Cobalt in PDB 5u7f: Co-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli

All present enzymatic activity of Co-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli:
3.6.1.67;

The structure of Co-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli, PDB code: 5u7f was solved by E.Nguyen, S.E.Hill, R.L.Lieberman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.20 / 1.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	54.600, 43.090, 57.230, 90.00, 91.87, 90.00
R / Rfree (%)	17.7 / 24

The binding sites of Cobalt atom in the Co-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli (pdb code 5u7f). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Co-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli, PDB code: 5u7f:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Co-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Co-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Co203 b:24.8 occ:0.81 O A:HOH386 2.0 31.0 1.0 OE2 A:GLU56 2.1 25.3 1.0 O A:HOH364 2.1 31.9 1.0 O A:HOH375 2.2 36.6 1.0 O4 A:SO4202 2.2 28.0 1.0 O A:HOH387 2.3 30.5 1.0 HH12 A:ARG55 3.0 32.6 1.0 CO A:CO206 3.0 31.3 0.8 CD A:GLU56 3.2 24.1 1.0 S A:SO4202 3.3 23.4 0.6 CO A:CO204 3.4 25.2 1.0 OE1 A:GLU56 3.5 26.6 1.0 H A:SER42 3.5 20.8 1.0 O3 A:SO4202 3.6 22.5 1.0 O2 A:SO4202 3.7 35.3 0.8 NH1 A:ARG55 3.8 27.2 1.0 HH22 A:ARG55 3.9 34.4 1.0 O A:HOH397 4.0 32.7 1.0 HA3 A:GLY41 4.0 21.0 1.0 HB2 A:SER42 4.1 27.4 1.0 HA2 A:GLY41 4.1 21.0 1.0 N A:SER42 4.2 17.3 1.0 HH11 A:ARG55 4.2 32.6 1.0 OE2 A:GLU59 4.4 39.7 1.0 O A:HOH374 4.4 29.5 1.0 OE2 A:GLU44 4.5 44.5 1.0 CA A:GLY41 4.5 17.5 1.0 O A:SER42 4.5 22.1 1.0 CG A:GLU56 4.5 17.7 1.0 O1 A:SO4202 4.5 30.5 1.0 O A:HOH316 4.6 42.0 1.0 NH2 A:ARG55 4.6 28.6 1.0 CZ A:ARG55 4.7 25.1 1.0 HG2 A:GLU56 4.7 21.3 1.0 HG3 A:GLU56 4.7 21.3 1.0 C A:GLY41 4.8 17.8 1.0 CB A:SER42 4.9 22.9 1.0 OE2 A:GLU117 4.9 36.8 1.0 CA A:SER42 5.0 23.1 1.0

Cobalt binding site 2 out of 4 in the Co-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Co-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Co204 b:25.2 occ:0.99 O A:HOH386 1.9 31.0 1.0 OE1 A:GLU56 2.1 26.6 1.0 OE2 A:GLU60 2.1 25.9 1.0 O A:HOH374 2.1 29.5 1.0 OE2 A:GLU117 2.1 36.8 1.0 O3 A:SO4202 2.2 22.5 1.0 CD A:GLU56 3.0 24.1 1.0 CD A:GLU60 3.1 26.0 1.0 CD A:GLU117 3.2 38.1 1.0 CO A:CO205 3.2 23.2 0.8 S A:SO4202 3.3 23.4 0.6 HG3 A:GLU60 3.3 28.5 1.0 HG2 A:GLU60 3.3 28.5 1.0 OE2 A:GLU56 3.4 25.3 1.0 CO A:CO203 3.4 24.8 0.8 CG A:GLU60 3.5 23.7 1.0 O A:HOH316 3.5 42.0 1.0 OE1 A:GLU117 3.5 29.9 1.0 CO A:CO206 3.6 31.3 0.8 O4 A:SO4202 3.6 28.0 1.0 O2 A:SO4202 3.7 35.3 0.8 O A:THR40 4.0 20.5 1.0 HA3 A:GLY41 4.2 21.0 1.0 OE2 A:GLU59 4.2 39.7 1.0 O A:HOH408 4.2 40.9 1.0 HB3 A:GLU56 4.2 23.7 1.0 OE1 A:GLU60 4.2 21.6 1.0 HA2 A:GLY41 4.3 21.0 1.0 HB2 A:GLU117 4.4 44.1 1.0 O A:HOH375 4.4 36.6 1.0 CG A:GLU56 4.4 17.7 1.0 CG A:GLU117 4.5 37.0 1.0 HA A:GLU56 4.5 25.6 1.0 O1 A:SO4202 4.6 30.5 1.0 CA A:GLY41 4.7 17.5 1.0 HB2 A:GLU59 4.7 36.5 1.0 HG3 A:GLU117 4.7 44.3 1.0 HG3 A:GLU56 4.8 21.3 1.0 CB A:GLU56 4.8 19.7 1.0 O A:HOH307 4.8 29.1 1.0 HH12 A:ARG55 4.8 32.6 1.0 O A:HOH387 4.8 30.5 1.0 CB A:GLU117 4.9 36.8 1.0 HB3 A:GLU59 4.9 36.5 1.0 O A:HOH305 4.9 35.0 1.0 HB3 A:GLU117 5.0 44.1 1.0 O A:HOH336 5.0 26.9 1.0

