Zinc in PDB 9iyk: Crystal Structure of HSOD1 in C121 Space Group

All present enzymatic activity of Crystal Structure of HSOD1 in C121 Space Group:
1.15.1.1;

The structure of Crystal Structure of HSOD1 in C121 Space Group, PDB code: 9iyk was solved by I.Yapici, H.Demirci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.92 / 2.34
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	178.19, 138.25, 112.93, 90, 129.2, 90
R / Rfree (%)	19.8 / 26.3

The structure of Crystal Structure of HSOD1 in C121 Space Group also contains other interesting chemical elements:

Copper

(Cu)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of HSOD1 in C121 Space Group (pdb code 9iyk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the Crystal Structure of HSOD1 in C121 Space Group, PDB code: 9iyk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in the Crystal Structure of HSOD1 in C121 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of HSOD1 in C121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:32.5 occ:1.00 OD1 A:ASP83 1.9 44.2 1.0 ND1 A:HIS80 1.9 32.9 1.0 ND1 A:HIS71 2.1 49.5 1.0 ND1 A:HIS63 2.3 33.2 1.0 OD2 A:ASP83 2.3 45.3 1.0 CG A:ASP83 2.4 45.0 1.0 CE1 A:HIS80 2.8 36.4 1.0 CE1 A:HIS71 2.9 42.3 1.0 CG A:HIS80 3.0 33.3 1.0 CG A:HIS63 3.2 42.2 1.0 CG A:HIS71 3.2 42.4 1.0 CE1 A:HIS63 3.3 42.4 1.0 CB A:HIS63 3.4 37.9 1.0 CB A:HIS80 3.4 34.1 1.0 CB A:HIS71 3.7 37.1 1.0 CB A:ASP83 3.9 39.4 1.0 NE2 A:HIS80 4.0 37.3 1.0 CA A:HIS71 4.0 36.5 1.0 O A:LYS136 4.0 43.9 1.0 CD2 A:HIS80 4.1 35.0 1.0 NE2 A:HIS71 4.1 41.0 1.0 CD2 A:HIS71 4.3 37.6 1.0 CD2 A:HIS63 4.3 46.8 1.0 CD2 A:HIS46 4.3 46.4 1.0 NE2 A:HIS63 4.3 41.8 1.0 CA A:ASP83 4.6 40.1 1.0 CA A:HIS80 4.7 35.8 1.0 N A:GLY72 4.7 39.6 1.0 N A:HIS80 4.7 37.1 1.0 CA A:HIS63 4.9 35.8 1.0 C A:HIS71 4.9 38.8 1.0 N A:ASP83 4.9 44.4 1.0

Zinc binding site 2 out of 13 in the Crystal Structure of HSOD1 in C121 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of HSOD1 in C121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:59.2 occ:1.00 NE2 A:HIS110 2.0 49.1 1.0 NE2 D:HIS-1 2.1 66.0 1.0 NE2 C:HIS110 2.2 50.7 1.0 NE2 B:HIS-1 2.4 59.5 1.0 CD2 B:HIS-1 2.8 56.7 1.0 CE1 A:HIS110 2.9 54.8 1.0 CE1 C:HIS110 2.9 43.3 1.0 CD2 D:HIS-1 3.0 62.4 1.0 CD2 A:HIS110 3.0 60.8 1.0 CE1 D:HIS-1 3.1 57.4 1.0 CD2 C:HIS110 3.3 56.5 1.0 CE1 B:HIS-1 3.6 52.4 1.0 ND1 A:HIS110 4.0 53.8 1.0 CG A:HIS110 4.1 57.0 1.0 ND1 C:HIS110 4.1 46.1 1.0 CG B:HIS-1 4.1 53.6 1.0 CG D:HIS-1 4.1 63.0 1.0 CB A:PRO66 4.1 47.7 1.0 ND1 D:HIS-1 4.1 60.7 1.0 CG C:HIS110 4.3 58.5 1.0 CB C:PRO66 4.4 35.9 1.0 ND1 B:HIS-1 4.5 55.8 1.0 O C:PRO66 4.8 28.8 1.0

