Zinc in PDB 4k2h: Crystal Structure of C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium

The structure of Crystal Structure of C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium, PDB code: 4k2h was solved by I.A.Shumilin, E.Niedzialkowska, M.J.Domagalski, J.Stam, W.F.Anderson, W.Minor, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.71 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	179.662, 113.751, 175.710, 90.00, 109.33, 90.00
R / Rfree (%)	17.2 / 20.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium (pdb code 4k2h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Crystal Structure of C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium, PDB code: 4k2h:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in the Crystal Structure of C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium


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 C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:30.8 occ:1.00 OE2 A:GLU14 1.8 23.3 1.0 OE1 A:GLU13 2.0 28.9 1.0 OD2 B:ASP22 2.0 24.7 1.0 ND1 A:HIS46 2.0 28.1 1.0 CD A:GLU14 2.7 23.7 1.0 CD A:GLU13 2.8 28.1 1.0 CE1 A:HIS46 2.8 29.5 1.0 OE2 A:GLU13 2.9 28.2 1.0 CG B:ASP22 3.0 25.1 1.0 OE1 A:GLU14 3.1 21.8 1.0 CG A:HIS46 3.2 29.5 1.0 CB B:ASP22 3.4 24.7 1.0 CB A:HIS46 3.7 28.1 1.0 NE2 A:HIS46 4.0 29.6 1.0 CG A:GLU14 4.1 23.9 1.0 CA B:ASP22 4.1 24.4 1.0 OD1 B:ASP22 4.1 26.7 1.0 CD2 A:HIS46 4.2 29.9 1.0 CG A:GLU13 4.2 27.4 1.0 N A:GLU14 4.2 24.3 1.0 N A:ALA15 4.2 27.3 1.0 NH2 B:ARG26 4.3 31.9 1.0 CB A:ALA15 4.4 29.4 1.0 N A:HIS46 4.4 28.7 1.0 CD2 A:TYR45 4.5 28.8 1.0 CA A:HIS46 4.7 28.8 1.0 CB A:TYR45 4.8 27.7 1.0 CA A:GLU13 4.8 24.8 1.0 O B:ASP22 4.8 24.9 1.0 C A:GLU13 4.9 24.5 1.0 C B:ASP22 4.9 25.1 1.0 CZ B:ARG26 4.9 30.3 1.0 NE B:ARG26 4.9 29.3 1.0 CA A:GLU14 5.0 24.2 1.0 CB A:GLU14 5.0 24.3 1.0 CA A:ALA15 5.0 28.7 1.0

Zinc binding site 2 out of 14 in the Crystal Structure of C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium


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 C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:34.7 occ:1.00 OE2 B:GLU14 1.9 29.7 1.0 ND1 B:HIS46 2.0 30.6 1.0 OE1 B:GLU13 2.1 34.6 1.0 OD1 A:ASP22 2.1 30.8 1.0 CE1 B:HIS46 2.7 32.7 1.0 CD B:GLU14 2.8 28.1 1.0 CD B:GLU13 2.9 33.6 1.0 OE2 B:GLU13 3.0 34.9 1.0 CG A:ASP22 3.1 28.9 1.0 OE1 B:GLU14 3.2 26.6 1.0 CG B:HIS46 3.2 31.4 1.0 CB A:ASP22 3.4 27.2 1.0 CB B:HIS46 3.8 30.3 1.0 NE2 B:HIS46 3.9 32.9 1.0 CA A:ASP22 4.1 27.9 1.0 CG B:GLU14 4.1 27.4 1.0 CD2 B:HIS46 4.2 32.1 1.0 NH2 A:ARG26 4.2 38.5 1.0 OD2 A:ASP22 4.2 29.5 1.0 CG B:GLU13 4.3 32.6 1.0 N B:ALA15 4.3 26.7 1.0 N B:GLU14 4.3 28.5 1.0 CB B:ALA15 4.5 29.5 1.0 N B:HIS46 4.5 29.5 1.0 CD2 B:TYR45 4.6 38.6 1.0 CA B:HIS46 4.8 30.0 1.0 CA B:GLU13 4.8 29.1 1.0 CZ A:ARG26 4.9 36.6 1.0 NE A:ARG26 4.9 36.5 1.0 C B:GLU13 4.9 28.6 1.0 CB B:TYR45 4.9 31.6 1.0 C A:ASP22 5.0 27.6 1.0

