Zinc in PDB 4y06: Crystal Structure of the Dap Bii (G675R) Dipeptide Complex

The structure of Crystal Structure of the Dap Bii (G675R) Dipeptide Complex, PDB code: 4y06 was solved by Y.Sakamoto, I.Iizuka, C.Tateoka, S.Roppongi, M.Fujimoto, T.Nonaka, W.Ogasawara, N.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.00 / 2.18
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	122.420, 122.420, 222.060, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 23.5

The binding sites of Zinc atom in the Crystal Structure of the Dap Bii (G675R) Dipeptide Complex (pdb code 4y06). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the Dap Bii (G675R) Dipeptide Complex, PDB code: 4y06:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of the Dap Bii (G675R) Dipeptide Complex


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 the Dap Bii (G675R) Dipeptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn809 b:60.9 occ:1.00 O A:HOH901 1.8 41.5 1.0 OE2 A:GLU635 1.9 71.4 1.0 CD A:GLU635 2.5 51.9 1.0 OE1 A:GLU635 2.7 46.4 1.0 CG A:GLU635 3.8 44.0 1.0 CD2 A:TYR631 4.4 34.6 1.0 CE2 A:TYR631 4.5 37.0 1.0 CB A:GLU635 4.7 42.9 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of the Dap Bii (G675R) Dipeptide Complex


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 the Dap Bii (G675R) Dipeptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn810 b:96.3 occ:1.00 OD2 A:ASP59 2.7 71.4 1.0 ND1 A:HIS252 3.5 48.2 1.0 CG A:ASP59 3.6 64.5 1.0 N A:TRP253 3.6 34.5 1.0 OD1 A:ASP59 3.8 70.5 1.0 O A:TRP253 3.8 31.2 1.0 CA A:HIS252 3.9 41.4 1.0 CB A:HIS252 4.2 41.4 1.0 O A:LYS251 4.2 46.3 1.0 CE3 A:TRP253 4.2 52.6 1.0 CG A:HIS252 4.2 48.9 1.0 C A:HIS252 4.3 37.4 1.0 CD2 A:TRP253 4.3 46.4 1.0 CZ3 A:TRP253 4.5 52.7 1.0 CE1 A:HIS252 4.5 50.5 1.0 C A:TRP253 4.6 35.7 1.0 CA A:TRP253 4.7 34.9 1.0 CE2 A:TRP253 4.7 49.0 1.0 CG A:TRP253 4.8 42.4 1.0 CH2 A:TRP253 4.8 53.1 1.0 CB A:ASP59 4.9 53.7 1.0 N A:HIS252 4.9 42.2 1.0 CZ2 A:TRP253 4.9 53.6 1.0 C A:LYS251 5.0 48.1 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of the Dap Bii (G675R) Dipeptide Complex


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 the Dap Bii (G675R) Dipeptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn811 b:47.5 occ:1.00 OE2 A:GLU438 2.0 42.9 1.0 CD A:GLU438 2.8 34.6 1.0 OE1 A:GLU438 2.9 33.4 1.0 CG A:GLU438 4.2 37.5 1.0 NZ A:LYS442 4.2 42.6 1.0 CD2 A:LEU507 4.7 47.9 1.0 CE A:LYS442 4.9 44.5 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of the Dap Bii (G675R) Dipeptide Complex


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 the Dap Bii (G675R) Dipeptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn811 b:50.6 occ:1.00 OE2 B:GLU438 2.1 47.3 1.0 CD B:GLU438 2.8 37.5 1.0 OE1 B:GLU438 2.8 39.2 1.0 NZ B:LYS442 4.2 43.4 1.0 CG B:GLU438 4.2 39.5 1.0 CE B:LYS442 5.0 42.6 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of the Dap Bii (G675R) Dipeptide Complex


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 the Dap Bii (G675R) Dipeptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn812 b:57.2 occ:1.00 O B:HOH902 1.8 52.5 1.0 OE2 B:GLU635 1.9 62.5 1.0 O B:HOH1141 2.0 41.8 1.0 CD B:GLU635 2.6 45.0 1.0 OE1 B:GLU635 2.7 46.0 1.0 CG B:GLU635 4.0 46.9 1.0 CD2 B:TYR631 4.5 30.0 1.0 CE2 B:TYR631 4.6 32.0 1.0 CB B:GLU635 4.7 38.8 1.0

Y.Sakamoto, Y.Suzuki, I.Iizuka, C.Tateoka, S.Roppongi, M.Fujimoto, K.Inaka, H.Tanaka, M.Yamada, K.Ohta, H.Gouda, T.Nonaka, W.Ogasawara, N.Tanaka. Structural and Mutational Analyses of Dipeptidyl Peptidase 11 From Porphyromonas Gingivalis Reveal the Molecular Basis For Strict Substrate Specificity. Sci Rep V. 5 11151 2015.
ISSN: ESSN 2045-2322
PubMed: 26057589
DOI: 10.1038/SREP11151