Zinc binding site 3 out of 13 in the Crystal Structure of HSOD1 in C121 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of HSOD1 in C121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn203 b:29.4 occ:1.00 OD1 C:ASP83 2.0 31.7 1.0 ND1 C:HIS71 2.0 35.8 1.0 ND1 C:HIS80 2.0 20.9 1.0 ND1 C:HIS63 2.2 35.1 1.0 OD2 C:ASP83 2.3 47.4 1.0 CG C:ASP83 2.4 46.6 1.0 CE1 C:HIS71 2.9 31.8 1.0 CE1 C:HIS80 3.0 27.6 1.0 CG C:HIS80 3.0 25.4 1.0 CG C:HIS63 3.1 23.2 1.0 CE1 C:HIS63 3.1 30.4 1.0 CG C:HIS71 3.1 25.3 1.0 CB C:HIS63 3.4 20.9 1.0 CB C:HIS80 3.4 32.5 1.0 CB C:HIS71 3.5 26.1 1.0 O C:LYS136 3.9 33.9 1.0 CB C:ASP83 3.9 38.9 1.0 CA C:HIS71 3.9 36.6 1.0 NE2 C:HIS71 4.1 42.4 1.0 NE2 C:HIS80 4.1 25.7 1.0 CD2 C:HIS80 4.1 21.7 1.0 NE2 C:HIS63 4.2 38.8 1.0 CD2 C:HIS63 4.2 30.9 1.0 CD2 C:HIS71 4.2 39.8 1.0 CA C:ASP83 4.6 29.9 1.0 CA C:HIS80 4.6 34.3 1.0 N C:HIS80 4.6 39.8 1.0 N C:GLY72 4.7 30.2 1.0 C C:LYS136 4.9 34.4 1.0 C C:HIS71 4.9 35.0 1.0 CA C:HIS63 4.9 31.9 1.0 N C:ASP83 4.9 32.7 1.0 CD2 C:HIS46 4.9 39.1 1.0 N C:HIS71 4.9 26.4 1.0

Zinc binding site 4 out of 13 in the Crystal Structure of HSOD1 in C121 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of HSOD1 in C121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn202 b:44.7 occ:1.00 OD1 K:ASP83 2.0 59.5 1.0 ND1 K:HIS63 2.1 51.0 1.0 ND1 K:HIS80 2.1 44.0 1.0 OD2 K:ASP83 2.2 38.9 1.0 ND1 K:HIS71 2.2 53.7 1.0 CG K:ASP83 2.4 51.6 1.0 CE1 K:HIS80 2.9 48.4 1.0 CG K:HIS63 2.9 43.4 1.0 CE1 K:HIS63 3.1 50.1 1.0 CE1 K:HIS71 3.1 50.4 1.0 CB K:HIS63 3.2 36.9 1.0 CG K:HIS80 3.2 42.7 1.0 CG K:HIS71 3.3 43.8 1.0 CB K:HIS71 3.6 46.4 1.0 CB K:HIS80 3.7 47.2 1.0 CB K:ASP83 3.8 49.1 1.0 O K:LYS136 4.0 52.6 1.0 CA K:HIS71 4.0 46.8 1.0 NE2 K:HIS80 4.1 50.1 1.0 CD2 K:HIS63 4.1 44.5 1.0 NE2 K:HIS63 4.2 40.6 1.0 CD2 K:HIS80 4.3 51.4 1.0 NE2 K:HIS71 4.3 49.3 1.0 CD2 K:HIS71 4.4 44.3 1.0 CA K:ASP83 4.4 48.7 1.0 CA K:HIS63 4.7 42.4 1.0 N K:HIS80 4.8 49.9 1.0 O K:HOH314 4.8 48.3 1.0 N K:ASP83 4.8 53.2 1.0 C K:LYS136 4.9 47.7 1.0 N K:GLY72 4.9 53.1 1.0 CA K:HIS80 4.9 47.3 1.0 N K:HIS71 5.0 50.0 1.0

