binary Complex of Mouse Tdt with Ssdna and Mn++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn603 b:28.5 occ:1.00 OP1 C:DA5 2.1 30.9 0.5 OD1 A:ASP343 2.1 26.2 1.0 OP1 C:DA5 2.2 38.1 0.5 OD2 A:ASP345 2.3 25.6 1.0 O A:HOH937 2.3 21.5 1.0 O C:HOH104 2.3 23.6 1.0 O A:HOH702 2.9 23.6 1.0 CG A:ASP343 3.3 26.0 1.0 CG A:ASP345 3.4 22.7 1.0 P C:DA5 3.5 32.0 0.5 P C:DA5 3.5 38.9 0.5 MN A:MN602 3.6 26.6 1.0 OD2 A:ASP343 3.7 30.4 1.0 OD1 A:ASP345 3.7 24.9 1.0 C5' C:DA5 3.8 43.8 0.5 O5' C:DA5 4.0 41.8 0.5 O5' C:DA5 4.0 28.4 0.5 O A:HOH938 4.0 39.3 1.0 C5' C:DA5 4.1 23.9 0.5 O A:ASP343 4.2 16.1 1.0 O C:HOH102 4.2 29.3 1.0 O A:HOH705 4.3 18.9 1.0 OP2 C:DA5 4.3 32.1 0.5 OP2 C:DA5 4.5 39.1 0.5 C A:ASP343 4.5 20.7 1.0 CB A:ASP343 4.5 20.2 1.0 O3' C:DA4 4.6 36.4 1.0 N A:GLY333 4.6 18.8 1.0 O C:HOH113 4.6 33.1 1.0 CA A:GLY332 4.6 16.1 1.0 CB A:ASP345 4.6 17.8 1.0 O C:HOH101 4.8 32.7 1.0 N A:ASP343 4.9 18.9 1.0 CA A:ASP343 4.9 18.2 1.0 C4' C:DA5 4.9 47.2 0.5

J.Gouge, S.Rosario, F.Romain, P.Beguin, M.Delarue. Structures of Intermediates Along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism. J.Mol.Biol. V. 425 4334 2013.
ISSN: ISSN 0022-2836
PubMed: 23856622
DOI: 10.1016/J.JMB.2013.07.009