Zinc in PDB 5k02: Structure of Human SOD1 with T2D Mutation

All present enzymatic activity of Structure of Human SOD1 with T2D Mutation:
1.15.1.1;

The structure of Structure of Human SOD1 with T2D Mutation, PDB code: 5k02 was solved by J.M.Fay, C.Zhu, W.Cui, H.Ke, N.V.Dokholyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	149.92 / 1.99
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	111.980, 111.961, 149.880, 89.86, 89.85, 60.13
R / Rfree (%)	14.6 / 16.2

The structure of Structure of Human SOD1 with T2D Mutation also contains other interesting chemical elements:

Copper

(Cu)

24 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Structure of Human SOD1 with T2D Mutation (pdb code 5k02). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Structure of Human SOD1 with T2D Mutation, PDB code: 5k02:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in the Structure of Human SOD1 with T2D Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human SOD1 with T2D Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:30.4 occ:1.00 OD1 A:ASP83 2.0 29.0 1.0 ND1 A:HIS80 2.1 30.2 1.0 ND1 A:HIS63 2.1 31.2 1.0 ND1 A:HIS71 2.1 29.7 1.0 CE1 A:HIS80 2.8 31.5 1.0 CG A:ASP83 2.9 27.4 1.0 CE1 A:HIS71 3.0 28.6 1.0 CG A:HIS63 3.1 31.7 1.0 CE1 A:HIS63 3.1 31.1 1.0 CG A:HIS71 3.1 28.9 1.0 OD2 A:ASP83 3.1 25.3 1.0 CG A:HIS80 3.3 31.0 1.0 CB A:HIS63 3.4 31.4 1.0 O A:LYS136 3.5 36.8 1.0 CB A:HIS71 3.6 30.6 1.0 CB A:HIS80 3.9 30.5 1.0 NE2 A:HIS80 4.0 30.0 1.0 NE2 A:HIS71 4.0 27.9 1.0 CA A:HIS71 4.1 32.2 1.0 CD2 A:HIS71 4.1 28.7 1.0 NE2 A:HIS63 4.2 33.6 1.0 CD2 A:HIS63 4.2 31.7 1.0 CD2 A:HIS80 4.2 30.5 1.0 CB A:ASP83 4.3 27.1 1.0 C A:LYS136 4.6 34.8 1.0 CA A:ASP83 4.8 28.3 1.0 N A:HIS80 4.8 31.5 1.0 CA A:THR137 4.9 35.3 1.0 CA A:HIS63 4.9 31.2 1.0 CA A:HIS80 5.0 31.6 1.0 O A:HOH320 5.0 31.4 1.0

Zinc binding site 2 out of 24 in the Structure of Human SOD1 with T2D Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human SOD1 with T2D Mutation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:30.2 occ:1.00 OD1 B:ASP83 2.0 29.7 1.0 ND1 B:HIS80 2.1 31.5 1.0 ND1 B:HIS71 2.1 33.8 1.0 ND1 B:HIS63 2.2 30.6 1.0 CE1 B:HIS80 2.8 32.0 1.0 CG B:HIS63 2.9 30.4 1.0 CE1 B:HIS63 3.0 28.6 1.0 CG B:ASP83 3.1 30.6 1.0 CG B:HIS71 3.1 34.6 1.0 CE1 B:HIS71 3.2 34.6 1.0 CB B:HIS63 3.3 31.5 1.0 CG B:HIS80 3.3 32.2 1.0 CB B:HIS71 3.3 34.6 1.0 OD2 B:ASP83 3.4 28.5 1.0 O B:LYS136 3.6 37.9 1.0 CB B:HIS80 3.8 32.2 1.0 CD2 B:HIS63 3.9 29.1 1.0 CA B:HIS71 3.9 34.3 1.0 NE2 B:HIS63 4.0 27.9 1.0 NE2 B:HIS80 4.1 30.2 1.0 CD2 B:HIS71 4.3 34.4 1.0 CD2 B:HIS80 4.3 31.5 1.0 NE2 B:HIS71 4.3 34.2 1.0 O B:HOH308 4.4 36.7 1.0 CB B:ASP83 4.4 30.5 1.0 C B:LYS136 4.5 38.9 1.0 CA B:THR137 4.7 37.8 1.0 CA B:HIS63 4.8 33.1 1.0 CA B:ASP83 4.9 31.9 1.0 N B:HIS71 4.9 33.6 1.0 O B:THR137 4.9 35.8 1.0 N B:GLY72 4.9 34.0 1.0 C B:HIS71 4.9 34.6 1.0 C B:THR137 5.0 37.6 1.0 N B:HIS80 5.0 34.8 1.0 N B:THR137 5.0 39.7 1.0

