Nickel in PDB 7kns: Cryo-Em Structure of Jack Bean Urease

All present enzymatic activity of Cryo-Em Structure of Jack Bean Urease:
3.5.1.5;

The binding sites of Nickel atom in the Cryo-Em Structure of Jack Bean Urease (pdb code 7kns). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Cryo-Em Structure of Jack Bean Urease, PDB code: 7kns:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Cryo-Em Structure of Jack Bean Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Cryo-Em Structure of Jack Bean Urease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni901 b:43.5 occ:1.00 O3 A:PO4902 1.9 38.1 1.0 OQ2 A:KCX490 2.1 27.4 1.0 ND1 A:HIS519 2.4 30.1 1.0 NE2 A:HIS545 2.6 30.5 1.0 CE1 A:HIS519 2.8 30.1 1.0 CX A:KCX490 3.0 27.4 1.0 OQ1 A:KCX490 3.1 27.4 1.0 CG A:HIS519 3.2 30.1 1.0 P A:PO4902 3.3 38.1 1.0 CE1 A:HIS545 3.5 30.5 1.0 CD2 A:HIS545 3.6 30.5 1.0 NE2 A:HIS492 3.7 28.9 1.0 O2 A:PO4902 3.8 38.1 1.0 NE2 A:HIS519 3.8 30.1 1.0 O1 A:PO4902 3.8 38.1 1.0 CB A:HIS519 3.9 30.1 1.0 CD2 A:HIS519 4.0 30.1 1.0 CE1 A:HIS407 4.1 26.7 1.0 NZ A:KCX490 4.2 27.4 1.0 NE2 A:HIS407 4.3 26.7 1.0 CD2 A:HIS492 4.3 28.9 1.0 O A:GLY550 4.3 34.3 1.0 O4 A:PO4902 4.4 38.1 1.0 CE1 A:HIS492 4.4 28.9 1.0 OD2 A:ASP633 4.5 28.6 1.0 OD1 A:ASP633 4.5 28.6 1.0 ND1 A:HIS545 4.7 30.5 1.0 CE A:KCX490 4.7 27.4 1.0 CG A:HIS545 4.7 30.5 1.0 C A:GLY550 4.8 34.3 1.0 O A:ALA440 4.9 28.5 1.0 CA A:HIS519 4.9 30.1 1.0 CG A:ASP633 4.9 28.6 1.0

Nickel binding site 2 out of 6 in the Cryo-Em Structure of Jack Bean Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Cryo-Em Structure of Jack Bean Urease within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni901 b:45.2 occ:1.00 O3 B:PO4902 1.9 31.6 1.0 OQ2 B:KCX490 1.9 27.2 1.0 ND1 B:HIS519 2.1 29.6 1.0 NE2 B:HIS545 2.1 30.6 1.0 CG B:HIS519 2.6 29.6 1.0 CE1 B:HIS545 2.8 30.6 1.0 CB B:HIS519 2.8 29.6 1.0 CX B:KCX490 3.0 27.2 1.0 CE1 B:HIS519 3.0 29.6 1.0 CD2 B:HIS545 3.3 30.6 1.0 P B:PO4902 3.3 31.6 1.0 OQ1 B:KCX490 3.5 27.2 1.0 CD2 B:HIS519 3.6 29.6 1.0 NE2 B:HIS519 3.8 29.6 1.0 NE2 B:HIS492 3.8 28.2 1.0 O4 B:PO4902 3.9 31.6 1.0 ND1 B:HIS545 4.0 30.6 1.0 NZ B:KCX490 4.0 27.2 1.0 CA B:HIS519 4.1 29.6 1.0 O2 B:PO4902 4.1 31.6 1.0 CD2 B:HIS492 4.1 28.2 1.0 O1 B:PO4902 4.2 31.6 1.0 CG B:HIS545 4.3 30.6 1.0 CE1 B:HIS407 4.3 26.5 1.0 CE B:KCX490 4.3 27.2 1.0 CE1 B:HIS492 4.5 28.2 1.0 NE2 B:HIS407 4.6 26.5 1.0 CB B:TYR544 4.7 27.9 1.0 O B:GLY550 4.8 33.9 1.0 N B:HIS519 4.9 29.6 1.0 CG B:HIS492 5.0 28.2 1.0

