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Nickel in PDB 5u7h: Ni-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli

Enzymatic activity of Ni-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli

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

Protein crystallography data

The structure of Ni-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli, PDB code: 5u7h 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) 33.55 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 53.680, 42.980, 57.050, 90.00, 91.36, 90.00
R / Rfree (%) 16.8 / 24.2

Nickel Binding Sites:

The binding sites of Nickel atom in the Ni-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli (pdb code 5u7h). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the Ni-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli, PDB code: 5u7h:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in 5u7h

Go back to Nickel Binding Sites List in 5u7h
Nickel binding site 1 out of 5 in the Ni-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Ni-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni204

b:21.1
occ:1.00
 OE2 A:GLU60 2.0 20.6 1.0
OE1 A:GLU56 2.0 17.7 1.0
OE2 A:GLU117 2.0 24.4 1.0
O A:HOH378 2.1 20.1 1.0
O3 A:SO4202 2.1 16.1 1.0
O A:HOH347 2.1 17.3 1.0
CD A:GLU60 3.0 20.2 1.0
CD A:GLU117 3.0 29.8 1.0
NI A:NI205 3.0 18.7 1.0
CD A:GLU56 3.1 14.8 1.0
S A:SO4202 3.2 20.3 1.0
CG A:GLU60 3.4 16.1 1.0
OE1 A:GLU117 3.4 20.9 1.0
OE2 A:GLU56 3.5 21.3 1.0
NI A:NI206 3.5 22.9 1.0
O4 A:SO4202 3.5 14.2 1.0
NI A:NI207 3.5 27.1 1.0
O A:HOH302 3.5 23.2 1.0
O2 A:SO4202 3.5 21.5 1.0
O A:THR40 4.0 17.2 1.0
OE1 A:GLU59 4.1 28.8 1.0
OE1 A:GLU60 4.2 20.1 1.0
O A:HOH396 4.3 32.0 1.0
CG A:GLU117 4.4 27.1 1.0
CG A:GLU56 4.4 15.7 1.0
O A:HOH337 4.4 22.8 1.0
O1 A:SO4202 4.4 20.0 1.0
O A:HOH314 4.6 27.7 1.0
O A:HOH387 4.7 23.0 1.0
CA A:GLY41 4.7 13.3 1.0
CB A:GLU56 4.7 17.0 1.0
O A:HOH345 4.7 19.6 1.0
CB A:GLU117 4.7 28.6 1.0
O A:HOH425 4.7 31.9 1.0
O A:HOH329 4.8 17.1 1.0
CB A:GLU60 4.9 19.8 1.0

Nickel binding site 2 out of 5 in 5u7h

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Nickel binding site 2 out of 5 in the Ni-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Ni-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni205

b:18.7
occ:1.00
 O A:THR40 2.0 17.2 1.0
O A:HOH345 2.0 19.6 1.0
O3 A:SO4202 2.0 16.1 1.0
OE2 A:GLU60 2.0 20.6 1.0
O A:HOH329 2.0 17.1 1.0
OE1 A:GLU117 2.1 20.9 1.0
CD A:GLU60 2.9 20.2 1.0
CD A:GLU117 3.0 29.8 1.0
NI A:NI204 3.0 21.1 1.0
C A:THR40 3.1 16.2 1.0
OE1 A:GLU60 3.2 20.1 1.0
OE2 A:GLU117 3.2 24.4 1.0
S A:SO4202 3.3 20.3 1.0
O1 A:SO4202 3.5 20.0 1.0
OG1 A:THR40 3.9 19.9 1.0
N A:GLY41 3.9 15.5 1.0
OE1 A:GLU56 4.0 17.7 1.0
N A:THR40 4.0 17.7 1.0
CA A:GLY41 4.0 13.3 1.0
O A:HOH314 4.0 27.7 1.0
CA A:THR40 4.0 18.4 1.0
O2 A:SO4202 4.1 21.5 1.0
NH1 A:ARG29 4.3 28.1 1.0
O4 A:SO4202 4.3 14.2 1.0
CG A:GLU60 4.3 16.1 1.0
OE1 A:GLN37 4.4 20.3 1.0
CG A:GLU117 4.5 27.1 1.0
CB A:THR40 4.6 19.6 1.0
O A:HOH378 4.7 20.1 1.0
CE1 A:HIS118 4.8 21.0 1.0
CD A:GLU56 4.8 14.8 1.0
O A:HOH347 4.9 17.3 1.0

