Zinc in PDB 8yaf: SOD1, NANOBODY1 and NANOBODY2 Complex

All present enzymatic activity of SOD1, NANOBODY1 and NANOBODY2 Complex:
1.15.1.1;

The structure of SOD1, NANOBODY1 and NANOBODY2 Complex, PDB code: 8yaf was solved by S.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.68 / 3.28
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	139.949, 218.892, 122.708, 90, 90, 90
R / Rfree (%)	20 / 24.9

The binding sites of Zinc atom in the SOD1, NANOBODY1 and NANOBODY2 Complex (pdb code 8yaf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the SOD1, NANOBODY1 and NANOBODY2 Complex, PDB code: 8yaf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the SOD1, NANOBODY1 and NANOBODY2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SOD1, NANOBODY1 and NANOBODY2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:61.4 occ:0.00 OD1 A:ASP83 1.3 51.1 1.0 CG A:ASP83 1.9 51.4 1.0 OD2 A:ASP83 1.9 49.1 1.0 ND1 A:HIS63 2.2 70.4 1.0 ND1 A:HIS71 2.2 63.6 1.0 ND1 A:HIS80 2.2 61.5 1.0 CE1 A:HIS71 2.3 69.2 1.0 CE1 A:HIS80 2.9 68.5 1.0 CG A:HIS63 3.0 71.2 1.0 CE1 A:HIS63 3.1 73.2 1.0 CB A:HIS63 3.2 64.5 1.0 CG A:HIS80 3.4 70.3 1.0 CB A:ASP83 3.5 49.9 1.0 CG A:HIS71 3.6 68.4 1.0 NE2 A:HIS71 3.6 65.8 1.0 O A:LYS136 3.7 68.4 1.0 CB A:HIS80 3.9 65.2 1.0 CD2 A:HIS63 4.0 70.5 1.0 NE2 A:HIS63 4.1 64.2 1.0 CA A:ASP83 4.1 55.7 1.0 NE2 A:HIS80 4.1 75.2 1.0 CD2 A:HIS71 4.2 64.0 1.0 CD2 A:HIS46 4.4 58.2 1.0 CD2 A:HIS80 4.4 66.8 1.0 CB A:HIS71 4.4 62.6 1.0 N A:ASP83 4.6 55.9 1.0 NE2 A:HIS46 4.7 61.5 1.0 CA A:HIS63 4.8 58.0 1.0 CG A:HIS46 4.8 60.4 1.0 CA A:HIS71 4.9 65.3 1.0 C A:LYS136 4.9 68.2 1.0 O A:THR137 4.9 56.6 1.0

Zinc binding site 2 out of 6 in the SOD1, NANOBODY1 and NANOBODY2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SOD1, NANOBODY1 and NANOBODY2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:104.5 occ:0.00 CE1 D:HIS80 1.7 56.6 1.0 O D:LYS136 1.9 60.3 1.0 ND1 D:HIS63 2.3 50.6 1.0 ND1 D:HIS80 2.3 51.4 1.0 ND1 D:HIS71 2.3 60.5 1.0 OD2 D:ASP83 2.6 43.9 1.0 OD1 D:ASP83 2.9 34.5 1.0 NE2 D:HIS80 2.9 61.4 1.0 CE1 D:HIS63 2.9 64.2 1.0 CG D:HIS71 3.0 61.9 1.0 C D:LYS136 3.1 55.0 1.0 CB D:HIS71 3.1 61.7 1.0 CG D:ASP83 3.2 42.3 1.0 CG D:HIS63 3.3 64.7 1.0 CE1 D:HIS71 3.4 62.4 1.0 CG D:HIS80 3.6 59.6 1.0 CA D:HIS71 3.7 60.2 1.0 CB D:HIS63 3.8 66.8 1.0 CD2 D:HIS80 3.9 56.0 1.0 N D:THR137 4.0 57.3 1.0 NE2 D:HIS63 4.0 63.0 1.0 CA D:LYS136 4.0 55.6 1.0 CA D:THR137 4.1 57.7 1.0 CD2 D:HIS63 4.2 60.8 1.0 CD2 D:HIS71 4.2 55.9 1.0 NE2 D:HIS71 4.4 53.0 1.0 N D:HIS71 4.4 56.3 1.0 C D:THR137 4.5 56.6 1.0 CB D:ASP83 4.8 44.2 1.0 N D:LYS136 4.8 57.0 1.0 CB D:HIS80 4.8 54.7 1.0 N D:GLY138 4.9 53.6 1.0 O D:THR135 4.9 66.8 1.0 C D:HIS71 5.0 59.2 1.0 O D:THR137 5.0 54.4 1.0

