Zinc in PDB 8k3l: SOD1 and NANOBODY3 Complex

All present enzymatic activity of SOD1 and NANOBODY3 Complex:
1.15.1.1;

The structure of SOD1 and NANOBODY3 Complex, PDB code: 8k3l was solved by S.Cheng, R.Liu, Y.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.07 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.214, 62.442, 314.928, 90, 90, 90
R / Rfree (%)	19.5 / 23.5

The structure of SOD1 and NANOBODY3 Complex also contains other interesting chemical elements:

Copper

(Cu)

4 atoms

The binding sites of Zinc atom in the SOD1 and NANOBODY3 Complex (pdb code 8k3l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the SOD1 and NANOBODY3 Complex, PDB code: 8k3l:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the SOD1 and NANOBODY3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SOD1 and NANOBODY3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:33.9 occ:1.00 OD1 A:ASP83 2.0 31.9 1.0 ND1 A:HIS63 2.2 31.2 1.0 ND1 A:HIS80 2.2 33.5 1.0 ND1 A:HIS71 2.2 29.8 1.0 CG A:ASP83 2.8 30.1 1.0 OD2 A:ASP83 2.9 29.8 1.0 CE1 A:HIS80 3.1 35.4 1.0 CG A:HIS63 3.1 36.2 1.0 CE1 A:HIS71 3.2 32.3 1.0 CE1 A:HIS63 3.2 34.8 1.0 CG A:HIS80 3.2 36.0 1.0 CG A:HIS71 3.2 34.8 1.0 CB A:HIS63 3.4 29.8 1.0 CB A:HIS71 3.5 34.0 1.0 CB A:HIS80 3.6 30.6 1.0 CA A:HIS71 3.9 35.6 1.0 O A:LYS136 4.0 35.6 1.0 CB A:ASP83 4.2 30.3 1.0 NE2 A:HIS80 4.2 36.7 1.0 CD2 A:HIS80 4.3 37.5 1.0 CD2 A:HIS63 4.3 35.0 1.0 NE2 A:HIS63 4.3 36.7 1.0 NE2 A:HIS71 4.3 38.2 1.0 CD2 A:HIS71 4.3 34.0 1.0 CA A:ASP83 4.7 29.8 1.0 N A:HIS80 4.8 32.3 1.0 CA A:HIS80 4.8 30.6 1.0 N A:GLY72 4.8 34.8 1.0 N A:HIS71 4.9 36.3 1.0 CD2 A:HIS46 4.9 33.0 1.0 N A:ASP83 4.9 27.9 1.0 C A:HIS71 4.9 36.8 1.0 CA A:HIS63 5.0 32.1 1.0 C A:LYS136 5.0 35.1 1.0

Zinc binding site 2 out of 4 in the SOD1 and NANOBODY3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SOD1 and NANOBODY3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:36.7 occ:1.00 CD2 C:HIS80 1.7 37.7 1.0 OD1 C:ASP83 2.0 34.1 1.0 ND1 C:HIS63 2.2 37.8 1.0 ND1 C:HIS71 2.3 37.8 1.0 NE2 C:HIS80 2.4 39.8 1.0 CG C:ASP83 2.8 36.3 1.0 OD2 C:ASP83 2.9 38.8 1.0 CG C:HIS80 2.9 38.1 1.0 CG C:HIS63 3.2 41.6 1.0 CE1 C:HIS71 3.2 38.6 1.0 CG C:HIS71 3.2 40.3 1.0 CE1 C:HIS63 3.3 43.8 1.0 CB C:HIS63 3.4 38.1 1.0 CB C:HIS71 3.6 37.9 1.0 CE1 C:HIS80 3.6 37.4 1.0 CB C:HIS80 3.8 38.6 1.0 ND1 C:HIS80 3.8 35.7 1.0 O C:LYS136 3.9 46.3 1.0 CA C:HIS71 3.9 39.4 1.0 CB C:ASP83 4.2 32.5 1.0 NE2 C:HIS71 4.3 41.6 1.0 CD2 C:HIS63 4.3 42.8 1.0 CD2 C:HIS71 4.3 42.5 1.0 NE2 C:HIS63 4.4 48.1 1.0 CA C:ASP83 4.7 32.9 1.0 N C:GLY72 4.7 41.3 1.0 N C:HIS80 4.7 34.1 1.0 C C:HIS71 4.9 44.4 1.0 CA C:HIS80 4.9 36.3 1.0 C C:LYS136 4.9 40.1 1.0 N C:ASP83 4.9 33.7 1.0 CA C:HIS63 5.0 36.6 1.0 N C:HIS71 5.0 38.6 1.0