Zinc binding site 3 out of 24 in the Structure of Human SOD1 with T2D Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human SOD1 with T2D Mutation within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:26.7 occ:1.00 OD1 C:ASP83 2.0 25.8 1.0 ND1 C:HIS80 2.1 25.8 1.0 ND1 C:HIS63 2.1 28.3 1.0 ND1 C:HIS71 2.2 30.1 1.0 CE1 C:HIS80 2.2 26.3 1.0 CG C:HIS63 3.0 30.7 1.0 CE1 C:HIS71 3.0 29.4 1.0 CG C:ASP83 3.0 24.6 1.0 CB C:HIS63 3.1 31.1 1.0 CG C:HIS71 3.2 31.6 1.0 CE1 C:HIS63 3.2 29.8 1.0 OD2 C:ASP83 3.4 24.0 1.0 CG C:HIS80 3.4 27.4 1.0 NE2 C:HIS80 3.5 24.2 1.0 CB C:HIS71 3.6 31.9 1.0 O C:LYS136 3.6 31.8 1.0 CD2 C:HIS80 4.1 26.3 1.0 CA C:HIS71 4.1 31.9 1.0 NE2 C:HIS71 4.2 32.0 1.0 CD2 C:HIS63 4.2 29.9 1.0 CB C:HIS80 4.3 28.8 1.0 NE2 C:HIS63 4.3 30.9 1.0 CD2 C:HIS71 4.3 30.4 1.0 CB C:ASP83 4.4 25.7 1.0 CA C:HIS63 4.7 32.6 1.0 C C:LYS136 4.7 32.7 1.0 CA C:ASP83 4.8 26.7 1.0 N C:ASP83 4.9 25.8 1.0 CD2 C:HIS46 5.0 28.0 1.0 N C:HIS71 5.0 32.4 1.0 N C:HIS80 5.0 31.9 1.0

Zinc binding site 4 out of 24 in the Structure of Human SOD1 with T2D Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human SOD1 with T2D Mutation within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:28.0 occ:1.00 OD1 D:ASP83 2.0 26.9 1.0 ND1 D:HIS80 2.1 25.0 1.0 ND1 D:HIS71 2.1 28.1 1.0 ND1 D:HIS63 2.1 29.6 1.0 CE1 D:HIS80 2.3 24.7 1.0 CG D:HIS63 2.9 31.0 1.0 CE1 D:HIS71 3.0 27.0 1.0 CE1 D:HIS63 3.0 28.6 1.0 CG D:ASP83 3.1 26.1 1.0 CG D:HIS71 3.2 27.6 1.0 CB D:HIS63 3.3 31.0 1.0 OD2 D:ASP83 3.4 25.6 1.0 CG D:HIS80 3.4 25.4 1.0 O D:LYS136 3.5 35.2 1.0 NE2 D:HIS80 3.6 23.1 1.0 CB D:HIS71 3.6 29.5 1.0 CD2 D:HIS63 4.0 30.4 1.0 NE2 D:HIS63 4.0 31.9 1.0 CA D:HIS71 4.1 30.0 1.0 NE2 D:HIS71 4.1 25.7 1.0 CD2 D:HIS80 4.2 24.4 1.0 CD2 D:HIS71 4.3 27.6 1.0 CB D:HIS80 4.3 27.8 1.0 CB D:ASP83 4.5 26.6 1.0 O D:HOH320 4.5 46.2 1.0 C D:LYS136 4.5 33.3 1.0 CA D:THR137 4.7 34.0 1.0 CA D:HIS63 4.8 32.3 1.0 CA D:ASP83 4.9 28.4 1.0 N D:HIS71 5.0 31.3 1.0 N D:GLY72 5.0 30.8 1.0