Cobalt binding site 3 out of 4 in the Co-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Co-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Co205 b:23.2 occ:0.77 O A:THR40 2.1 20.5 1.0 OE2 A:GLU60 2.1 25.9 1.0 O3 A:SO4202 2.1 22.5 1.0 OE1 A:GLU117 2.2 29.9 1.0 O A:HOH307 2.2 29.1 1.0 O A:HOH336 2.2 26.9 1.0 CD A:GLU60 3.0 26.0 1.0 CD A:GLU117 3.1 38.1 1.0 HG1 A:THR40 3.1 37.6 1.0 C A:THR40 3.1 23.0 1.0 CO A:CO204 3.2 25.2 1.0 OE1 A:GLU60 3.2 21.6 1.0 H A:THR40 3.3 20.7 1.0 OE2 A:GLU117 3.3 36.8 1.0 S A:SO4202 3.3 23.4 0.6 HA2 A:GLY41 3.5 21.0 1.0 O1 A:SO4202 3.5 30.5 1.0 HH12 A:ARG29 3.6 42.1 1.0 OG1 A:THR40 3.7 31.4 1.0 N A:THR40 3.9 17.3 1.0 CA A:THR40 4.0 17.8 1.0 N A:GLY41 4.0 21.1 1.0 OE1 A:GLU56 4.1 26.6 1.0 CA A:GLY41 4.1 17.5 1.0 O2 A:SO4202 4.1 35.3 0.8 HA3 A:GLY41 4.1 21.0 1.0 HE1 A:HIS118 4.1 31.1 1.0 NH1 A:ARG29 4.4 35.1 1.0 CG A:GLU60 4.4 23.7 1.0 O4 A:SO4202 4.4 28.0 1.0 CB A:THR40 4.5 23.8 1.0 OE1 A:GLN37 4.5 24.7 1.0 CG A:GLU117 4.5 37.0 1.0 HH11 A:ARG29 4.6 42.1 1.0 O A:HOH305 4.6 35.0 1.0 HG2 A:GLU60 4.6 28.5 1.0 HG2 A:GLU117 4.6 44.3 1.0 HG3 A:GLU60 4.6 28.5 1.0 HG13 A:VAL39 4.7 21.5 1.0 HZ1 A:LYS7 4.7 51.9 1.0 O A:HOH386 4.7 31.0 1.0 CE1 A:HIS118 4.8 25.9 1.0 H A:GLY41 4.8 25.3 1.0 HE2 A:HIS118 4.9 27.3 1.0 HA A:THR40 4.9 21.3 1.0 HA A:VAL39 4.9 22.0 1.0 CD A:GLU56 4.9 24.1 1.0 HB3 A:GLU117 4.9 44.1 1.0 HB A:THR40 5.0 28.5 1.0

Cobalt binding site 4 out of 4 in the Co-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Co-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Co206 b:31.3 occ:0.84 O A:HOH316 2.0 42.0 1.0 O A:HOH387 2.2 30.5 1.0 O2 A:SO4202 2.2 35.3 0.8 O A:HOH386 2.3 31.0 1.0 O A:HOH388 2.3 39.9 1.0 CO A:CO203 3.0 24.8 0.8 S A:SO4202 3.1 23.4 0.6 O4 A:SO4202 3.1 28.0 1.0 CO A:CO204 3.6 25.2 1.0 O3 A:SO4202 3.6 22.5 1.0 OE2 A:GLU117 3.6 36.8 1.0 O A:HOH305 3.6 35.0 1.0 O A:HOH375 3.8 36.6 1.0 O A:HOH397 4.0 32.7 1.0 HE2 A:LYS7 4.3 51.5 1.0 O1 A:SO4202 4.4 30.5 1.0 O A:HOH374 4.5 29.5 1.0 HZ1 A:LYS7 4.5 51.9 1.0 CD A:GLU117 4.5 38.1 1.0 O A:HOH364 4.8 31.9 1.0 OE2 A:GLU56 4.8 25.3 1.0 HZ3 A:LYS7 4.9 51.9 1.0

S.E.Hill, E.Nguyen, C.U.Ukachukwu, D.M.Freeman, S.Quirk, R.L.Lieberman. Metal Ion Coordination in the E. Coli Nudix Hydrolase Dihydroneopterin Triphosphate Pyrophosphatase: New Clues Into Catalytic Mechanism. Plos One V. 12 80241 2017.
ISSN: ESSN 1932-6203
PubMed: 28742822
DOI: 10.1371/JOURNAL.PONE.0180241