Zinc binding site 3 out of 6 in the SOD1, NANOBODY1 and NANOBODY2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of SOD1, NANOBODY1 and NANOBODY2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn201 b:88.6 occ:0.00 OD1 H:ASP83 1.4 48.8 1.0 OD2 H:ASP83 1.7 42.6 1.0 CG H:ASP83 1.8 47.2 1.0 ND1 H:HIS80 2.1 57.5 1.0 ND1 H:HIS63 2.1 59.2 1.0 ND1 H:HIS71 2.4 56.2 1.0 CB H:HIS63 2.4 67.5 1.0 CG H:HIS63 2.4 67.3 1.0 CE1 H:HIS71 2.9 62.6 1.0 CG H:HIS80 3.0 63.7 1.0 CE1 H:HIS80 3.1 63.6 1.0 CB H:HIS80 3.3 61.0 1.0 CE1 H:HIS63 3.3 65.3 1.0 CB H:ASP83 3.4 44.1 1.0 CG H:HIS71 3.7 65.8 1.0 CD2 H:HIS63 3.7 64.3 1.0 CA H:HIS63 3.9 58.8 1.0 NE2 H:HIS63 4.0 65.5 1.0 CA H:ASP83 4.1 56.9 1.0 CD2 H:HIS80 4.2 61.3 1.0 NE2 H:HIS71 4.2 58.3 1.0 NE2 H:HIS80 4.2 67.0 1.0 O H:LYS136 4.3 68.2 1.0 CB H:HIS71 4.3 66.9 1.0 N H:ASP83 4.3 55.6 1.0 CA H:HIS80 4.5 56.0 1.0 CD2 H:HIS71 4.5 54.8 1.0 C H:HIS63 4.6 58.0 1.0 N H:HIS80 4.7 59.1 1.0 CA H:HIS71 4.7 63.5 1.0 CD2 H:HIS46 4.7 56.3 1.0 N H:HIS63 4.8 53.8 1.0 C H:GLY82 4.9 52.7 1.0 O H:HIS63 4.9 61.0 1.0

Zinc binding site 4 out of 6 in the SOD1, NANOBODY1 and NANOBODY2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of SOD1, NANOBODY1 and NANOBODY2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn201 b:59.7 occ:0.00 OD1 L:ASP83 1.5 45.5 1.0 OD2 L:ASP83 1.7 49.4 1.0 CG L:ASP83 1.9 46.5 1.0 ND1 L:HIS63 2.1 65.0 1.0 ND1 L:HIS80 2.1 50.5 1.0 ND1 L:HIS71 2.2 63.3 1.0 CE1 L:HIS71 2.6 67.0 1.0 CE1 L:HIS80 2.7 59.9 1.0 CG L:HIS63 2.8 68.1 1.0 CB L:HIS63 3.0 64.5 1.0 CE1 L:HIS63 3.2 67.5 1.0 CG L:HIS80 3.4 63.7 1.0 CG L:HIS71 3.5 64.3 1.0 CB L:ASP83 3.5 50.6 1.0 O L:LYS136 3.6 67.6 1.0 NE2 L:HIS71 3.9 59.7 1.0 NE2 L:HIS80 4.0 64.3 1.0 CB L:HIS80 4.0 65.0 1.0 CD2 L:HIS63 4.0 70.3 1.0 NE2 L:HIS63 4.1 67.8 1.0 CB L:HIS71 4.2 61.7 1.0 CA L:ASP83 4.3 61.3 1.0 CD2 L:HIS80 4.3 57.4 1.0 CD2 L:HIS71 4.3 61.9 1.0 CA L:HIS71 4.5 60.2 1.0 CA L:HIS63 4.6 59.6 1.0 C L:LYS136 4.7 64.7 1.0 N L:ASP83 4.8 61.8 1.0 CD2 L:HIS46 4.8 63.5 1.0 CA L:THR137 4.9 65.8 1.0 NE2 L:HIS46 4.9 65.0 1.0 O L:THR137 4.9 61.4 1.0 N L:GLY72 5.0 56.2 1.0 C L:THR137 5.0 62.7 1.0