Zinc binding site 5 out of 13 in the Crystal Structure of HSOD1 in C121 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of HSOD1 in C121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn202 b:52.7 occ:1.00 OD1 F:ASP83 1.8 65.8 1.0 ND1 F:HIS63 1.9 61.4 1.0 ND1 F:HIS80 2.1 56.1 1.0 ND1 F:HIS71 2.1 57.7 1.0 CG F:ASP83 2.8 61.1 1.0 CE1 F:HIS80 2.8 59.8 1.0 CE1 F:HIS71 2.9 62.7 1.0 CE1 F:HIS63 2.9 60.4 1.0 CG F:HIS63 2.9 60.7 1.0 OD2 F:ASP83 3.2 63.8 1.0 CG F:HIS71 3.2 59.9 1.0 CG F:HIS80 3.3 67.6 1.0 CB F:HIS63 3.3 61.8 1.0 CB F:HIS71 3.7 62.5 1.0 O F:LYS136 3.8 55.5 1.0 CB F:HIS80 3.9 65.3 1.0 CB F:ASP83 4.0 58.7 1.0 NE2 F:HIS80 4.0 65.0 1.0 NE2 F:HIS63 4.0 59.1 1.0 CD2 F:HIS63 4.0 59.2 1.0 NE2 F:HIS71 4.1 63.8 1.0 CA F:HIS71 4.1 63.6 1.0 CD2 F:HIS71 4.2 59.7 1.0 CD2 F:HIS80 4.3 65.5 1.0 CA F:ASP83 4.5 56.0 1.0 CD2 F:HIS46 4.7 64.2 1.0 N F:ASP83 4.7 57.6 1.0 C F:LYS136 4.8 61.3 1.0 CA F:HIS63 4.8 61.0 1.0 N F:GLY72 4.9 64.0 1.0 N F:HIS80 5.0 64.8 1.0

Zinc binding site 6 out of 13 in the Crystal Structure of HSOD1 in C121 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of HSOD1 in C121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn202 b:54.0 occ:1.00 OD1 E:ASP83 1.9 52.1 1.0 ND1 E:HIS80 2.0 47.4 1.0 ND1 E:HIS71 2.1 59.2 1.0 ND1 E:HIS63 2.1 43.3 1.0 CE1 E:HIS80 2.6 55.8 1.0 CG E:ASP83 2.8 53.6 1.0 CE1 E:HIS71 2.9 53.4 1.0 CG E:HIS63 3.0 43.6 1.0 CE1 E:HIS63 3.1 45.6 1.0 CG E:HIS71 3.2 49.4 1.0 OD2 E:ASP83 3.2 56.8 1.0 CG E:HIS80 3.2 58.9 1.0 CB E:HIS63 3.3 45.1 1.0 CB E:HIS71 3.6 49.7 1.0 CB E:HIS80 3.8 52.1 1.0 NE2 E:HIS80 3.9 54.6 1.0 O E:LYS136 4.0 51.4 1.0 NE2 E:HIS71 4.0 47.8 1.0 CB E:ASP83 4.1 48.2 1.0 CD2 E:HIS80 4.2 48.1 1.0 CA E:HIS71 4.2 47.9 1.0 CD2 E:HIS63 4.2 52.4 1.0 CD2 E:HIS71 4.2 53.9 1.0 NE2 E:HIS63 4.2 47.9 1.0 CA E:ASP83 4.5 42.8 1.0 CD2 E:HIS46 4.8 44.8 1.0 CA E:HIS63 4.8 46.5 1.0 N E:HIS80 4.9 50.3 1.0 N E:ASP83 4.9 40.3 1.0 N E:GLY72 4.9 57.9 1.0 C E:LYS136 4.9 53.4 1.0 CA E:HIS80 5.0 53.0 1.0

