Zinc in PDB 3iib: Crystal Structure of Peptidase M28 Precursor (YP_926796.1) From Shewanella Amazonensis SB2B at 1.70 A Resolution

The structure of Crystal Structure of Peptidase M28 Precursor (YP_926796.1) From Shewanella Amazonensis SB2B at 1.70 A Resolution, PDB code: 3iib was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.37 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.442, 84.867, 80.114, 90.00, 115.85, 90.00
R / Rfree (%)	15.1 / 18.2

The binding sites of Zinc atom in the Crystal Structure of Peptidase M28 Precursor (YP_926796.1) From Shewanella Amazonensis SB2B at 1.70 A Resolution (pdb code 3iib). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Peptidase M28 Precursor (YP_926796.1) From Shewanella Amazonensis SB2B at 1.70 A Resolution, PDB code: 3iib:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Peptidase M28 Precursor (YP_926796.1) From Shewanella Amazonensis SB2B at 1.70 A Resolution


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 Peptidase M28 Precursor (YP_926796.1) From Shewanella Amazonensis SB2B at 1.70 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:5.5 occ:0.50 OD2 A:ASP292 2.0 8.2 1.0 O A:HOH589 2.1 9.1 1.0 O A:HOH648 2.1 13.3 1.0 OE1 A:GLU327 2.2 6.4 1.0 NE2 A:HIS425 2.3 5.9 1.0 OE2 A:GLU327 2.3 10.4 1.0 CD A:GLU327 2.6 10.9 1.0 CG A:ASP292 3.0 9.6 1.0 CE1 A:HIS425 3.2 5.6 1.0 CD2 A:HIS425 3.3 4.1 1.0 OD1 A:ASP292 3.3 5.6 1.0 ZN A:ZN2 3.5 7.0 0.5 NE2 A:HIS424 3.6 6.1 1.0 O A:HOH587 4.0 16.6 1.0 O A:HOH1063 4.1 13.1 0.5 CG A:GLU327 4.1 8.8 1.0 OE1 A:GLU326 4.1 10.7 1.0 CD2 A:HIS424 4.1 7.0 1.0 O A:HOH676 4.2 5.2 1.0 CB A:ASP292 4.4 5.0 1.0 ND1 A:HIS425 4.4 4.8 1.0 CG A:HIS425 4.4 4.9 1.0 CD1 A:TRP284 4.4 4.4 1.0 CE1 A:HIS280 4.5 3.7 1.0 O A:HOH588 4.6 27.0 1.0 NE2 A:HIS280 4.6 3.8 1.0 CE1 A:HIS424 4.6 7.8 1.0 NE1 A:TRP284 4.6 5.3 1.0 O A:HOH746 4.8 7.0 1.0 CB A:GLU327 4.9 4.3 1.0 OH A:TYR420 5.0 7.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Peptidase M28 Precursor (YP_926796.1) From Shewanella Amazonensis SB2B at 1.70 A Resolution


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 Peptidase M28 Precursor (YP_926796.1) From Shewanella Amazonensis SB2B at 1.70 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:7.0 occ:0.50 O A:HOH589 1.9 9.1 1.0 OD1 A:ASP292 2.1 5.6 1.0 OD1 A:ASP354 2.1 7.2 1.0 NE2 A:HIS280 2.2 3.8 1.0 OD2 A:ASP354 2.3 8.2 1.0 O A:HOH587 2.4 16.6 1.0 CG A:ASP354 2.5 8.3 1.0 CG A:ASP292 3.1 9.6 1.0 CE1 A:HIS280 3.1 3.7 1.0 CD2 A:HIS280 3.2 6.5 1.0 OD2 A:ASP292 3.5 8.2 1.0 ZN A:ZN1 3.5 5.5 0.5 O A:HOH588 3.7 27.0 1.0 OE1 A:GLU326 3.7 10.7 1.0 O A:HOH708 3.9 6.6 1.0 OH A:TYR420 4.0 7.5 1.0 O A:HOH648 4.0 13.3 1.0 CB A:ASP354 4.1 5.7 1.0 CD A:GLU326 4.2 10.2 1.0 CB A:ASP293 4.2 3.9 1.0 OE2 A:GLU327 4.2 10.4 1.0 ND1 A:HIS280 4.2 4.0 1.0 OE2 A:GLU326 4.3 18.7 1.0 CG A:HIS280 4.3 5.4 1.0 CB A:ASP292 4.4 5.0 1.0 O A:ASP354 4.4 8.5 1.0 CA A:ASP292 4.6 6.0 1.0 CG A:ASP293 4.7 5.4 1.0 CD A:GLU327 4.7 10.9 1.0 CA A:ASP354 4.8 5.0 1.0 C A:ASP354 4.9 7.8 1.0 OE1 A:GLU327 4.9 6.4 1.0 C A:ASP292 4.9 3.3 1.0 OD2 A:ASP293 4.9 6.4 1.0

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.