Zinc in PDB 4koy: Crystal Structure of A Gnat Superfamily Acetyltransferase PA4794 in Complex with Cephalosporin C

The structure of Crystal Structure of A Gnat Superfamily Acetyltransferase PA4794 in Complex with Cephalosporin C, PDB code: 4koy was solved by K.A.Majorek, P.J.Porebski, M.Chruszcz, M.Cymborowski, A.Joachimiak, W.Minor, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.94 / 1.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.000, 76.059, 39.303, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 17.3

The binding sites of Zinc atom in the Crystal Structure of A Gnat Superfamily Acetyltransferase PA4794 in Complex with Cephalosporin C (pdb code 4koy). 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 A Gnat Superfamily Acetyltransferase PA4794 in Complex with Cephalosporin C, PDB code: 4koy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Gnat Superfamily Acetyltransferase PA4794 in Complex with Cephalosporin C


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 A Gnat Superfamily Acetyltransferase PA4794 in Complex with Cephalosporin C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn215 b:53.8 occ:0.50 ZN A:ZN215 0.0 53.8 0.5 CE1 A:HIS5 1.9 19.4 0.5 NE2 A:HIS5 2.0 20.5 0.5 O A:HOH516 2.5 34.5 0.5 NE2 A:HIS5 2.6 20.2 0.5 O A:HOH435 2.7 32.0 1.0 CD2 A:HIS5 2.9 19.0 0.5 ND1 A:HIS5 3.0 18.3 0.5 CE1 A:HIS5 3.1 20.6 0.5 ZN A:ZN215 3.2 45.0 0.5 O A:HOH385 3.4 36.5 1.0 O A:HOH371 3.7 26.4 1.0 O A:HOH344 3.8 24.0 1.0 CD2 A:HIS5 3.9 19.3 0.5 CG A:HIS5 4.1 18.1 0.5 CG A:HIS5 4.1 18.5 0.5 ND1 A:HIS5 4.1 19.5 0.5 O A:HOH379 4.7 42.9 1.0 O A:HOH502 4.7 29.7 0.5 CG1 A:VAL99 4.8 14.8 1.0 O A:HOH392 4.9 38.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Gnat Superfamily Acetyltransferase PA4794 in Complex with Cephalosporin C


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 A Gnat Superfamily Acetyltransferase PA4794 in Complex with Cephalosporin C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn215 b:45.0 occ:0.50 ZN A:ZN215 0.0 45.0 0.5 CE1 A:HIS5 2.2 20.6 0.5 NE2 A:HIS5 2.2 20.2 0.5 NE2 A:HIS5 2.7 20.5 0.5 O A:HOH379 2.9 42.9 1.0 CE1 A:HIS5 3.2 19.4 0.5 CD2 A:HIS5 3.2 19.3 0.5 ZN A:ZN215 3.2 53.8 0.5 ND1 A:HIS5 3.4 19.5 0.5 O A:HOH516 3.9 34.5 0.5 CD2 A:HIS5 4.1 19.0 0.5 O A:HOH349 4.1 34.0 1.0 ND1 A:HIS5 4.3 18.3 0.5 CG A:HIS5 4.3 18.1 0.5 CG A:HIS5 4.4 18.5 0.5 O A:HOH371 4.5 26.4 1.0 O A:HOH327 4.7 27.3 1.0 O A:HOH447 4.9 49.0 1.0 CG2 A:VAL99 5.0 15.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Gnat Superfamily Acetyltransferase PA4794 in Complex with Cephalosporin C


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 A Gnat Superfamily Acetyltransferase PA4794 in Complex with Cephalosporin C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn216 b:32.0 occ:0.60 O A:HOH529 1.9 49.0 1.0 O A:HOH462 2.1 46.1 1.0 NE2 A:HIS57 2.1 27.1 1.0 O A:HOH490 2.2 48.1 0.6 O A:HOH463 2.3 31.9 0.5 O A:HOH463 2.4 33.2 0.5 CE1 A:HIS57 3.0 28.1 1.0 CD2 A:HIS57 3.2 25.8 1.0 ND1 A:HIS57 4.1 27.0 1.0 CB A:ASP58 4.2 30.1 1.0 OD2 A:ASP58 4.2 37.3 1.0 CG A:HIS57 4.3 24.7 1.0 CG A:ASP58 4.6 35.2 1.0 O A:HOH450 5.0 53.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Gnat Superfamily Acetyltransferase PA4794 in Complex with Cephalosporin C


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 A Gnat Superfamily Acetyltransferase PA4794 in Complex with Cephalosporin C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn217 b:19.7 occ:0.20 O A:HOH429 1.9 36.4 1.0 NE2 A:HIS142 2.0 18.5 0.2 CE1 A:HIS142 2.0 22.6 0.8 O A:HOH456 2.1 21.6 0.2 O A:HOH507 2.1 17.4 0.2 O A:HOH517 2.3 34.1 1.0 NE2 A:HIS142 2.6 22.5 0.8 CE1 A:HIS142 2.8 18.2 0.2 OE1 A:GLU140 2.8 34.7 0.8 CD2 A:HIS142 3.1 18.2 0.2 ND1 A:HIS142 3.3 22.1 0.8 O A:HOH399 3.8 41.5 1.0 OE2 A:GLU140 3.8 17.5 0.2 CD A:GLU140 3.9 30.1 0.8 CD2 A:HIS142 3.9 22.3 0.8 ND1 A:HIS142 4.0 17.8 0.2 CG A:HIS142 4.2 17.5 0.2 CG A:HIS142 4.2 20.1 0.8 CD A:GLU140 4.4 17.6 0.2 O2 A:EDO207 4.4 30.6 0.7 CG A:GLU140 4.6 16.6 0.2 CG A:GLU140 4.7 23.1 0.8 OE2 A:GLU140 4.8 32.2 0.8

K.A.Majorek, M.L.Kuhn, M.Chruszcz, W.F.Anderson, W.Minor. Structural, Functional, and Inhibition Studies of A GCN5-Related N-Acetyltransferase (Gnat) Superfamily Protein PA4794: A New C-Terminal Lysine Protein Acetyltransferase From Pseudomonas Aeruginosa. J.Biol.Chem. V. 288 30223 2013.
ISSN: ISSN 0021-9258
PubMed: 24003232
DOI: 10.1074/JBC.M113.501353