Cobalt in PDB 6nnd: Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis in Complex with Nadph and Dihydrofolate

All present enzymatic activity of Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis in Complex with Nadph and Dihydrofolate:
1.5.1.3;

The structure of Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis in Complex with Nadph and Dihydrofolate, PDB code: 6nnd was solved by J.A.Ribeiro, S.M.Chavez-Pacheco, M.V.B.Dias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.56 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.981, 70.863, 72.110, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.9

The binding sites of Cobalt atom in the Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis in Complex with Nadph and Dihydrofolate (pdb code 6nnd). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis in Complex with Nadph and Dihydrofolate, PDB code: 6nnd:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis in Complex with Nadph and Dihydrofolate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis in Complex with Nadph and Dihydrofolate within 5.0Å range: probe atom residue distance (Å) B Occ A:Co202 b:20.0 occ:1.00 O B:HOH383 2.1 16.9 1.0 NE2 B:HIS157 2.1 18.2 1.0 O A:HOH314 2.1 18.6 1.0 O B:HOH395 2.1 20.9 1.0 NE2 A:HIS38 2.1 20.4 1.0 O A:HOH353 2.2 15.8 1.0 CD2 A:HIS38 3.1 18.3 1.0 CD2 B:HIS157 3.1 19.2 1.0 CE1 B:HIS157 3.1 24.0 1.0 CE1 A:HIS38 3.2 23.9 1.0 OE2 A:GLU90 3.8 24.7 1.0 O A:ILE34 3.8 16.8 1.0 OG1 B:THR108 4.0 22.5 1.0 O A:MET36 4.1 17.3 1.0 OE1 A:GLU90 4.2 27.3 1.0 ND1 B:HIS157 4.2 21.2 1.0 CG B:HIS157 4.2 22.9 1.0 CG A:HIS38 4.2 20.9 1.0 ND1 A:HIS38 4.3 19.8 1.0 CD A:GLU90 4.3 27.6 1.0 O B:ARG158 4.4 33.1 1.0 O A:GLU33 4.4 17.6 1.0 O A:HOH394 4.5 24.2 1.0 C A:ILE34 4.7 18.7 1.0

Cobalt binding site 2 out of 3 in the Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis in Complex with Nadph and Dihydrofolate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis in Complex with Nadph and Dihydrofolate within 5.0Å range: probe atom residue distance (Å) B Occ A:Co203 b:30.1 occ:0.45 ND1 B:HIS30 2.0 28.3 1.0 OE1 A:GLU138 2.1 41.6 1.0 NE2 A:HIS157 2.2 41.6 1.0 CE1 B:HIS30 2.7 25.2 1.0 CE1 A:HIS157 2.9 44.0 1.0 CD A:GLU138 3.1 45.6 1.0 CG B:HIS30 3.2 24.3 1.0 CD2 A:HIS157 3.3 41.3 1.0 CG A:GLU138 3.5 39.9 1.0 CB B:HIS30 3.7 18.7 1.0 NE2 B:HIS30 3.9 25.7 1.0 CD1 B:LEU153 4.0 33.3 1.0 ND1 A:HIS157 4.1 41.2 1.0 CD2 B:HIS30 4.1 25.9 1.0 O A:HOH347 4.2 37.9 1.0 OE2 A:GLU138 4.3 44.9 1.0 CA B:HIS30 4.3 16.0 1.0 CG A:HIS157 4.3 36.2 1.0 NE A:ARG136 4.5 48.7 1.0 CD1 B:ILE34 4.9 32.4 1.0 O B:HIS30 5.0 18.7 1.0

Cobalt binding site 3 out of 3 in the Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis in Complex with Nadph and Dihydrofolate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis in Complex with Nadph and Dihydrofolate within 5.0Å range: probe atom residue distance (Å) B Occ B:Co202 b:28.2 occ:1.00 O A:HOH416 1.8 26.4 1.0 O A:HOH415 2.0 29.5 1.0 O B:HOH322 2.1 25.0 1.0 NE2 B:HIS38 2.1 23.8 1.0 O B:HOH357 2.1 26.9 1.0 O B:HOH361 2.2 21.4 1.0 CE1 B:HIS38 3.1 21.1 1.0 CD2 B:HIS38 3.1 21.3 1.0 O B:ILE34 3.8 22.3 1.0 OE2 B:GLU90 3.9 29.9 1.0 O B:HOH328 4.1 32.6 1.0 OE1 B:GLU90 4.1 30.6 1.0 ND1 B:HIS38 4.2 23.7 1.0 O B:MET36 4.2 15.1 1.0 CG B:HIS38 4.3 20.6 1.0 O B:HOH392 4.3 43.6 1.0 CD B:GLU90 4.3 33.0 1.0 O A:ARG158 4.5 27.5 1.0 O B:HOH429 4.5 45.5 1.0 CB A:THR108 4.6 21.1 1.0 CG2 A:THR108 4.6 23.5 1.0 O B:GLU33 4.6 21.3 1.0 O A:SER159 4.6 36.6 1.0 OG1 A:THR108 4.6 22.8 1.0 CA A:SER159 4.6 25.9 1.0 C B:ILE34 4.7 17.0 1.0

J.A.Ribeiro, S.M.Chavez-Pacheco, G.S.De Oliveira, C.D.S.Silva, J.H.P.Giudice, G.A.Libreros-Zuniga, M.V.B.Dias. Crystal Structures of the Closed Form of Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with Dihydrofolate and Antifolates. Acta Crystallogr D Struct V. 75 682 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 31282477
DOI: 10.1107/S205979831900901X