Copper 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:

Zinc

(Zn)

4 atoms

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

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of SOD1 and NANOBODY3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu201 b:41.3 occ:1.00 O A:HOH305 1.8 30.9 1.0 ND1 A:HIS46 2.1 35.4 1.0 NE2 A:HIS120 2.2 31.8 1.0 NE2 A:HIS48 2.2 36.3 1.0 CD2 A:HIS120 2.9 32.2 1.0 CG A:HIS46 3.1 32.9 1.0 CD2 A:HIS48 3.1 30.5 1.0 NE2 A:HIS63 3.1 36.7 1.0 CE1 A:HIS48 3.2 32.2 1.0 CE1 A:HIS46 3.2 31.7 1.0 CB A:HIS46 3.3 32.0 1.0 CE1 A:HIS120 3.3 34.4 1.0 CD2 A:HIS63 3.5 35.0 1.0 CG1 A:VAL118 4.0 32.5 1.0 O A:HOH352 4.0 27.1 1.0 CG A:HIS120 4.1 33.3 1.0 CE1 A:HIS63 4.2 34.8 1.0 CB A:VAL118 4.2 30.0 1.0 CD2 A:HIS46 4.2 33.0 1.0 NE2 A:HIS46 4.3 35.9 1.0 ND1 A:HIS48 4.3 38.1 1.0 CG A:HIS48 4.3 35.3 1.0 ND1 A:HIS120 4.3 34.2 1.0 CA A:HIS46 4.3 29.9 1.0 N A:HIS46 4.4 30.5 1.0 O A:VAL118 4.5 32.3 1.0 O A:HIS46 4.6 32.0 1.0 CG A:HIS63 4.7 36.2 1.0 C A:HIS46 4.7 31.8 1.0 ND1 A:HIS63 4.9 31.2 1.0

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of SOD1 and NANOBODY3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu201 b:41.7 occ:1.00 NE2 C:HIS120 2.0 36.0 1.0 NE2 C:HIS48 2.1 40.9 1.0 ND1 C:HIS46 2.2 40.9 1.0 CE1 C:HIS120 2.9 38.1 1.0 CD2 C:HIS120 3.0 35.7 1.0 CE1 C:HIS48 3.0 39.2 1.0 CE1 C:HIS46 3.1 37.0 1.0 NE2 C:HIS63 3.2 48.1 1.0 CG C:HIS46 3.2 38.6 1.0 CD2 C:HIS48 3.2 38.8 1.0 CB C:HIS46 3.5 33.9 1.0 CD2 C:HIS63 3.6 42.8 1.0 O C:HOH345 3.8 33.6 1.0 ND1 C:HIS120 4.0 41.1 1.0 CG C:HIS120 4.1 42.2 1.0 CE1 C:HIS63 4.1 43.8 1.0 ND1 C:HIS48 4.2 44.2 1.0 CG1 C:VAL118 4.2 35.2 1.0 NE2 C:HIS46 4.2 38.4 1.0 CG C:HIS48 4.3 39.2 1.0 CD2 C:HIS46 4.3 37.0 1.0 CB C:VAL118 4.4 36.3 1.0 CG C:HIS63 4.6 41.6 1.0 CA C:HIS46 4.7 32.5 1.0 N C:HIS46 4.8 32.2 1.0 ND1 C:HIS63 4.9 37.8 1.0 O C:VAL118 4.9 37.9 1.0

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of SOD1 and NANOBODY3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu201 b:47.9 occ:1.00 O E:HOH302 1.9 36.9 1.0 ND1 E:HIS46 2.2 49.6 1.0 NE2 E:HIS120 2.2 41.0 1.0 CE1 E:HIS48 2.3 42.9 1.0 NE2 E:HIS63 2.6 47.2 1.0 NE2 E:HIS48 2.7 39.8 1.0 CE1 E:HIS46 2.9 43.9 1.0 CE1 E:HIS120 2.9 42.5 1.0 CG E:HIS46 3.0 46.3 1.0 CD2 E:HIS120 3.1 47.6 1.0 CD2 E:HIS63 3.2 48.1 1.0 ND1 E:HIS48 3.4 43.5 1.0 CB E:HIS46 3.5 38.8 1.0 CE1 E:HIS63 3.7 48.4 1.0 NE2 E:HIS46 3.9 47.3 1.0 CD2 E:HIS46 4.0 45.0 1.0 CD2 E:HIS48 4.0 41.7 1.0 ND1 E:HIS120 4.0 48.7 1.0 CG E:HIS120 4.1 48.6 1.0 CG E:HIS48 4.3 41.9 1.0 CG E:HIS63 4.4 39.9 1.0 CG1 E:VAL118 4.5 42.2 1.0 ND1 E:HIS63 4.6 47.1 1.0 CB E:VAL118 4.6 37.7 1.0 CA E:HIS46 4.7 38.5 1.0 N E:HIS46 4.9 38.3 1.0

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of SOD1 and NANOBODY3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Cu201 b:47.1 occ:1.00 NE2 G:HIS120 1.9 40.6 1.0 NE2 G:HIS48 2.0 44.5 1.0 ND1 G:HIS46 2.1 48.2 1.0 CE1 G:HIS48 2.7 42.0 1.0 CE1 G:HIS120 2.7 41.8 1.0 NE2 G:HIS63 3.0 46.5 1.0 CD2 G:HIS120 3.0 37.3 1.0 CE1 G:HIS46 3.0 41.4 1.0 CG G:HIS46 3.1 46.4 1.0 CD2 G:HIS48 3.2 37.1 1.0 CD2 G:HIS63 3.2 46.1 1.0 CB G:HIS46 3.4 37.5 1.0 ND1 G:HIS120 3.9 42.0 1.0 ND1 G:HIS48 3.9 45.1 1.0 CG G:HIS120 4.0 43.0 1.0 NE2 G:HIS46 4.1 45.0 1.0 CG G:HIS48 4.2 40.7 1.0 CD2 G:HIS46 4.2 41.1 1.0 CG1 G:VAL118 4.2 41.3 1.0 CE1 G:HIS63 4.2 46.1 1.0 CB G:VAL118 4.3 40.7 1.0 CA G:HIS46 4.5 38.7 1.0 CG G:HIS63 4.6 42.3 1.0 N G:HIS46 4.6 41.4 1.0 O G:VAL118 5.0 43.2 1.0

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