Nickel binding site 3 out of 6 in the Cryo-Em Structure of Jack Bean Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Cryo-Em Structure of Jack Bean Urease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni901 b:52.1 occ:1.00 O4 C:PO4902 1.9 33.4 1.0 OQ1 C:KCX490 1.9 27.6 1.0 O2 C:PO4902 1.9 33.4 1.0 OQ2 C:KCX490 1.9 27.6 1.0 CX C:KCX490 2.2 27.6 1.0 P C:PO4902 2.3 33.4 1.0 NE2 C:HIS407 2.7 27.1 1.0 CE1 C:HIS407 2.9 27.1 1.0 OD1 C:ASP633 3.3 28.4 1.0 O1 C:PO4902 3.4 33.4 1.0 NE2 C:HIS545 3.5 30.8 1.0 O3 C:PO4902 3.5 33.4 1.0 NZ C:KCX490 3.5 27.6 1.0 CD2 C:HIS545 3.8 30.8 1.0 ND1 C:HIS519 3.9 29.8 1.0 NE2 C:HIS409 3.9 26.3 1.0 NE2 C:HIS492 4.0 28.6 1.0 CG C:ASP633 4.0 28.4 1.0 CD2 C:HIS407 4.0 27.1 1.0 OD2 C:ASP633 4.1 28.4 1.0 ND1 C:HIS407 4.2 27.1 1.0 CE1 C:HIS409 4.2 26.3 1.0 CD2 C:HIS492 4.3 28.6 1.0 CE C:KCX490 4.5 27.6 1.0 O C:ALA440 4.6 28.4 1.0 CD2 C:TYR544 4.7 28.3 1.0 CE1 C:HIS545 4.7 30.8 1.0 CG C:HIS519 4.7 29.8 1.0 CE1 C:HIS519 4.7 29.8 1.0 CB C:HIS519 4.8 29.8 1.0 CG C:HIS407 4.8 27.1 1.0

Nickel binding site 4 out of 6 in the Cryo-Em Structure of Jack Bean Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Cryo-Em Structure of Jack Bean Urease within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni901 b:47.7 occ:1.00 O1 D:PO4902 1.8 32.7 1.0 OQ1 D:KCX490 1.9 27.6 1.0 NE2 D:HIS545 2.1 30.5 1.0 ND1 D:HIS519 2.1 29.6 1.0 CE1 D:HIS545 3.0 30.5 1.0 CX D:KCX490 3.0 27.6 1.0 CG D:HIS519 3.1 29.6 1.0 CD2 D:HIS545 3.1 30.5 1.0 CE1 D:HIS519 3.2 29.6 1.0 P D:PO4902 3.2 32.7 1.0 CB D:HIS519 3.3 29.6 1.0 OQ2 D:KCX490 3.4 27.6 1.0 O3 D:PO4902 3.7 32.7 1.0 O4 D:PO4902 3.8 32.7 1.0 NE2 D:HIS492 3.9 28.7 1.0 CE1 D:HIS407 3.9 27.1 1.0 ND1 D:HIS545 4.1 30.5 1.0 NZ D:KCX490 4.1 27.6 1.0 CG D:HIS545 4.2 30.5 1.0 NE2 D:HIS407 4.2 27.1 1.0 CD2 D:HIS519 4.2 29.6 1.0 NE2 D:HIS519 4.2 29.6 1.0 CD2 D:HIS492 4.3 28.7 1.0 O2 D:PO4902 4.3 32.7 1.0 CA D:HIS519 4.4 29.6 1.0 CE D:KCX490 4.5 27.6 1.0 O D:GLY550 4.6 33.5 1.0 CB D:TYR544 4.6 28.2 1.0 CE1 D:HIS492 4.7 28.7 1.0 OD1 D:ASP633 4.9 28.5 1.0 OD2 D:ASP633 4.9 28.5 1.0

