Nickel in PDB 4epe: Final Urease Structure For Radiation Damage Experiment at 300 K

All present enzymatic activity of Final Urease Structure For Radiation Damage Experiment at 300 K:
3.5.1.5;

The structure of Final Urease Structure For Radiation Damage Experiment at 300 K, PDB code: 4epe was solved by M.Warkentin, R.Badeau, J.B.Hopkins, R.E.Thorne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.66 / 2.05
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	170.697, 170.697, 170.697, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 18.5

The binding sites of Nickel atom in the Final Urease Structure For Radiation Damage Experiment at 300 K (pdb code 4epe). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Final Urease Structure For Radiation Damage Experiment at 300 K, PDB code: 4epe:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Final Urease Structure For Radiation Damage Experiment at 300 K


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Final Urease Structure For Radiation Damage Experiment at 300 K within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1601 b:47.1 occ:1.00 OQ2 C:KCX1217 2.0 34.3 1.0 ND1 C:HIS1246 2.1 34.9 1.0 NE2 C:HIS1272 2.2 33.2 1.0 O C:HOH1702 2.2 41.0 1.0 CX C:KCX1217 3.0 33.2 1.0 CE1 C:HIS1246 3.0 34.8 1.0 CD2 C:HIS1272 3.1 33.5 1.0 CG C:HIS1246 3.1 32.6 1.0 CE1 C:HIS1272 3.2 33.1 1.0 OQ1 C:KCX1217 3.2 32.6 1.0 O C:GLY1277 3.4 38.9 1.0 NE2 C:HIS1219 3.5 33.4 1.0 CB C:HIS1246 3.5 29.0 1.0 NI C:NI1602 3.6 42.4 1.0 O C:HOH1701 3.6 42.3 1.0 O C:HOH1703 3.8 38.7 1.0 CD2 C:HIS1219 3.9 32.8 1.0 CE1 C:HIS1134 4.2 33.5 1.0 NE2 C:HIS1246 4.2 35.2 1.0 CD2 C:HIS1246 4.2 34.9 1.0 CG C:HIS1272 4.3 33.3 1.0 NE2 C:HIS1134 4.3 33.2 1.0 NZ C:KCX1217 4.3 31.6 1.0 ND1 C:HIS1272 4.3 34.5 1.0 OD2 C:ASP1360 4.3 36.3 1.0 C C:GLY1277 4.4 38.4 1.0 CE1 C:HIS1219 4.5 33.3 1.0 CE C:KCX1217 4.8 29.9 1.0 CA C:HIS1246 4.8 28.1 1.0 CE1 C:HIS1320 4.9 52.5 0.5 OD1 C:ASP1360 4.9 30.7 1.0 NE2 C:HIS1320 4.9 53.0 0.5

Nickel binding site 2 out of 2 in the Final Urease Structure For Radiation Damage Experiment at 300 K


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Final Urease Structure For Radiation Damage Experiment at 300 K within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1602 b:42.4 occ:1.00 NE2 C:HIS1136 2.0 27.1 1.0 OQ1 C:KCX1217 2.1 32.6 1.0 OD1 C:ASP1360 2.1 30.7 1.0 O C:HOH1703 2.1 38.7 1.0 NE2 C:HIS1134 2.2 33.2 1.0 CE1 C:HIS1136 2.9 26.7 1.0 CG C:ASP1360 2.9 31.6 1.0 CX C:KCX1217 3.1 33.2 1.0 CD2 C:HIS1134 3.1 32.7 1.0 CD2 C:HIS1136 3.2 26.5 1.0 CE1 C:HIS1134 3.2 33.5 1.0 OD2 C:ASP1360 3.3 36.3 1.0 O C:HOH1702 3.3 41.0 1.0 OQ2 C:KCX1217 3.5 34.3 1.0 NI C:NI1601 3.6 47.1 1.0 O C:HOH1701 4.0 42.3 1.0 ND1 C:HIS1136 4.1 28.0 1.0 CG2 C:THR1169 4.2 25.4 1.0 O C:ALA1363 4.2 33.8 1.0 CG C:HIS1136 4.2 26.1 1.0 CB C:ASP1360 4.3 25.5 1.0 NZ C:KCX1217 4.3 31.6 1.0 CG C:HIS1134 4.3 30.9 1.0 ND1 C:HIS1134 4.4 33.5 1.0 CB C:ALA1363 4.5 28.1 1.0 O C:ALA1167 4.5 29.2 1.0 CA C:ASP1360 4.5 24.2 1.0 NE2 C:HIS1272 4.9 33.2 1.0 CD2 C:HIS1272 5.0 33.5 1.0 N C:THR1169 5.0 25.8 1.0

M.Warkentin, R.Badeau, J.B.Hopkins, R.E.Thorne. Spatial Distribution of Radiation Damage to Crystalline Proteins at 25-300 K. Acta Crystallogr.,Sect.D V. 68 1108 2012.
ISSN: ISSN 0907-4449
PubMed: 22948911
DOI: 10.1107/S0907444912021361