Zinc in PDB 1sed: Crystal Structure of Protein of Unknown Function Yhal From Bacillus Subtilis

The structure of Crystal Structure of Protein of Unknown Function Yhal From Bacillus Subtilis, PDB code: 1sed was solved by Y.Kim, A.Joachimiak, E.Evdokimova, A.Savchenko, A.Edwards, Midwest Centerfor Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.81 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.784, 64.550, 64.503, 111.37, 107.19, 107.13
R / Rfree (%)	18.9 / 20.9

The structure of Crystal Structure of Protein of Unknown Function Yhal From Bacillus Subtilis also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

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

Zinc binding site 1 out of 3 in the Crystal Structure of Protein of Unknown Function Yhal 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 Protein of Unknown Function Yhal From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:26.1 occ:0.95 OE1 A:GLU55 2.0 27.1 1.0 OE1 A:GLU52 2.1 27.3 1.0 OE2 A:GLU55 2.6 34.7 1.0 CD A:GLU55 2.6 29.7 1.0 CD A:GLU52 2.8 28.2 1.0 OE2 A:GLU52 2.9 25.8 1.0 O A:HOH851 3.6 31.2 1.0 NH1 A:ARG48 4.1 24.9 1.0 CG A:GLU55 4.1 28.0 1.0 CG A:GLU52 4.3 23.8 1.0 NH2 A:ARG48 4.4 25.2 1.0 CB A:ASP51 4.7 24.8 1.0 CB A:GLU55 4.7 28.2 1.0 CZ A:ARG48 4.7 28.0 1.0 CA A:GLU52 4.7 25.6 1.0 N A:GLU52 4.8 24.8 1.0 C A:ASP51 4.9 23.4 1.0 O A:ASP51 4.9 26.1 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Protein of Unknown Function Yhal 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 Protein of Unknown Function Yhal From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:26.6 occ:0.95 OE1 B:GLU55 2.0 31.3 1.0 OE2 B:GLU52 2.2 30.5 1.0 OE2 B:GLU55 2.5 39.5 1.0 CD B:GLU55 2.6 30.9 1.0 OE1 B:GLU52 2.8 22.1 1.0 CD B:GLU52 2.9 27.3 1.0 O B:HOH850 3.5 30.2 1.0 NH1 B:ARG48 4.1 22.2 1.0 CG B:GLU55 4.1 29.1 1.0 CG B:GLU52 4.4 26.2 1.0 NH2 B:ARG48 4.4 24.5 1.0 CB B:ASP51 4.7 27.4 1.0 CZ B:ARG48 4.7 24.9 1.0 CA B:GLU52 4.8 25.8 1.0 CB B:GLU55 4.8 29.6 1.0 N B:GLU52 4.8 24.8 1.0 C B:ASP51 4.9 26.2 1.0 O B:ASP51 4.9 26.2 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Protein of Unknown Function Yhal 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 Protein of Unknown Function Yhal From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn503 b:26.4 occ:0.95 OE2 C:GLU52 2.0 29.6 1.0 OE2 C:GLU55 2.2 32.3 1.0 OE1 C:GLU55 2.5 39.5 1.0 CD C:GLU55 2.7 33.6 1.0 CD C:GLU52 2.8 30.9 1.0 OE1 C:GLU52 2.9 28.6 1.0 O C:HOH857 3.5 31.8 1.0 NH1 C:ARG48 4.0 20.8 1.0 CG C:GLU55 4.2 32.4 1.0 CG C:GLU52 4.3 28.1 1.0 NH2 C:ARG48 4.4 27.3 1.0 CB C:ASP51 4.7 27.1 1.0 CZ C:ARG48 4.7 23.7 1.0 CA C:GLU52 4.8 25.1 1.0 N C:GLU52 4.8 23.6 1.0 CB C:GLU55 4.8 30.5 1.0 O C:ASP51 4.9 25.2 1.0 C C:ASP51 4.9 24.6 1.0

Y.Kim, A.Joachimiak, E.Evdokimova, A.Savchenko, A.Edwards. The Crystal Structure of the Hypothetical Protein Yhai, APC1180 From Bacillus Subtilis To Be Published.