Nickel binding site 5 out of 6 in the Cryo-Em Structure of Jack Bean Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Cryo-Em Structure of Jack Bean Urease within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni901 b:43.5 occ:1.00 O1 E:PO4902 1.8 31.6 1.0 OQ1 E:KCX490 1.9 27.4 1.0 ND1 E:HIS519 2.1 29.7 1.0 NE2 E:HIS545 2.4 30.4 1.0 CX E:KCX490 2.8 27.4 1.0 CG E:HIS519 3.0 29.7 1.0 P E:PO4902 3.1 31.6 1.0 CE1 E:HIS519 3.1 29.7 1.0 OQ2 E:KCX490 3.1 27.4 1.0 CE1 E:HIS545 3.3 30.4 1.0 CB E:HIS519 3.3 29.7 1.0 CD2 E:HIS545 3.4 30.4 1.0 O4 E:PO4902 3.4 31.6 1.0 NE2 E:HIS492 3.6 28.6 1.0 O2 E:PO4902 3.6 31.6 1.0 NZ E:KCX490 3.9 27.4 1.0 CD2 E:HIS492 4.0 28.6 1.0 CE1 E:HIS407 4.0 26.6 1.0 NE2 E:HIS519 4.2 29.7 1.0 CD2 E:HIS519 4.2 29.7 1.0 NE2 E:HIS407 4.2 26.6 1.0 O3 E:PO4902 4.3 31.6 1.0 CE E:KCX490 4.4 27.4 1.0 ND1 E:HIS545 4.4 30.4 1.0 CE1 E:HIS492 4.4 28.6 1.0 CG E:HIS545 4.5 30.4 1.0 CA E:HIS519 4.5 29.7 1.0 O E:GLY550 4.6 33.6 1.0 OD1 E:ASP633 4.9 28.3 1.0 CB E:TYR544 4.9 28.2 1.0 OD2 E:ASP633 5.0 28.3 1.0

Nickel binding site 6 out of 6 in the Cryo-Em Structure of Jack Bean Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Cryo-Em Structure of Jack Bean Urease within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni901 b:41.2 occ:1.00 O1 F:PO4902 2.0 40.2 1.0 OQ1 F:KCX490 2.4 27.3 1.0 ND1 F:HIS519 2.4 29.7 1.0 NE2 F:HIS545 2.6 30.5 1.0 CE1 F:HIS519 2.9 29.7 1.0 CX F:KCX490 3.1 27.3 1.0 OQ2 F:KCX490 3.1 27.3 1.0 P F:PO4902 3.3 40.2 1.0 CD2 F:HIS545 3.5 30.5 1.0 CG F:HIS519 3.5 29.7 1.0 NE2 F:HIS492 3.5 28.3 1.0 CE1 F:HIS545 3.7 30.5 1.0 O2 F:PO4902 3.7 40.2 1.0 O4 F:PO4902 3.9 40.2 1.0 NE2 F:HIS519 4.0 29.7 1.0 CB F:HIS519 4.1 29.7 1.0 OD2 F:ASP633 4.2 28.4 1.0 CD2 F:HIS492 4.2 28.3 1.0 CE1 F:HIS492 4.2 28.3 1.0 CD2 F:HIS519 4.3 29.7 1.0 CE1 F:HIS407 4.3 26.5 1.0 OD1 F:ASP633 4.3 28.4 1.0 NZ F:KCX490 4.3 27.3 1.0 O F:GLY550 4.3 34.2 1.0 NE2 F:HIS407 4.3 26.5 1.0 O3 F:PO4902 4.4 40.2 1.0 O F:ALA440 4.6 28.0 1.0 CG F:ASP633 4.6 28.4 1.0 CG F:HIS545 4.7 30.5 1.0 ND1 F:HIS545 4.8 30.5 1.0 C F:GLY550 4.8 34.2 1.0 CE F:KCX490 5.0 27.3 1.0

J.R.Feathers, K.A.Spoth, J.C.Fromme. Experimental Evaluation of Super-Resolution Imaging and Magnification Choice in Single-Particle Cryo-Em J.Struct.Biol. 2021.
ISSN: ESSN 1095-8657