Zinc binding site 3 out of 14 in the Crystal Structure of C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium


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 C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:35.8 occ:1.00 OE2 C:GLU14 1.9 31.3 1.0 ND1 C:HIS46 2.0 32.5 1.0 OD2 D:ASP22 2.0 30.2 1.0 OE1 C:GLU13 2.1 37.4 1.0 CD C:GLU13 2.7 35.0 1.0 OE2 C:GLU13 2.8 35.8 1.0 CE1 C:HIS46 2.8 33.5 1.0 CD C:GLU14 2.8 29.5 1.0 CG D:ASP22 3.0 30.3 1.0 OE1 C:GLU14 3.1 27.6 1.0 CG C:HIS46 3.2 33.3 1.0 CB D:ASP22 3.4 29.4 1.0 CB C:HIS46 3.7 31.1 1.0 NE2 C:HIS46 4.0 33.1 1.0 CA D:ASP22 4.1 30.8 1.0 OD1 D:ASP22 4.1 31.2 1.0 CG C:GLU13 4.2 34.2 1.0 CG C:GLU14 4.2 29.8 1.0 NH2 D:ARG26 4.2 41.8 1.0 CD2 C:HIS46 4.2 32.6 1.0 N C:GLU14 4.3 29.5 1.0 N C:ALA15 4.4 30.2 1.0 CB C:ALA15 4.5 31.7 1.0 CD2 C:TYR45 4.5 36.4 1.0 N C:HIS46 4.5 32.2 1.0 CZ D:ARG26 4.8 39.2 1.0 CA C:HIS46 4.8 31.8 1.0 NE D:ARG26 4.9 38.6 1.0 C C:GLU13 4.9 30.0 1.0 CA C:GLU13 4.9 30.1 1.0 CB C:TYR45 4.9 31.7 1.0 C D:ASP22 5.0 30.6 1.0

Zinc binding site 4 out of 14 in the Crystal Structure of C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium


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 C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:30.9 occ:1.00 OE2 D:GLU14 1.9 24.0 1.0 OD1 C:ASP22 2.0 28.4 1.0 ND1 D:HIS46 2.0 26.8 1.0 OE1 D:GLU13 2.1 30.5 1.0 CD D:GLU14 2.8 24.3 1.0 CE1 D:HIS46 2.8 27.9 1.0 CD D:GLU13 2.8 29.5 1.0 OE2 D:GLU13 2.9 29.1 1.0 CG C:ASP22 3.0 27.8 1.0 CG D:HIS46 3.1 27.2 1.0 OE1 D:GLU14 3.2 22.9 1.0 CB C:ASP22 3.5 27.7 1.0 CB D:HIS46 3.6 26.6 1.0 NE2 D:HIS46 4.0 28.2 1.0 OD2 C:ASP22 4.1 28.1 1.0 CA C:ASP22 4.1 26.8 1.0 CG D:GLU14 4.2 24.9 1.0 CD2 D:HIS46 4.2 27.2 1.0 N D:GLU14 4.3 24.5 1.0 NH2 C:ARG26 4.3 32.5 1.0 CG D:GLU13 4.3 28.8 1.0 N D:ALA15 4.3 27.8 1.0 CD2 D:TYR45 4.4 29.6 1.0 N D:HIS46 4.5 26.9 1.0 CB D:ALA15 4.5 29.2 1.0 CA D:HIS46 4.7 26.7 1.0 CB D:TYR45 4.7 26.9 1.0 CA D:GLU13 4.9 25.3 1.0 C C:ASP22 4.9 26.7 1.0 CZ C:ARG26 4.9 30.7 1.0 O C:ASP22 4.9 27.3 1.0 C D:GLU13 4.9 25.2 1.0 NE C:ARG26 4.9 29.5 1.0 CG D:TYR45 4.9 28.1 1.0