Nickel binding site 3 out of 5 in 5u7h

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Nickel binding site 3 out of 5 in the Ni-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Ni-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni206

b:22.9
occ:1.00
 O4 A:SO4202 2.0 14.2 1.0
O A:HOH337 2.0 22.8 1.0
OE2 A:GLU56 2.0 21.3 1.0
O A:HOH378 2.0 20.1 1.0
O A:HOH353 2.2 18.3 1.0
O A:HOH387 2.2 23.0 1.0
CD A:GLU56 3.0 14.8 1.0
NI A:NI207 3.1 27.1 1.0
S A:SO4202 3.1 20.3 1.0
OE1 A:GLU56 3.4 17.7 1.0
NI A:NI204 3.5 21.1 1.0
O2 A:SO4202 3.5 21.5 1.0
O3 A:SO4202 3.6 16.1 1.0
O A:HOH311 3.9 31.2 1.0
NH1 A:ARG55 4.0 21.2 1.0
O A:HOH425 4.0 31.9 1.0
N A:SER42 4.1 19.0 1.0
OE1 A:GLU59 4.2 28.8 1.0
O A:HOH347 4.3 17.3 1.0
O1 A:SO4202 4.3 20.0 1.0
OE2 A:GLU44 4.3 46.0 1.0
CG A:GLU56 4.4 15.7 1.0
O A:SER42 4.4 18.4 1.0
CA A:GLY41 4.5 13.3 1.0
NH2 A:ARG55 4.8 22.2 1.0
C A:GLY41 4.8 15.9 1.0
O A:HOH302 4.8 23.2 1.0
O A:HOH305 4.8 23.9 1.0
CZ A:ARG55 4.8 21.6 1.0
OE2 A:GLU117 4.8 24.4 1.0
CB A:SER42 4.9 14.2 1.0
CA A:SER42 5.0 17.6 1.0

Nickel binding site 4 out of 5 in 5u7h

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Nickel binding site 4 out of 5 in the Ni-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Ni-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni207

b:27.1
occ:1.00
 O2 A:SO4202 2.0 21.5 1.0
O A:HOH302 2.1 23.2 1.0
O A:HOH305 2.2 23.9 1.0
O A:HOH378 2.2 20.1 1.0
O A:HOH387 2.2 23.0 1.0
O A:HOH425 2.4 31.9 1.0
S A:SO4202 3.1 20.3 1.0
NI A:NI206 3.1 22.9 1.0
O4 A:SO4202 3.2 14.2 1.0
OE2 A:GLU117 3.3 24.4 1.0
NI A:NI204 3.5 21.1 1.0
O3 A:SO4202 3.6 16.1 1.0
O A:HOH314 3.7 27.7 1.0
O A:HOH337 4.0 22.8 1.0
O4 A:SO4203 4.0 41.9 1.0
O A:HOH311 4.1 31.2 1.0
CD A:GLU117 4.2 29.8 1.0
O A:HOH347 4.3 17.3 1.0
O1 A:SO4202 4.3 20.0 1.0
OE2 A:GLU56 4.8 21.3 1.0
O A:HOH412 4.8 39.0 1.0
OE1 A:GLU56 4.9 17.7 1.0
OE1 A:GLU117 4.9 20.9 1.0
NZ A:LYS7 4.9 29.4 1.0
O A:HOH353 4.9 18.3 1.0
O3 A:SO4203 5.0 55.6 1.0

Nickel binding site 5 out of 5 in 5u7h

Go back to Nickel Binding Sites List in 5u7h
Nickel binding site 5 out of 5 in the Ni-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Ni-Bound Dihydroneopterin Triphosphate Pyrophosphohydrolase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni208

b:58.5
occ:1.00
 NE2 A:HIS109 2.1 27.4 1.0
CE1 A:HIS109 3.1 24.1 1.0
CD2 A:HIS109 3.1 26.7 1.0
ND1 A:HIS109 4.2 27.2 1.0
CG A:HIS109 4.2 29.7 1.0
CB A:PRO108 4.8 22.9 1.0

Reference:

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
Page generated: Thu Oct 10 08:06:27 2024

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