Zinc binding site 5 out of 24 in the Structure of Human SOD1 with T2D Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Human SOD1 with T2D Mutation within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn202 b:33.8 occ:1.00 OD1 E:ASP83 2.0 33.1 1.0 ND1 E:HIS63 2.1 32.5 1.0 ND1 E:HIS80 2.1 32.5 1.0 ND1 E:HIS71 2.1 37.5 1.0 OD2 E:ASP83 2.4 34.8 1.0 CG E:ASP83 2.5 33.5 1.0 CE1 E:HIS80 2.8 32.4 1.0 CG E:HIS80 2.9 32.0 1.0 CE1 E:HIS71 3.0 38.6 1.0 CG E:HIS63 3.1 32.2 1.0 CE1 E:HIS63 3.1 32.4 1.0 CG E:HIS71 3.2 39.5 1.0 CB E:HIS63 3.4 32.3 1.0 CB E:HIS80 3.4 30.8 1.0 CB E:HIS71 3.7 40.4 1.0 NE2 E:HIS80 3.8 30.6 1.0 CD2 E:HIS80 3.8 30.7 1.0 O E:LYS136 4.0 38.3 1.0 CB E:ASP83 4.0 32.5 1.0 CA E:HIS71 4.1 41.0 1.0 NE2 E:HIS71 4.2 39.5 1.0 NE2 E:HIS63 4.3 30.6 1.0 CD2 E:HIS63 4.3 32.1 1.0 CD2 E:HIS71 4.3 40.0 1.0 N E:HIS80 4.4 30.6 1.0 CA E:HIS80 4.5 30.8 1.0 CA E:ASP83 4.7 31.0 1.0 O E:GLY72 4.8 43.5 1.0 N E:GLY72 4.8 41.5 1.0 O E:HOH320 4.8 33.5 1.0 N E:ASP83 4.9 29.4 1.0 CA E:HIS63 4.9 32.6 1.0 C E:HIS71 5.0 41.7 1.0

Zinc binding site 6 out of 24 in the Structure of Human SOD1 with T2D Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Human SOD1 with T2D Mutation within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn202 b:31.6 occ:1.00 OD1 F:ASP83 2.0 29.1 1.0 ND1 F:HIS80 2.1 27.9 1.0 ND1 F:HIS71 2.1 33.6 1.0 ND1 F:HIS63 2.2 34.3 1.0 CG F:ASP83 2.8 29.8 1.0 CE1 F:HIS80 2.8 27.4 1.0 OD2 F:ASP83 2.9 31.7 1.0 CG F:HIS63 3.1 35.0 1.0 CE1 F:HIS71 3.1 35.6 1.0 CE1 F:HIS63 3.1 33.9 1.0 CG F:HIS71 3.2 35.4 1.0 CG F:HIS80 3.3 27.5 1.0 CB F:HIS63 3.3 34.6 1.0 CB F:HIS71 3.5 35.8 1.0 O F:LYS136 3.7 38.7 1.0 CB F:HIS80 3.8 28.3 1.0 CA F:HIS71 4.0 36.5 1.0 NE2 F:HIS80 4.1 25.4 1.0 CB F:ASP83 4.2 29.6 1.0 CD2 F:HIS63 4.2 34.9 1.0 NE2 F:HIS63 4.2 35.7 1.0 NE2 F:HIS71 4.2 36.0 1.0 CD2 F:HIS80 4.3 26.4 1.0 CD2 F:HIS71 4.3 35.4 1.0 N F:HIS80 4.6 30.9 1.0 N F:GLY72 4.8 36.7 1.0 CA F:HIS80 4.8 29.6 1.0 CA F:ASP83 4.8 29.3 1.0 CA F:HIS63 4.9 35.1 1.0 C F:LYS136 4.9 37.1 1.0 C F:HIS71 4.9 38.0 1.0 N F:HIS71 5.0 37.2 1.0 N F:ASP83 5.0 28.2 1.0

