Nickel in PDB 4epd: Initial Urease Structure For Radiation Damage Experiment at 300 K

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

The structure of Initial Urease Structure For Radiation Damage Experiment at 300 K, PDB code: 4epd 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)	19.63 / 1.70
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	170.765, 170.765, 170.765, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / 16.4

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

Nickel binding site 1 out of 2 in the Initial 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 Initial Urease Structure For Radiation Damage Experiment at 300 K within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1601 b:29.1 occ:1.00 ND1 C:HIS1246 2.0 20.1 1.0 OQ2 C:KCX1217 2.0 23.1 1.0 NE2 C:HIS1272 2.1 21.1 1.0 O C:HOH1702 2.1 24.7 1.0 O C:HOH1703 2.2 29.8 1.0 CE1 C:HIS1246 2.9 20.5 1.0 CE1 C:HIS1272 3.0 21.2 1.0 CD2 C:HIS1272 3.1 22.1 1.0 CX C:KCX1217 3.1 22.6 1.0 CG C:HIS1246 3.1 19.7 1.0 O C:GLY1277 3.2 24.6 1.0 OQ1 C:KCX1217 3.3 21.9 1.0 NE2 C:HIS1219 3.6 22.2 1.0 CB C:HIS1246 3.6 17.0 1.0 O C:HOH1701 3.6 26.6 1.0 NI C:NI1602 3.7 26.2 1.0 O C:HOH1704 3.8 25.4 1.0 CD2 C:HIS1219 4.0 21.8 1.0 NE2 C:HIS1246 4.1 20.4 1.0 CE1 C:HIS1134 4.1 20.8 1.0 ND1 C:HIS1272 4.2 22.4 1.0 CG C:HIS1272 4.2 21.4 1.0 CD2 C:HIS1246 4.2 21.2 1.0 C C:GLY1277 4.2 24.7 1.0 OD2 C:ASP1360 4.3 22.2 1.0 NZ C:KCX1217 4.3 19.8 1.0 NE2 C:HIS1134 4.3 21.0 1.0 CE1 C:HIS1219 4.5 22.3 1.0 CE C:KCX1217 4.7 19.2 1.0 CA C:HIS1246 4.8 16.9 1.0 CE1 C:HIS1320 4.9 28.5 0.5 NE2 C:HIS1320 5.0 29.2 0.5 OD1 C:ASP1360 5.0 18.9 1.0

Nickel binding site 2 out of 2 in the Initial 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 Initial Urease Structure For Radiation Damage Experiment at 300 K within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1602 b:26.2 occ:1.00 OD1 C:ASP1360 2.0 18.9 1.0 NE2 C:HIS1136 2.0 18.0 1.0 OQ1 C:KCX1217 2.0 21.9 1.0 NE2 C:HIS1134 2.1 21.0 1.0 O C:HOH1702 2.2 24.7 1.0 O C:HOH1704 2.2 25.4 1.0 CG C:ASP1360 2.9 21.3 1.0 CE1 C:HIS1136 2.9 17.7 1.0 CD2 C:HIS1134 3.1 20.7 1.0 CE1 C:HIS1134 3.1 20.8 1.0 CX C:KCX1217 3.1 22.6 1.0 OD2 C:ASP1360 3.2 22.2 1.0 CD2 C:HIS1136 3.2 18.1 1.0 O C:HOH1703 3.4 29.8 1.0 OQ2 C:KCX1217 3.5 23.1 1.0 NI C:NI1601 3.7 29.1 1.0 CG2 C:THR1169 4.1 16.8 1.0 ND1 C:HIS1136 4.1 18.0 1.0 O C:HOH1701 4.1 26.6 1.0 CB C:ASP1360 4.2 16.3 1.0 O C:ALA1363 4.2 21.0 1.0 CG C:HIS1134 4.2 20.0 1.0 ND1 C:HIS1134 4.2 21.3 1.0 CG C:HIS1136 4.2 16.2 1.0 NZ C:KCX1217 4.2 19.8 1.0 CA C:ASP1360 4.4 14.8 1.0 CB C:ALA1363 4.4 17.5 1.0 O C:ALA1167 4.5 17.7 1.0 NE2 C:HIS1272 4.8 21.1 1.0 CD2 C:HIS1272 4.9 22.1 1.0 N C:THR1169 5.0 15.8 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