Nickel in PDB 4epb: Final Urease Structure For Radiation Damage Experiment at 100 K

All present enzymatic activity of Final Urease Structure For Radiation Damage Experiment at 100 K:
3.5.1.5;

The structure of Final Urease Structure For Radiation Damage Experiment at 100 K, PDB code: 4epb 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)	30.89 / 1.75
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	169.212, 169.212, 169.212, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 19.7

The binding sites of Nickel atom in the Final Urease Structure For Radiation Damage Experiment at 100 K (pdb code 4epb). 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 100 K, PDB code: 4epb:
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 100 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 100 K within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1601 b:33.3 occ:1.00 ND1 C:HIS1246 2.0 21.7 1.0 NE2 C:HIS1272 2.1 24.1 1.0 OQ2 C:KCX1217 2.1 23.7 1.0 O C:HOH1702 2.2 32.3 1.0 CE1 C:HIS1246 2.9 21.6 1.0 CE1 C:HIS1272 3.0 24.4 1.0 CG C:HIS1246 3.1 21.8 1.0 CD2 C:HIS1272 3.1 24.1 1.0 CX C:KCX1217 3.2 24.2 1.0 OQ1 C:KCX1217 3.5 23.4 1.0 O C:GLY1277 3.5 30.7 1.0 CB C:HIS1246 3.5 19.9 1.0 NE2 C:HIS1219 3.6 24.2 1.0 NI C:NI1602 3.7 29.5 1.0 O C:HOH1701 3.7 36.3 1.0 O C:HOH1703 3.8 29.9 1.0 CD2 C:HIS1219 4.0 24.0 1.0 NE2 C:HIS1246 4.0 22.3 1.0 ND1 C:HIS1272 4.1 25.2 1.0 CD2 C:HIS1246 4.1 22.6 1.0 CE1 C:HIS1134 4.1 22.5 1.0 CG C:HIS1272 4.2 24.1 1.0 OD2 C:ASP1360 4.3 25.0 1.0 NZ C:KCX1217 4.4 23.1 1.0 NE2 C:HIS1134 4.4 21.9 1.0 C C:GLY1277 4.5 29.5 1.0 CE1 C:HIS1219 4.6 23.8 1.0 CA C:HIS1246 4.7 20.1 1.0 CE C:KCX1217 4.8 22.8 1.0 OD1 C:ASP1360 5.0 22.7 1.0

Nickel binding site 2 out of 2 in the Final Urease Structure For Radiation Damage Experiment at 100 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 100 K within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1602 b:29.5 occ:1.00 NE2 C:HIS1136 2.0 19.0 1.0 OD1 C:ASP1360 2.1 22.7 1.0 NE2 C:HIS1134 2.1 21.9 1.0 OQ1 C:KCX1217 2.1 23.4 1.0 O C:HOH1703 2.3 29.9 1.0 CE1 C:HIS1136 2.9 19.5 1.0 CG C:ASP1360 3.0 25.1 1.0 CE1 C:HIS1134 3.1 22.5 1.0 CD2 C:HIS1134 3.1 22.2 1.0 CX C:KCX1217 3.1 24.2 1.0 CD2 C:HIS1136 3.2 19.8 1.0 OD2 C:ASP1360 3.3 25.0 1.0 OQ2 C:KCX1217 3.4 23.7 1.0 O C:HOH1702 3.5 32.3 1.0 NI C:NI1601 3.7 33.3 1.0 O C:HOH1701 4.0 36.3 1.0 ND1 C:HIS1136 4.1 19.3 1.0 CG2 C:THR1169 4.1 22.0 1.0 ND1 C:HIS1134 4.2 24.0 1.0 CG C:HIS1134 4.2 22.3 1.0 NZ C:KCX1217 4.2 23.1 1.0 CG C:HIS1136 4.2 17.3 1.0 CB C:ASP1360 4.2 22.4 1.0 O C:ALA1363 4.4 31.6 1.0 O C:ALA1167 4.4 20.3 1.0 CA C:ASP1360 4.5 21.1 1.0 CB C:ALA1363 4.5 23.1 1.0 NE2 C:HIS1272 4.8 24.1 1.0 CD2 C:HIS1272 4.9 24.1 1.0 N C:THR1169 5.0 18.6 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