Cobalt in PDB 1kej: Crystal Structure of Murine Terminal Deoxynucleotidyl Transferase Complexed with Ddatp

All present enzymatic activity of Crystal Structure of Murine Terminal Deoxynucleotidyl Transferase Complexed with Ddatp:
2.7.7.31;

The structure of Crystal Structure of Murine Terminal Deoxynucleotidyl Transferase Complexed with Ddatp, PDB code: 1kej was solved by M.Delarue, J.B.Boule, J.Lescar, N.Expert-Bezancon, N.Jourdan, N.Sukumar, F.Rougeon, C.Papanicolaou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.900, 85.300, 108.300, 90.00, 90.00, 90.00
R / Rfree (%)	26.3 / 30.9

The structure of Crystal Structure of Murine Terminal Deoxynucleotidyl Transferase Complexed with Ddatp also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Cobalt atom in the Crystal Structure of Murine Terminal Deoxynucleotidyl Transferase Complexed with Ddatp (pdb code 1kej). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of Murine Terminal Deoxynucleotidyl Transferase Complexed with Ddatp, PDB code: 1kej:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Murine Terminal Deoxynucleotidyl Transferase Complexed with Ddatp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Murine Terminal Deoxynucleotidyl Transferase Complexed with Ddatp within 5.0Å range: probe atom residue distance (Å) B Occ A:Co701 b:63.7 occ:1.00 OD1 A:ASP343 1.7 47.1 1.0 O2G A:DAD601 1.7 65.2 1.0 OD2 A:ASP345 1.8 59.9 1.0 O2B A:DAD601 2.7 57.5 1.0 CG A:ASP345 2.8 54.2 1.0 CG A:ASP343 2.9 46.0 1.0 O1A A:DAD601 3.1 65.2 1.0 PG A:DAD601 3.2 65.2 1.0 O A:ASP343 3.2 41.9 1.0 O3A A:DAD601 3.4 61.6 1.0 OD1 A:ASP345 3.5 56.0 1.0 OD2 A:ASP343 3.5 52.2 1.0 PB A:DAD601 3.5 61.5 1.0 CO A:CO702 3.5 61.6 1.0 PA A:DAD601 3.7 66.0 1.0 C A:ASP343 3.7 43.4 1.0 O3B A:DAD601 3.8 64.2 1.0 CB A:ASP345 4.0 50.4 1.0 O1G A:DAD601 4.0 65.6 1.0 N A:ASP343 4.0 41.8 1.0 CB A:ASP343 4.1 43.7 1.0 O3G A:DAD601 4.1 67.3 1.0 CA A:ASP343 4.1 42.8 1.0 N A:ASP345 4.2 46.5 1.0 O5' A:DAD601 4.5 66.4 1.0 N A:VAL344 4.5 44.7 1.0 N A:GLY333 4.6 40.7 1.0 CA A:ASP345 4.7 46.9 1.0 C A:VAL344 4.9 46.2 1.0 O1B A:DAD601 4.9 58.9 1.0 CA A:GLY332 5.0 41.2 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Murine Terminal Deoxynucleotidyl Transferase Complexed with Ddatp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Murine Terminal Deoxynucleotidyl Transferase Complexed with Ddatp within 5.0Å range: probe atom residue distance (Å) B Occ A:Co702 b:61.6 occ:1.00 O1A A:DAD601 2.0 65.2 1.0 OD1 A:ASP434 2.3 55.1 1.0 OD1 A:ASP345 2.4 56.0 1.0 OD2 A:ASP343 2.4 52.2 1.0 CG A:ASP343 3.2 46.0 1.0 CG A:ASP345 3.2 54.2 1.0 OD1 A:ASP343 3.2 47.1 1.0 OD2 A:ASP345 3.3 59.9 1.0 PA A:DAD601 3.3 66.0 1.0 CG A:ASP434 3.4 55.4 1.0 O5' A:DAD601 3.5 66.4 1.0 CO A:CO701 3.5 63.7 1.0 CB A:ASP434 4.2 53.2 1.0 NH2 A:ARG432 4.2 57.1 1.0 O3A A:DAD601 4.3 61.6 1.0 O2A A:DAD601 4.3 66.4 1.0 OD2 A:ASP434 4.4 61.2 1.0 O2G A:DAD601 4.5 65.2 1.0 C5' A:DAD601 4.5 72.0 1.0 CB A:ASP343 4.6 43.7 1.0 CB A:ASP345 4.7 50.4 1.0 CZ3 A:TRP450 4.9 55.4 1.0

M.Delarue, J.B.Boule, J.Lescar, N.Expert-Bezancon, N.Jourdan, N.Sukumar, F.Rougeon, C.Papanicolaou. Crystal Structures of A Template-Independent Dna Polymerase: Murine Terminal Deoxynucleotidyltransferase. Embo J. V. 21 427 2002.
ISSN: ISSN 0261-4189
PubMed: 11823435
DOI: 10.1093/EMBOJ/21.3.427