Zinc binding site 5 out of 14 in the Crystal Structure of C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium


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 C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:36.3 occ:1.00 OE2 E:GLU14 1.7 30.3 1.0 OE1 E:GLU13 1.8 38.8 1.0 OD1 F:ASP22 2.0 31.1 1.0 ND1 E:HIS46 2.0 35.0 1.0 CD E:GLU13 2.7 36.5 1.0 CE1 E:HIS46 2.8 34.4 1.0 CD E:GLU14 2.9 29.4 1.0 CG F:ASP22 3.0 31.0 1.0 OE2 E:GLU13 3.1 38.7 1.0 CG E:HIS46 3.2 34.3 1.0 OE1 E:GLU14 3.4 28.6 1.0 CB F:ASP22 3.4 30.6 1.0 CB E:HIS46 3.7 32.2 1.0 NE2 E:HIS46 4.0 34.1 1.0 CA F:ASP22 4.0 30.8 1.0 OD2 F:ASP22 4.1 32.5 1.0 CG E:GLU13 4.1 34.5 1.0 CG E:GLU14 4.1 29.2 1.0 NH2 F:ARG26 4.1 34.7 1.0 CD2 E:HIS46 4.2 34.4 1.0 N E:ALA15 4.3 28.4 1.0 N E:GLU14 4.4 28.8 1.0 CD2 E:TYR45 4.4 36.7 1.0 N E:HIS46 4.5 32.0 1.0 CB E:ALA15 4.6 29.9 1.0 CZ F:ARG26 4.7 35.7 1.0 NE F:ARG26 4.8 35.6 1.0 CA E:HIS46 4.8 32.0 1.0 O F:ASP22 4.8 29.8 1.0 C F:ASP22 4.8 30.2 1.0 CB E:TYR45 4.8 33.0 1.0 CA E:GLU13 4.9 29.8 1.0 C E:GLU13 5.0 29.2 1.0

Zinc binding site 6 out of 14 in the Crystal Structure of C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium


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 C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:34.2 occ:1.00 OD2 E:ASP22 1.8 28.2 1.0 OE2 F:GLU13 1.8 36.7 1.0 OE2 F:GLU14 2.0 29.1 1.0 ND1 F:HIS46 2.0 31.0 1.0 CD F:GLU13 2.7 35.4 1.0 CE1 F:HIS46 2.8 31.8 1.0 CD F:GLU14 2.9 27.5 1.0 CG E:ASP22 2.9 27.2 1.0 OE1 F:GLU13 3.0 36.8 1.0 OE1 F:GLU14 3.2 25.2 1.0 CG F:HIS46 3.2 31.4 1.0 CB E:ASP22 3.4 25.6 1.0 CB F:HIS46 3.8 30.5 1.0 NE2 F:HIS46 4.0 32.0 1.0 OD1 E:ASP22 4.0 27.8 1.0 CA E:ASP22 4.1 25.0 1.0 CG F:GLU13 4.1 33.6 1.0 NH2 E:ARG26 4.2 37.8 1.0 CG F:GLU14 4.2 27.7 1.0 CD2 F:HIS46 4.2 31.7 1.0 N F:GLU14 4.3 28.9 1.0 CD2 F:TYR45 4.3 37.9 1.0 N F:ALA15 4.4 28.8 1.0 N F:HIS46 4.4 31.0 1.0 CB F:ALA15 4.5 31.0 1.0 NE E:ARG26 4.7 34.0 1.0 CZ E:ARG26 4.7 35.5 1.0 CA F:HIS46 4.7 30.7 1.0 CB F:TYR45 4.8 34.6 1.0 CA F:GLU13 4.8 29.5 1.0 C F:GLU13 4.9 29.2 1.0 CG F:TYR45 5.0 36.2 1.0 C E:ASP22 5.0 25.8 1.0

