Zinc in PDB 6jzv: Crystal Structure of Sufu From Bacillus Subtilis

The structure of Crystal Structure of Sufu From Bacillus Subtilis, PDB code: 6jzv was solved by T.Fujishiro, Y.Takahashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.41 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	35.320, 54.450, 70.380, 68.99, 75.86, 72.54
R / Rfree (%)	21.2 / 24.2

The binding sites of Zinc atom in the Crystal Structure of Sufu From Bacillus Subtilis (pdb code 6jzv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Sufu From Bacillus Subtilis, PDB code: 6jzv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Sufu From Bacillus Subtilis


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 Sufu From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:34.3 occ:1.00 OD2 A:ASP43 2.0 40.5 1.0 OD1 A:ASP43 2.1 40.4 1.0 SG A:CYS41 2.3 36.2 1.0 SG A:CYS66 2.4 28.9 1.0 CG A:ASP43 2.4 35.3 1.0 SG A:CYS128 2.4 32.3 1.0 CB A:CYS41 3.1 36.9 1.0 CB A:CYS128 3.4 30.6 1.0 CB A:CYS66 3.4 28.6 1.0 CB A:ASP43 3.9 29.1 1.0 N A:CYS66 4.1 23.7 1.0 OG A:SER69 4.2 28.7 1.0 NH2 A:ARG125 4.3 35.3 1.0 CA A:CYS128 4.3 30.0 1.0 OD1 A:ASN38 4.3 80.0 1.0 NE A:ARG125 4.4 32.1 1.0 CA A:CYS66 4.4 25.8 1.0 CB A:SER69 4.4 27.1 1.0 O A:HOH311 4.5 44.1 1.0 CA A:CYS41 4.6 40.8 1.0 CZ A:ARG125 4.8 35.5 1.0 O A:HOH308 4.8 39.7 1.0 N A:ASP43 4.9 34.5 1.0 CA A:ASP43 4.9 32.1 1.0 C A:CYS41 4.9 41.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Sufu From Bacillus Subtilis


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 Sufu From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:33.8 occ:1.00 OD2 B:ASP43 2.0 37.9 1.0 OD1 B:ASP43 2.1 36.1 1.0 SG B:CYS128 2.3 37.4 1.0 SG B:CYS66 2.3 25.8 1.0 SG B:CYS41 2.3 42.7 1.0 CG B:ASP43 2.4 29.7 1.0 CB B:CYS41 3.0 42.0 1.0 CB B:CYS66 3.4 24.8 1.0 CB B:CYS128 3.4 36.2 1.0 ND2 B:ASN38 3.7 45.7 1.0 CB B:ASP43 3.9 29.7 1.0 N B:CYS66 4.1 26.3 1.0 OG B:SER69 4.2 32.5 1.0 CA B:CYS128 4.3 32.0 1.0 CB B:SER69 4.3 30.4 1.0 CA B:CYS66 4.4 26.3 1.0 CA B:CYS41 4.4 42.9 1.0 NE B:ARG125 4.4 36.2 1.0 NH2 B:ARG125 4.5 35.0 1.0 C B:CYS41 4.7 44.8 1.0 N B:ASP43 4.7 31.3 1.0 CA B:ASP43 4.8 29.5 1.0 CG B:ASN38 4.9 47.0 1.0 CZ B:ARG125 4.9 37.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Sufu From Bacillus Subtilis


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 Sufu From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:33.2 occ:1.00 OD2 C:ASP43 2.0 35.9 1.0 OD1 C:ASP43 2.1 31.3 1.0 SG C:CYS41 2.3 33.4 1.0 SG C:CYS66 2.4 25.3 1.0 CG C:ASP43 2.4 31.2 1.0 SG C:CYS128 2.4 34.0 1.0 CB C:CYS41 3.1 34.2 1.0 CB C:CYS66 3.3 23.2 1.0 CB C:CYS128 3.5 29.1 1.0 CB C:ASP43 3.9 34.5 1.0 ND2 C:ASN38 4.0 43.2 1.0 N C:CYS66 4.1 27.7 1.0 OG C:SER69 4.1 27.2 1.0 CB C:SER69 4.3 23.9 1.0 CA C:CYS66 4.3 25.5 1.0 CA C:CYS128 4.4 31.0 1.0 NH2 C:ARG125 4.4 38.9 1.0 CA C:CYS41 4.5 43.2 1.0 NE C:ARG125 4.5 36.7 1.0 N C:ASP43 4.7 39.1 1.0 C C:CYS41 4.7 51.5 1.0 CA C:ASP43 4.8 36.1 1.0 CZ C:ARG125 4.9 40.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Sufu From Bacillus Subtilis


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 Sufu From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:31.2 occ:1.00 OD2 D:ASP43 2.0 37.7 1.0 OD1 D:ASP43 2.2 34.8 1.0 SG D:CYS128 2.3 29.0 1.0 SG D:CYS66 2.3 28.1 1.0 SG D:CYS41 2.3 42.5 1.0 CG D:ASP43 2.4 30.6 1.0 CB D:CYS41 3.1 48.3 1.0 CB D:CYS128 3.3 27.6 1.0 CB D:CYS66 3.4 29.0 1.0 CB D:ASP43 3.9 30.6 1.0 N D:CYS66 4.2 23.4 1.0 OG D:SER69 4.2 29.1 1.0 CA D:CYS128 4.2 26.3 1.0 CB D:SER69 4.3 28.1 1.0 NH2 D:ARG125 4.3 25.8 1.0 CA D:CYS66 4.4 23.2 1.0 NE D:ARG125 4.5 30.9 1.0 CA D:CYS41 4.5 53.0 1.0 C D:CYS41 4.8 53.6 1.0 N D:ASP43 4.8 42.3 1.0 CZ D:ARG125 4.9 33.8 1.0 CA D:ASP43 4.9 32.5 1.0 OD1 D:ASN38 5.0 69.4 1.0

T.Fujishiro, T.Terahata, Y.Shimada, Y.Takahashi. Zinc-Persulfide Complex For Sulfur Mobilization By Sufu in Suf-Like Machinery For Fe-S Cluster Biosynthesis To Be Published.