Zinc binding site 7 out of 24 in the Structure of Human SOD1 with T2D Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Human SOD1 with T2D Mutation within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn202 b:32.6 occ:1.00 OD1 G:ASP83 2.0 27.9 1.0 ND1 G:HIS63 2.1 29.6 1.0 ND1 G:HIS80 2.1 33.8 1.0 ND1 G:HIS71 2.2 34.5 1.0 OD2 G:ASP83 2.3 28.4 1.0 CG G:ASP83 2.5 27.5 1.0 CE1 G:HIS71 2.9 33.3 1.0 CE1 G:HIS80 3.0 33.5 1.0 CE1 G:HIS63 3.0 29.4 1.0 CG G:HIS80 3.0 35.3 1.0 CG G:HIS63 3.2 29.4 1.0 CG G:HIS71 3.3 35.6 1.0 CB G:HIS80 3.4 35.3 1.0 CB G:HIS63 3.6 29.9 1.0 CB G:HIS71 3.8 37.5 1.0 CB G:ASP83 4.0 28.9 1.0 NE2 G:HIS80 4.0 33.1 1.0 CD2 G:HIS80 4.0 34.0 1.0 CA G:HIS71 4.0 38.8 1.0 NE2 G:HIS71 4.2 34.7 1.0 N G:HIS80 4.2 37.2 1.0 NE2 G:HIS63 4.2 28.6 1.0 CD2 G:HIS63 4.3 28.2 1.0 CD2 G:HIS71 4.3 35.2 1.0 CA G:HIS80 4.4 37.0 1.0 O G:LYS136 4.4 45.1 1.0 N G:GLY72 4.6 39.0 1.0 CA G:ASP83 4.7 29.7 1.0 O G:GLY72 4.7 35.4 1.0 C G:HIS71 4.9 39.6 1.0 N G:ASP83 4.9 29.4 1.0 O G:HIS80 5.0 36.9 1.0

Zinc binding site 8 out of 24 in the Structure of Human SOD1 with T2D Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Human SOD1 with T2D Mutation within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn202 b:36.3 occ:1.00 OD1 H:ASP83 2.0 32.4 1.0 ND1 H:HIS80 2.1 37.2 1.0 ND1 H:HIS63 2.1 35.3 1.0 ND1 H:HIS71 2.1 36.9 1.0 CG H:ASP83 2.8 33.8 1.0 OD2 H:ASP83 2.8 32.6 1.0 CE1 H:HIS71 2.9 35.8 1.0 CE1 H:HIS80 3.0 36.1 1.0 CE1 H:HIS63 3.0 34.0 1.0 CG H:HIS80 3.2 35.9 1.0 CG H:HIS63 3.2 34.4 1.0 CG H:HIS71 3.3 37.0 1.0 CB H:HIS80 3.6 36.6 1.0 CB H:HIS63 3.6 35.1 1.0 CB H:HIS71 3.8 37.1 1.0 O H:LYS136 3.9 33.8 1.0 CA H:HIS71 4.1 37.5 1.0 NE2 H:HIS80 4.1 35.5 1.0 NE2 H:HIS71 4.1 35.8 1.0 NE2 H:HIS63 4.2 34.3 1.0 CD2 H:HIS80 4.2 36.6 1.0 CB H:ASP83 4.2 33.4 1.0 CD2 H:HIS63 4.3 34.4 1.0 CD2 H:HIS71 4.3 36.9 1.0 N H:HIS80 4.5 37.1 1.0 CA H:HIS80 4.6 36.8 1.0 CA H:ASP83 4.8 33.6 1.0 N H:GLY72 4.8 35.6 1.0 N H:ASP83 5.0 33.8 1.0 C H:LYS136 5.0 32.8 1.0 N H:HIS71 5.0 37.6 1.0