Zinc binding site 7 out of 14 in the Crystal Structure of C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium


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 C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn201 b:47.5 occ:1.00 OE1 G:GLU13 2.0 50.6 1.0 OD1 H:ASP22 2.0 43.8 1.0 OE2 G:GLU14 2.0 42.0 1.0 ND1 G:HIS46 2.1 42.8 1.0 CD G:GLU13 2.9 45.7 1.0 CD G:GLU14 2.9 38.0 1.0 CG H:ASP22 3.0 43.9 1.0 CE1 G:HIS46 3.0 43.6 1.0 CG G:HIS46 3.2 42.9 1.0 OE2 G:GLU13 3.2 48.1 1.0 OE1 G:GLU14 3.2 35.9 1.0 CB H:ASP22 3.3 41.3 1.0 CB G:HIS46 3.6 40.0 1.0 CA H:ASP22 4.0 40.7 1.0 OD2 H:ASP22 4.1 41.9 1.0 NE2 G:HIS46 4.2 44.6 1.0 N G:GLU14 4.2 34.8 1.0 CG G:GLU14 4.3 36.8 1.0 CD2 G:HIS46 4.3 44.4 1.0 CG G:GLU13 4.3 43.2 1.0 N G:ALA15 4.3 34.9 1.0 NH2 H:ARG26 4.3 52.0 1.0 N G:HIS46 4.4 38.5 1.0 CB G:ALA15 4.5 39.7 1.0 CA G:HIS46 4.7 39.1 1.0 NE H:ARG26 4.7 47.7 1.0 CD2 G:TYR45 4.7 46.3 1.0 CB G:TYR45 4.8 40.6 1.0 C H:ASP22 4.9 41.0 1.0 CA G:GLU13 4.9 36.6 1.0 CZ H:ARG26 4.9 49.4 1.0 C G:GLU13 4.9 36.1 1.0

Zinc binding site 8 out of 14 in the Crystal Structure of C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium


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 C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn201 b:43.4 occ:1.00 OE2 H:GLU14 2.0 38.8 1.0 OE2 H:GLU13 2.0 46.5 1.0 ND1 H:HIS46 2.1 38.2 1.0 OD2 G:ASP22 2.1 39.0 1.0 CD H:GLU14 2.9 37.9 1.0 CE1 H:HIS46 2.9 39.5 1.0 CD H:GLU13 3.1 43.7 1.0 CG G:ASP22 3.1 38.8 1.0 OE1 H:GLU14 3.1 35.6 1.0 CG H:HIS46 3.2 37.4 1.0 CB G:ASP22 3.4 37.8 1.0 OE1 H:GLU13 3.5 47.8 1.0 CB H:HIS46 3.7 38.1 1.0 CA G:ASP22 4.1 37.1 1.0 NE2 H:HIS46 4.1 38.9 1.0 OD1 G:ASP22 4.2 39.8 1.0 CG H:GLU14 4.2 36.7 1.0 CD2 H:HIS46 4.2 38.3 1.0 NH2 G:ARG26 4.3 48.4 1.0 CG H:GLU13 4.4 42.5 1.0 CD2 H:TYR45 4.4 48.1 1.0 N H:HIS46 4.4 38.2 1.0 N H:GLU14 4.4 35.3 1.0 N H:ALA15 4.5 34.0 1.0 CB H:ALA15 4.7 37.6 1.0 CA H:HIS46 4.7 37.7 1.0 CB H:TYR45 4.8 43.0 1.0 NE G:ARG26 4.9 45.3 1.0 CZ G:ARG26 4.9 46.8 1.0 C G:ASP22 4.9 36.0 1.0 CG H:TYR45 4.9 46.1 1.0 O G:ASP22 5.0 35.0 1.0 CA H:GLU13 5.0 36.7 1.0

