Zinc in PDB 1s7d: Crystal Structure of Refined Tetragonal Crystal of Yoda From Escherichia Coli

The structure of Crystal Structure of Refined Tetragonal Crystal of Yoda From Escherichia Coli, PDB code: 1s7d was solved by D.H.Shin, H.Yokota, R.Kim, S.H.Kim, Berkeley Structural Genomics Center(Bsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.45 / 2.17
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.009, 55.009, 153.785, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25.5

The binding sites of Zinc atom in the Crystal Structure of Refined Tetragonal Crystal of Yoda From Escherichia Coli (pdb code 1s7d). 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 Refined Tetragonal Crystal of Yoda From Escherichia Coli, PDB code: 1s7d:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Refined Tetragonal Crystal of Yoda From Escherichia Coli


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 Refined Tetragonal Crystal of Yoda From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:38.4 occ:0.70 NE2 A:HIS155 2.2 35.7 1.0 NE2 A:HIS144 2.3 29.7 1.0 O A:HOH368 2.4 30.5 1.0 O A:HOH301 2.5 25.6 1.0 CE1 A:HIS144 2.8 28.1 1.0 O A:HOH366 2.9 26.2 1.0 CE1 A:HIS155 3.1 34.3 1.0 CD2 A:HIS155 3.2 30.9 1.0 CD2 A:HIS144 3.6 29.2 1.0 ND1 A:HIS144 4.0 29.9 1.0 ND1 A:HIS155 4.2 32.0 1.0 CG A:HIS155 4.2 30.6 1.0 O A:HOH323 4.4 43.1 1.0 CG A:HIS144 4.5 29.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Refined Tetragonal Crystal of Yoda From Escherichia Coli


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 Refined Tetragonal Crystal of Yoda From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:50.9 occ:0.70 OE1 A:GLU189 2.3 47.9 1.0 NE2 A:HIS193 2.4 0.2 1.0 CE1 A:HIS153 2.7 38.1 1.0 OE2 A:GLU189 2.7 46.0 1.0 CD A:GLU189 2.9 46.3 1.0 CD2 A:HIS193 2.9 0.8 1.0 CE1 A:HIS193 3.0 1.0 1.0 ND1 A:HIS153 3.2 37.8 1.0 O A:HOH373 3.5 45.9 1.0 CG A:HIS193 3.7 1.0 1.0 ND1 A:HIS193 3.7 0.0 1.0 NE2 A:HIS153 3.8 38.6 1.0 CG A:GLU189 4.4 44.7 1.0 O A:HOH350 4.5 52.4 1.0 CG A:HIS153 4.5 35.3 1.0 O A:GLU189 4.6 42.1 1.0 OH A:TYR177 4.7 27.6 1.0 CD2 A:HIS153 4.8 37.0 1.0 CB A:HIS193 4.9 1.0 1.0 CB A:SER152 4.9 37.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Refined Tetragonal Crystal of Yoda From Escherichia Coli


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 Refined Tetragonal Crystal of Yoda From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:40.0 occ:1.00 ND1 A:HIS95 2.1 19.0 1.0 CG A:HIS95 3.1 19.7 1.0 CE1 A:HIS95 3.1 19.1 1.0 CB A:HIS95 3.4 18.6 1.0 CG2 A:THR100 3.9 48.5 1.0 NE2 A:HIS95 4.2 20.8 1.0 CE A:MET84 4.2 43.8 1.0 CD2 A:HIS95 4.2 19.4 1.0 CA A:HIS95 4.5 24.5 1.0 O A:GLU99 4.9 41.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Refined Tetragonal Crystal of Yoda From Escherichia Coli


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 Refined Tetragonal Crystal of Yoda From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:33.1 occ:1.00 OD2 A:ASP24 2.2 32.4 1.0 O A:HOH380 2.3 14.9 1.0 O A:HOH337 2.4 28.2 1.0 CG A:ASP24 3.0 32.5 1.0 CB A:ASP24 3.3 32.0 1.0 O A:HOH308 4.1 37.6 1.0 OD1 A:ASP24 4.1 34.1 1.0 CA A:ASP24 4.8 26.8 1.0 CD1 A:ILE112 4.8 22.7 1.0

D.H.Shin, H.Yokota, R.Kim, S.H.Kim. Crystal Structure of Refined Tetragonal Crystal of Yoda From Escherichia Coli To Be Published.