Zinc binding site 9 out of 24 in the Structure of Human SOD1 with T2D Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Human SOD1 with T2D Mutation within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn202 b:32.1 occ:1.00 OD1 I:ASP83 2.0 26.8 1.0 ND1 I:HIS63 2.1 31.6 1.0 ND1 I:HIS80 2.1 30.4 1.0 ND1 I:HIS71 2.2 33.9 1.0 CE1 I:HIS71 2.9 33.7 1.0 CG I:HIS80 2.9 30.8 1.0 CE1 I:HIS80 3.0 30.0 1.0 CG I:ASP83 3.0 25.8 1.0 CG I:HIS63 3.0 33.7 1.0 CE1 I:HIS63 3.1 30.7 1.0 CG I:HIS71 3.3 34.7 1.0 CB I:HIS63 3.3 34.6 1.0 CB I:HIS80 3.3 31.2 1.0 OD2 I:ASP83 3.4 27.0 1.0 CB I:HIS71 3.8 34.1 1.0 O I:LYS136 3.9 31.9 1.0 CD2 I:HIS80 3.9 29.3 1.0 NE2 I:HIS80 3.9 27.9 1.0 NE2 I:HIS71 4.1 35.4 1.0 CA I:HIS71 4.1 35.1 1.0 CD2 I:HIS63 4.2 31.7 1.0 NE2 I:HIS63 4.2 31.5 1.0 CB I:ASP83 4.3 25.9 1.0 CD2 I:HIS71 4.3 34.4 1.0 N I:HIS80 4.3 34.4 1.0 CA I:HIS80 4.4 33.1 1.0 N I:GLY72 4.7 33.5 1.0 CA I:ASP83 4.8 25.9 1.0 CA I:HIS63 4.8 37.2 1.0 N I:ASP83 4.9 25.4 1.0 O I:GLY72 5.0 32.2 1.0 C I:HIS71 5.0 34.4 1.0

Zinc binding site 10 out of 24 in the Structure of Human SOD1 with T2D Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Human SOD1 with T2D Mutation within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn202 b:32.9 occ:1.00 OD1 J:ASP83 2.0 32.2 1.0 ND1 J:HIS80 2.1 30.3 1.0 ND1 J:HIS63 2.1 33.6 1.0 ND1 J:HIS71 2.1 33.8 1.0 OD2 J:ASP83 2.6 31.6 1.0 CG J:ASP83 2.6 31.0 1.0 CE1 J:HIS63 2.9 33.6 1.0 CG J:HIS80 3.0 29.5 1.0 CE1 J:HIS80 3.1 28.1 1.0 CE1 J:HIS71 3.1 32.8 1.0 CG J:HIS71 3.1 33.9 1.0 CG J:HIS63 3.1 33.9 1.0 CB J:HIS80 3.3 29.8 1.0 CB J:HIS71 3.4 34.5 1.0 CB J:HIS63 3.6 33.9 1.0 O J:LYS136 3.8 33.4 1.0 CA J:HIS71 3.8 35.8 1.0 NE2 J:HIS63 4.0 33.1 1.0 CD2 J:HIS80 4.1 28.5 1.0 NE2 J:HIS80 4.1 27.9 1.0 CB J:ASP83 4.1 30.4 1.0 CD2 J:HIS63 4.1 33.6 1.0 NE2 J:HIS71 4.2 34.2 1.0 CD2 J:HIS71 4.3 33.5 1.0 N J:HIS80 4.3 31.2 1.0 CA J:HIS80 4.4 31.0 1.0 N J:GLY72 4.5 37.2 1.0 CA J:ASP83 4.7 30.9 1.0 C J:HIS71 4.7 36.1 1.0 N J:ASP83 4.8 30.5 1.0 O J:GLY72 4.8 37.0 1.0 C J:LYS136 4.8 31.4 1.0 N J:HIS71 4.9 36.6 1.0

J.M.Fay, C.Zhu, E.A.Proctor, Y.Tao, W.Cui, H.Ke, N.V.Dokholyan. A Phosphomimetic Mutation Stabilizes SOD1 and Rescues Cell Viability in the Context of An Als-Associated Mutation. Structure V. 24 1898 2016.
ISSN: ISSN 0969-2126
PubMed: 27667694
DOI: 10.1016/J.STR.2016.08.011