Zinc binding site 9 out of 14 in the Crystal Structure of C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium


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 C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:39.6 occ:1.00 OE2 I:GLU14 1.8 34.0 1.0 OD2 J:ASP22 1.9 35.0 1.0 OE1 I:GLU13 2.0 38.6 1.0 ND1 I:HIS46 2.1 34.0 1.0 CD I:GLU14 2.7 30.4 1.0 CE1 I:HIS46 2.8 34.9 1.0 CD I:GLU13 2.8 34.6 1.0 OE2 I:GLU13 3.0 33.4 1.0 CG J:ASP22 3.0 33.6 1.0 OE1 I:GLU14 3.1 29.8 1.0 CG I:HIS46 3.2 34.3 1.0 CB J:ASP22 3.6 32.5 1.0 CB I:HIS46 3.8 33.3 1.0 NE2 I:HIS46 4.0 36.3 1.0 NH2 J:ARG26 4.0 41.6 1.0 CG I:GLU14 4.1 30.9 1.0 OD1 J:ASP22 4.1 32.3 1.0 CA J:ASP22 4.2 31.8 1.0 CG I:GLU13 4.2 34.4 1.0 N I:GLU14 4.2 30.1 1.0 CD2 I:HIS46 4.2 35.9 1.0 N I:ALA15 4.4 29.9 1.0 N I:HIS46 4.4 33.9 1.0 CD2 I:TYR45 4.5 41.0 1.0 CB I:ALA15 4.6 31.9 1.0 CZ J:ARG26 4.7 40.3 1.0 NE J:ARG26 4.7 40.1 1.0 CA I:HIS46 4.8 33.4 1.0 C I:GLU13 4.8 29.8 1.0 CA I:GLU13 4.8 31.2 1.0 CB I:TYR45 4.9 36.2 1.0

Zinc binding site 10 out of 14 in the Crystal Structure of C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium


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 C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn201 b:40.4 occ:1.00 OE2 J:GLU14 1.8 32.5 1.0 ND1 J:HIS46 1.8 32.1 1.0 OD2 I:ASP22 1.9 36.3 1.0 OE1 J:GLU13 2.0 40.1 1.0 CE1 J:HIS46 2.4 34.1 1.0 CD J:GLU14 2.8 31.4 1.0 CD J:GLU13 2.8 37.9 1.0 CG I:ASP22 3.0 35.7 1.0 OE2 J:GLU13 3.0 40.0 1.0 CG J:HIS46 3.1 32.3 1.0 OE1 J:GLU14 3.1 33.6 1.0 CB I:ASP22 3.5 34.2 1.0 NE2 J:HIS46 3.7 33.3 1.0 CB J:HIS46 3.8 32.2 1.0 CD2 J:HIS46 4.0 33.2 1.0 CA I:ASP22 4.0 34.0 1.0 OD1 I:ASP22 4.1 36.5 1.0 NH2 I:ARG26 4.1 37.6 1.0 CG J:GLU14 4.1 29.8 1.0 CG J:GLU13 4.3 36.0 1.0 N J:GLU14 4.3 29.6 1.0 CD2 J:TYR45 4.4 39.6 1.0 N J:HIS46 4.4 32.2 1.0 N J:ALA15 4.5 31.1 1.0 CB J:ALA15 4.7 33.5 1.0 CZ I:ARG26 4.7 36.7 1.0 NE I:ARG26 4.8 37.0 1.0 CA J:HIS46 4.8 32.1 1.0 C I:ASP22 4.9 33.4 1.0 O I:ASP22 4.9 33.5 1.0 CA J:GLU13 4.9 31.1 1.0 CB J:TYR45 4.9 33.6 1.0 C J:GLU13 5.0 31.3 1.0

I.A.Shumilin, E.Niedzialkowska, M.J.Domagalski, J.Stam, W.F.Anderson, W.Minor, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of C103A Mutant of Dj-1 Superfamily Protein STM1931 From Salmonella Typhimurium To Be Published.