Zinc binding site 7 out of 13 in the Crystal Structure of HSOD1 in C121 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of HSOD1 in C121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:84.6 occ:1.00 OD1 D:ASP83 1.7 100.8 1.0 ND1 D:HIS63 2.1 90.5 1.0 ND1 D:HIS71 2.1 102.2 1.0 ND1 D:HIS80 2.2 92.2 1.0 CG D:ASP83 2.6 95.9 1.0 OD2 D:ASP83 2.8 91.0 1.0 CE1 D:HIS80 2.9 93.3 1.0 CE1 D:HIS71 2.9 93.8 1.0 CG D:HIS63 2.9 90.2 1.0 CB D:HIS63 3.1 91.3 1.0 CE1 D:HIS63 3.2 90.0 1.0 CG D:HIS71 3.3 92.0 1.0 CG D:HIS80 3.4 95.2 1.0 CB D:HIS71 3.8 93.3 1.0 CB D:HIS80 3.9 95.6 1.0 CB D:ASP83 4.0 89.0 1.0 O D:LYS136 4.1 93.6 1.0 NE2 D:HIS71 4.1 97.0 1.0 NE2 D:HIS80 4.1 94.3 1.0 CD2 D:HIS63 4.1 89.8 1.0 CA D:HIS71 4.2 93.6 1.0 NE2 D:HIS63 4.2 89.7 1.0 CD2 D:HIS71 4.3 94.0 1.0 CD2 D:HIS80 4.4 93.9 1.0 CD2 D:HIS46 4.4 87.5 1.0 CA D:ASP83 4.5 88.0 1.0 CA D:HIS63 4.7 93.8 1.0 N D:HIS80 4.9 94.5 1.0 N D:ASP83 4.9 96.0 1.0 N D:GLY72 5.0 100.8 1.0

Zinc binding site 8 out of 13 in the Crystal Structure of HSOD1 in C121 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of HSOD1 in C121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:49.1 occ:1.00 ND1 B:HIS80 1.9 51.2 1.0 OD1 B:ASP83 1.9 54.4 1.0 ND1 B:HIS71 2.0 62.4 1.0 OD2 B:ASP83 2.1 49.3 1.0 ND1 B:HIS63 2.2 49.5 1.0 CG B:ASP83 2.3 53.9 1.0 CE1 B:HIS80 2.8 58.9 1.0 CG B:HIS80 2.9 51.5 1.0 CE1 B:HIS71 3.0 62.0 1.0 CG B:HIS71 3.1 53.7 1.0 CG B:HIS63 3.1 56.7 1.0 CE1 B:HIS63 3.2 47.6 1.0 CB B:HIS80 3.3 54.0 1.0 CB B:HIS63 3.4 54.1 1.0 CB B:HIS71 3.5 54.2 1.0 CA B:HIS71 3.8 54.8 1.0 CB B:ASP83 3.8 50.9 1.0 NE2 B:HIS80 3.8 65.8 1.0 CD2 B:HIS80 3.9 54.0 1.0 O B:LYS136 4.0 54.1 1.0 NE2 B:HIS71 4.1 60.5 1.0 CD2 B:HIS71 4.2 58.7 1.0 CD2 B:HIS63 4.3 55.1 1.0 NE2 B:HIS63 4.3 53.8 1.0 N B:HIS80 4.5 51.7 1.0 CA B:HIS80 4.5 50.9 1.0 CA B:ASP83 4.6 49.8 1.0 N B:GLY72 4.6 62.6 1.0 C B:HIS71 4.8 60.2 1.0 N B:HIS71 4.8 60.9 1.0 CD2 B:HIS46 4.8 55.4 1.0 N B:ASP83 4.9 51.0 1.0 CA B:HIS63 4.9 58.8 1.0