Zinc binding site 5 out of 6 in the SOD1, NANOBODY1 and NANOBODY2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of SOD1, NANOBODY1 and NANOBODY2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn201 b:68.6 occ:0.00 CD2 P:HIS63 1.3 58.8 1.0 OD1 P:ASP83 1.6 42.5 1.0 CG P:HIS63 1.7 63.8 1.0 NE2 P:HIS63 1.9 68.0 1.0 ND1 P:HIS80 2.3 45.4 1.0 ND1 P:HIS63 2.4 64.2 1.0 ND1 P:HIS71 2.4 52.2 1.0 CE1 P:HIS63 2.5 59.2 1.0 CE1 P:HIS71 2.6 59.1 1.0 CB P:HIS63 2.7 65.0 1.0 CE1 P:HIS80 2.7 50.9 1.0 CG P:ASP83 2.7 48.8 1.0 OD2 P:ASP83 3.0 48.2 1.0 CG P:HIS80 3.6 57.6 1.0 CG P:HIS71 3.7 56.8 1.0 O P:LYS136 3.9 55.6 1.0 NE2 P:HIS71 3.9 53.1 1.0 NE2 P:HIS80 4.0 57.5 1.0 CA P:HIS63 4.0 55.0 1.0 CB P:ASP83 4.2 50.8 1.0 CB P:HIS80 4.3 59.7 1.0 CD2 P:HIS46 4.4 59.0 1.0 CD2 P:HIS71 4.5 51.6 1.0 CD2 P:HIS80 4.5 50.5 1.0 CG P:HIS46 4.5 58.3 1.0 CB P:HIS71 4.6 56.2 1.0 CA P:ASP83 4.6 59.1 1.0 O P:THR137 4.7 46.8 1.0 N P:HIS63 4.8 53.6 1.0 NE2 P:HIS46 4.8 60.3 1.0 CA P:THR137 4.8 47.7 1.0 C P:THR137 4.8 50.4 1.0 CB P:HIS46 4.9 55.2 1.0 C P:LYS136 5.0 51.8 1.0 ND1 P:HIS46 5.0 59.4 1.0

Zinc binding site 6 out of 6 in the SOD1, NANOBODY1 and NANOBODY2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of SOD1, NANOBODY1 and NANOBODY2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ T:Zn201 b:103.7 occ:0.00 OD1 T:ASP83 1.4 51.7 1.0 OD2 T:ASP83 1.8 39.5 1.0 CG T:ASP83 1.9 49.4 1.0 ND1 T:HIS63 2.2 69.8 1.0 ND1 T:HIS80 2.2 51.0 1.0 ND1 T:HIS71 2.3 56.8 1.0 CG T:HIS63 2.4 63.7 1.0 CE1 T:HIS71 2.5 62.4 1.0 CB T:HIS63 2.6 61.7 1.0 CE1 T:HIS80 2.9 60.3 1.0 CE1 T:HIS63 3.1 73.1 1.0 CD2 T:HIS63 3.3 66.7 1.0 CG T:HIS80 3.4 59.8 1.0 CB T:ASP83 3.5 48.9 1.0 CG T:HIS71 3.6 65.3 1.0 NE2 T:HIS63 3.7 70.1 1.0 NE2 T:HIS71 3.8 60.6 1.0 CB T:HIS80 3.8 59.5 1.0 O T:LYS136 3.9 63.6 1.0 CA T:HIS63 4.1 54.3 1.0 NE2 T:HIS80 4.2 59.5 1.0 CA T:ASP83 4.2 58.7 1.0 CD2 T:HIS71 4.4 58.2 1.0 CD2 T:HIS80 4.4 57.1 1.0 CB T:HIS71 4.5 62.0 1.0 N T:ASP83 4.7 62.2 1.0 CD2 T:HIS46 4.7 58.6 1.0 N T:HIS63 4.9 57.2 1.0 NE2 T:HIS46 4.9 59.2 1.0 CA T:HIS71 4.9 58.5 1.0 C T:HIS63 4.9 55.2 1.0 CG T:HIS46 5.0 58.3 1.0

S.Cheng, S.Cheng. N/A N/A.