Zinc binding site 3 out of 4 in the SOD1 and NANOBODY3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of SOD1 and NANOBODY3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn202 b:37.7 occ:1.00 OD1 E:ASP83 2.0 37.4 1.0 ND1 E:HIS80 2.2 34.3 1.0 ND1 E:HIS63 2.3 47.1 1.0 ND1 E:HIS71 2.3 40.9 1.0 CG E:ASP83 2.7 42.6 1.0 OD2 E:ASP83 2.8 37.8 1.0 CG E:HIS71 3.1 40.8 1.0 CE1 E:HIS80 3.1 42.0 1.0 CG E:HIS63 3.2 39.9 1.0 CG E:HIS80 3.2 41.8 1.0 CE1 E:HIS71 3.2 38.4 1.0 CE1 E:HIS63 3.3 48.4 1.0 CB E:HIS63 3.4 39.1 1.0 CB E:HIS71 3.4 39.9 1.0 CB E:HIS80 3.5 41.7 1.0 O E:LYS136 3.7 49.5 1.0 CA E:HIS71 3.9 39.5 1.0 CB E:ASP83 4.2 36.1 1.0 NE2 E:HIS80 4.3 43.8 1.0 CD2 E:HIS71 4.3 45.3 1.0 NE2 E:HIS71 4.3 44.4 1.0 CD2 E:HIS80 4.3 45.9 1.0 CD2 E:HIS63 4.3 48.1 1.0 NE2 E:HIS63 4.4 47.2 1.0 N E:HIS80 4.6 44.7 1.0 CA E:HIS80 4.6 43.0 1.0 CA E:ASP83 4.7 40.2 1.0 CD2 E:HIS46 4.7 45.0 1.0 C E:LYS136 4.8 50.6 1.0 N E:HIS71 4.8 42.7 1.0 N E:GLY72 4.8 42.7 1.0 CA E:HIS63 4.9 37.2 1.0 C E:HIS71 4.9 45.3 1.0 N E:ASP83 5.0 38.7 1.0

Zinc binding site 4 out of 4 in the SOD1 and NANOBODY3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of SOD1 and NANOBODY3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn202 b:39.2 occ:1.00 OD1 G:ASP83 1.9 36.0 1.0 ND1 G:HIS80 2.2 32.0 1.0 ND1 G:HIS71 2.2 39.9 1.0 ND1 G:HIS63 2.3 43.9 1.0 CG G:ASP83 2.7 40.3 1.0 OD2 G:ASP83 3.0 36.0 1.0 CG G:HIS63 3.0 42.3 1.0 CE1 G:HIS63 3.1 46.1 1.0 CE1 G:HIS71 3.1 38.2 1.0 CG G:HIS80 3.1 39.4 1.0 CE1 G:HIS80 3.2 39.2 1.0 CG G:HIS71 3.3 42.0 1.0 CB G:HIS63 3.4 37.0 1.0 CB G:HIS80 3.4 35.8 1.0 CB G:HIS71 3.7 37.2 1.0 CD2 G:HIS63 3.9 46.1 1.0 NE2 G:HIS63 3.9 46.5 1.0 O G:LYS136 3.9 45.0 1.0 CA G:HIS71 4.0 42.5 1.0 CB G:ASP83 4.2 38.5 1.0 NE2 G:HIS80 4.2 42.9 1.0 CD2 G:HIS80 4.3 40.5 1.0 NE2 G:HIS71 4.3 47.5 1.0 CD2 G:HIS71 4.4 44.9 1.0 CA G:ASP83 4.7 39.8 1.0 CA G:HIS80 4.7 38.5 1.0 N G:HIS80 4.7 42.7 1.0 N G:ASP83 4.8 33.4 1.0 N G:GLY72 4.9 42.4 1.0 CA G:HIS63 4.9 36.5 1.0 CD2 G:HIS46 4.9 41.1 1.0 C G:LYS136 5.0 48.8 1.0

C.Shihao, S.Cheng, R.Liu, Y.Ding. N/A N/A.