Zinc binding site 9 out of 13 in the Crystal Structure of HSOD1 in C121 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of HSOD1 in C121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn202 b:67.8 occ:1.00 ND1 G:HIS63 2.1 65.3 1.0 ND1 G:HIS80 2.1 77.9 1.0 ND1 G:HIS71 2.1 82.0 1.0 OD1 G:ASP83 2.1 64.8 1.0 OD2 G:ASP83 2.2 84.5 1.0 CG G:ASP83 2.4 70.1 1.0 CE1 G:HIS71 2.8 65.9 1.0 CE1 G:HIS80 2.9 75.3 1.0 CG G:HIS63 3.0 63.3 1.0 CE1 G:HIS63 3.1 60.6 1.0 CG G:HIS71 3.2 70.3 1.0 CG G:HIS80 3.2 76.3 1.0 CB G:HIS63 3.3 65.0 1.0 CB G:HIS80 3.7 72.8 1.0 CB G:HIS71 3.8 74.6 1.0 CB G:ASP83 3.9 63.9 1.0 O G:LYS136 3.9 77.3 1.0 NE2 G:HIS71 4.0 63.0 1.0 NE2 G:HIS80 4.1 78.3 1.0 NE2 G:HIS63 4.2 61.5 1.0 CD2 G:HIS63 4.2 60.6 1.0 CD2 G:HIS71 4.2 68.8 1.0 CD2 G:HIS80 4.3 78.5 1.0 CA G:HIS71 4.3 83.7 1.0 CA G:ASP83 4.5 61.2 1.0 N G:HIS80 4.8 87.0 1.0 C G:LYS136 4.8 81.6 1.0 CD2 G:HIS46 4.8 57.9 1.0 CA G:HIS63 4.8 67.0 1.0 N G:GLY72 4.9 77.9 1.0 CA G:HIS80 4.9 75.8 1.0 O G:GLY72 4.9 73.3 1.0

Zinc binding site 10 out of 13 in the Crystal Structure of HSOD1 in C121 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of HSOD1 in C121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn202 b:59.8 occ:1.00 ND1 I:HIS80 1.9 66.8 1.0 OD1 I:ASP83 2.0 70.1 1.0 ND1 I:HIS63 2.1 67.2 1.0 OD2 I:ASP83 2.2 72.1 1.0 ND1 I:HIS71 2.2 80.8 1.0 CG I:ASP83 2.3 67.8 1.0 CG I:HIS80 2.9 74.6 1.0 CE1 I:HIS80 2.9 67.3 1.0 CE1 I:HIS71 3.1 69.6 1.0 CG I:HIS63 3.1 68.0 1.0 CE1 I:HIS63 3.2 68.0 1.0 CB I:HIS80 3.2 72.8 1.0 CG I:HIS71 3.2 70.6 1.0 CB I:HIS63 3.4 68.6 1.0 CB I:HIS71 3.6 70.9 1.0 CB I:ASP83 3.9 71.1 1.0 CA I:HIS71 3.9 70.4 1.0 CD2 I:HIS80 4.0 78.4 1.0 NE2 I:HIS80 4.0 72.5 1.0 O I:LYS136 4.0 66.0 1.0 NE2 I:HIS71 4.2 71.3 1.0 CD2 I:HIS63 4.3 66.9 1.0 NE2 I:HIS63 4.3 67.8 1.0 CD2 I:HIS71 4.3 71.9 1.0 CA I:HIS80 4.5 74.3 1.0 CA I:ASP83 4.5 76.7 1.0 N I:HIS80 4.6 84.0 1.0 N I:GLY72 4.7 74.2 1.0 N I:ASP83 4.8 67.5 1.0 CA I:HIS63 4.9 70.6 1.0 C I:HIS71 4.9 79.4 1.0 N I:HIS71 4.9 71.1 1.0 CD2 I:HIS46 4.9 67.3 1.0

I.Yapici, H.Demirci. The New Crystal Form of HSOD1 To Be Published.