Nickel in PDB 6h6s: Sad Phasing on Nickel-Substituted Human Carbonic Anhydrase II

All present enzymatic activity of Sad Phasing on Nickel-Substituted Human Carbonic Anhydrase II:
4.2.1.1;

The structure of Sad Phasing on Nickel-Substituted Human Carbonic Anhydrase II, PDB code: 6h6s was solved by V.Calderone, M.Fragai, J.P.Silva, C.Luchinat, E.Ravera, C.F.G.C.Geraldes, A.L.Macedo, L.Cerofolini, S.Giuntini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.34 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.480, 41.180, 84.040, 90.00, 109.25, 90.00
R / Rfree (%)	15 / 20.4

The binding sites of Nickel atom in the Sad Phasing on Nickel-Substituted Human Carbonic Anhydrase II (pdb code 6h6s). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Sad Phasing on Nickel-Substituted Human Carbonic Anhydrase II, PDB code: 6h6s:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Sad Phasing on Nickel-Substituted Human Carbonic Anhydrase II


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Sad Phasing on Nickel-Substituted Human Carbonic Anhydrase II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:31.7 occ:1.00 N A:HIS2 1.9 34.8 1.0 ND1 A:HIS3 1.9 26.8 1.0 N A:HIS3 2.0 21.8 1.0 O A:HOH455 2.1 27.6 1.0 C A:HIS2 2.8 31.1 1.0 CA A:HIS2 2.8 47.8 1.0 CG A:HIS3 2.9 30.6 1.0 CE1 A:HIS3 2.9 30.5 1.0 CA A:HIS3 3.0 23.2 1.0 CB A:HIS3 3.2 30.2 1.0 N A:TRP4 3.5 18.8 1.0 O A:HOH665 3.6 47.2 1.0 C A:HIS3 3.7 24.4 1.0 O A:HIS2 3.9 49.4 1.0 CD2 A:HIS3 4.0 26.1 1.0 NE2 A:HIS3 4.1 31.8 1.0 CB A:HIS2 4.1 67.0 1.0 CD1 A:TRP4 4.1 15.6 1.0 CG A:HIS2 4.5 83.9 1.0 CA A:TRP4 4.7 16.6 1.0 CD2 A:HIS2 4.8 76.4 1.0 O A:HIS3 4.9 34.5 1.0 CG A:TRP4 4.9 15.7 1.0 NE1 A:TRP4 5.0 15.2 1.0

Nickel binding site 2 out of 4 in the Sad Phasing on Nickel-Substituted Human Carbonic Anhydrase II


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Sad Phasing on Nickel-Substituted Human Carbonic Anhydrase II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:9.7 occ:1.00 NE2 A:HIS93 2.0 11.0 1.0 ND1 A:HIS118 2.0 8.9 1.0 O A:HOH564 2.0 12.2 1.0 NE2 A:HIS95 2.1 9.2 1.0 O A:HOH401 2.1 33.2 1.0 O A:HOH589 2.3 13.2 1.0 CE1 A:HIS118 2.9 8.8 1.0 CE1 A:HIS93 3.0 8.4 1.0 CE1 A:HIS95 3.0 10.0 1.0 CD2 A:HIS93 3.0 10.2 1.0 CD2 A:HIS95 3.1 9.5 1.0 CG A:HIS118 3.2 7.6 1.0 O A:HOH592 3.5 23.1 1.0 CB A:HIS118 3.6 8.3 1.0 OG1 A:THR197 3.6 11.0 1.0 O A:HOH690 3.9 27.5 1.0 OE1 A:GLU105 4.0 11.4 1.0 O A:HOH633 4.1 27.0 1.0 NE2 A:HIS118 4.1 7.9 1.0 ND1 A:HIS93 4.1 8.8 1.0 ND1 A:HIS95 4.1 10.6 1.0 CG A:HIS93 4.2 9.0 1.0 O A:HOH572 4.2 29.7 1.0 CG A:HIS95 4.2 8.2 1.0 CD2 A:HIS118 4.2 8.8 1.0 CD A:GLU105 4.9 11.3 1.0 CB A:THR197 5.0 9.3 1.0 CH2 A:TRP207 5.0 9.8 1.0

Nickel binding site 3 out of 4 in the Sad Phasing on Nickel-Substituted Human Carbonic Anhydrase II


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Sad Phasing on Nickel-Substituted Human Carbonic Anhydrase II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:51.3 occ:1.00 N B:HIS2 2.0 72.0 1.0 N B:HIS3 2.1 16.2 1.0 C B:HIS2 2.1 45.0 1.0 O B:HOH408 2.4 29.2 1.0 CA B:HIS2 2.5 71.2 1.0 ND1 B:HIS3 2.5 41.3 1.0 CA B:HIS3 2.6 27.7 1.0 CB B:HIS3 2.9 40.2 1.0 CG B:HIS3 3.1 50.5 1.0 O B:HIS2 3.1 50.3 1.0 N B:TRP4 3.6 21.1 1.0 CE1 B:HIS3 3.7 56.4 1.0 C B:HIS3 3.7 33.4 1.0 CB B:HIS2 3.8 87.6 1.0 CD2 B:HIS3 4.4 60.6 1.0 CG B:HIS2 4.6 90.3 1.0 NE2 B:HIS3 4.6 53.9 1.0 O B:HIS3 5.0 54.7 1.0

Nickel binding site 4 out of 4 in the Sad Phasing on Nickel-Substituted Human Carbonic Anhydrase II


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Sad Phasing on Nickel-Substituted Human Carbonic Anhydrase II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni302 b:9.7 occ:1.00 NE2 B:HIS93 2.0 10.6 1.0 O B:HOH560 2.0 14.9 1.0 ND1 B:HIS118 2.1 8.8 1.0 NE2 B:HIS95 2.1 8.9 1.0 O B:HOH596 2.2 13.2 1.0 O B:HOH402 2.2 23.2 1.0 CE1 B:HIS118 3.0 9.6 1.0 CE1 B:HIS93 3.0 9.1 1.0 CE1 B:HIS95 3.1 9.2 1.0 CD2 B:HIS93 3.1 9.6 1.0 CD2 B:HIS95 3.1 9.3 1.0 CG B:HIS118 3.2 9.5 1.0 O B:HOH632 3.4 30.9 1.0 CB B:HIS118 3.6 7.6 1.0 OG1 B:THR197 3.9 12.2 1.0 OE1 B:GLU105 4.0 13.2 1.0 ND1 B:HIS93 4.2 9.4 1.0 NE2 B:HIS118 4.2 8.8 1.0 CG B:HIS93 4.2 9.1 1.0 ND1 B:HIS95 4.2 9.3 1.0 O B:HOH565 4.2 23.7 1.0 CD2 B:HIS118 4.3 8.7 1.0 CG B:HIS95 4.3 7.8 1.0 O B:HOH664 4.3 23.9 1.0 CH2 B:TRP207 4.8 10.6 1.0 CD B:GLU105 5.0 13.4 1.0

J.M.Silva, S.Giuntini, L.Cerofolini, C.F.G.C.Geraldes, A.L.Macedo, E.Ravera, M.Fragai, C.Luchinat, V.Calderone. Non-Crystallographic Symmetry in Proteins: Jahn-Teller-Like and Butterfly-Like Effects? J. Biol. Inorg. Chem. V. 24 91 2019.
ISSN: ESSN 1432-1327
PubMed: 30470900
DOI: 10.1007/S00775-018-1630-0