Cobalt in PDB 3tw3: Crystal Structure of Rtca.Atp.Co Ternary Complex

All present enzymatic activity of Crystal Structure of Rtca.Atp.Co Ternary Complex:
6.5.1.4;

The structure of Crystal Structure of Rtca.Atp.Co Ternary Complex, PDB code: 3tw3 was solved by A.K.Chakravarty, P.Smith, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.37 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	69.660, 82.950, 51.780, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 26.3

The binding sites of Cobalt atom in the Crystal Structure of Rtca.Atp.Co Ternary Complex (pdb code 3tw3). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Crystal Structure of Rtca.Atp.Co Ternary Complex, PDB code: 3tw3:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Crystal Structure of Rtca.Atp.Co Ternary Complex


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 Rtca.Atp.Co Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co501 b:29.9 occ:0.35 OE2 A:GLU14 1.9 38.0 1.0 O1B A:ATP401 1.9 38.8 1.0 O2A A:ATP401 2.0 39.7 1.0 O1G A:ATP401 2.0 37.9 1.0 O A:HOH423 2.2 32.7 1.0 O A:HOH370 2.3 43.0 1.0 CD A:GLU14 3.0 38.4 1.0 PB A:ATP401 3.2 40.5 1.0 PA A:ATP401 3.2 40.4 1.0 PG A:ATP401 3.4 43.8 1.0 OE1 A:GLU14 3.5 35.9 1.0 O3A A:ATP401 3.7 41.4 1.0 NH2 A:ARG43 3.7 49.9 1.0 O3B A:ATP401 3.7 55.3 1.0 NH1 A:ARG43 3.7 56.9 1.0 O1A A:ATP401 4.0 39.2 1.0 CZ A:ARG43 4.1 52.2 1.0 O3G A:ATP401 4.2 51.1 1.0 CG A:GLU14 4.3 36.2 1.0 O A:HOH373 4.3 31.0 1.0 O2B A:ATP401 4.5 42.7 1.0 O2G A:ATP401 4.5 35.8 1.0 O5' A:ATP401 4.5 33.5 1.0 ND2 A:ASN309 4.5 31.4 1.0 O A:HOH472 4.8 46.9 1.0 OG A:SER129 4.9 47.2 1.0 C5' A:ATP401 5.0 25.9 1.0 CA A:GLY16 5.0 24.7 1.0

Cobalt binding site 2 out of 3 in the Crystal Structure of Rtca.Atp.Co Ternary Complex


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 Rtca.Atp.Co Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co340 b:91.6 occ:0.50 NE2 A:HIS225 2.7 51.0 1.0 CE1 A:HIS225 3.4 51.6 1.0 CD2 A:HIS225 3.8 49.2 1.0 O A:HOH479 4.5 40.1 1.0 ND1 A:HIS225 4.6 50.6 1.0 O A:HOH353 4.7 44.4 1.0 CG A:HIS225 4.8 47.1 1.0 OE2 A:GLU195 5.0 62.0 1.0

Cobalt binding site 3 out of 3 in the Crystal Structure of Rtca.Atp.Co Ternary Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Rtca.Atp.Co Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co341 b:0.2 occ:1.00 NE2 A:HIS158 2.8 40.8 1.0 CD2 A:HIS158 3.6 41.1 1.0 CE1 A:HIS158 3.8 39.9 1.0 CD1 A:LEU197 4.5 41.6 1.0 CD2 A:LEU227 4.7 39.6 1.0 CG A:HIS158 4.8 39.4 1.0 CD2 A:LEU155 4.9 45.6 1.0 ND1 A:HIS158 4.9 39.7 1.0

A.K.Chakravarty, P.Smith, S.Shuman. Structures of Rna 3'-Phosphate Cyclase Bound to Atp Reveal the Mechanism of Nucleotidyl Transfer and Metal-Assisted Catalysis. Proc.Natl.Acad.Sci.Usa V. 108 21034 2011.
ISSN: ISSN 0027-8424
PubMed: 22167800
DOI: 10.1073/PNAS.1115560108