Zinc in PDB 4xaf: Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes

The structure of Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes, PDB code: 4xaf was solved by C.J.Jackson, E.Campbell, M.Kaltenbach, N.Tokuriki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.71 / 1.66
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.687, 85.733, 88.380, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 22

The structure of Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes (pdb code 4xaf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes, PDB code: 4xaf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2401 b:19.5 occ:0.60 O1 A:CAC2403 2.0 34.4 0.7 NE2 A:HIS57 2.1 18.9 1.0 OD1 A:ASP301 2.1 21.9 1.0 OQ2 A:KCX169 2.3 32.1 1.0 NE2 A:HIS55 2.3 21.3 1.0 CE1 A:HIS57 3.0 19.4 1.0 CG A:ASP301 3.0 23.0 1.0 CD2 A:HIS55 3.1 19.9 1.0 CD2 A:HIS57 3.1 14.1 1.0 CX A:KCX169 3.2 42.7 1.0 OD2 A:ASP301 3.3 27.6 1.0 AS A:CAC2403 3.4 56.5 0.7 CE1 A:HIS55 3.4 18.2 1.0 OQ1 A:KCX169 3.7 33.8 1.0 ZN A:ZN2402 3.9 21.9 0.3 C2 A:CAC2403 4.0 35.3 0.7 O2 A:CAC2403 4.1 35.4 0.7 CG2 A:VAL101 4.1 16.1 1.0 ND1 A:HIS57 4.1 18.6 1.0 NZ A:KCX169 4.2 31.5 1.0 CG A:HIS57 4.2 14.5 1.0 CE1 A:HIS230 4.3 35.2 1.0 CG A:HIS55 4.3 19.9 1.0 CB A:ASP301 4.4 20.1 1.0 ND1 A:HIS55 4.4 23.6 1.0 O A:HOH2643 4.6 42.2 1.0 NE2 A:HIS230 4.6 29.5 1.0 CA A:ASP301 4.8 18.6 1.0 C1 A:CAC2403 5.0 48.7 0.7

Zinc binding site 2 out of 4 in the Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2402 b:21.9 occ:0.31 OQ1 A:KCX169 1.8 33.8 1.0 NE2 A:HIS230 2.1 29.5 1.0 ND1 A:HIS201 2.2 34.2 1.0 O2 A:CAC2403 2.3 35.4 0.7 CX A:KCX169 2.9 42.7 1.0 CE1 A:HIS230 3.0 35.2 1.0 O1 A:CAC2403 3.1 34.4 0.7 CG A:HIS201 3.1 41.7 1.0 CE1 A:HIS201 3.1 50.2 1.0 CD2 A:HIS230 3.2 46.8 1.0 OQ2 A:KCX169 3.3 32.1 1.0 NH2 A:ARG254 3.3 43.3 0.4 CB A:HIS201 3.4 35.5 1.0 AS A:CAC2403 3.4 56.5 0.7 ZN A:ZN2401 3.9 19.5 0.6 NE1 A:TRP131 3.9 30.6 1.0 NZ A:KCX169 4.1 31.5 1.0 ND1 A:HIS230 4.2 46.2 1.0 NE2 A:HIS201 4.2 41.5 1.0 CD2 A:HIS201 4.2 44.0 1.0 CZ A:ARG254 4.3 44.4 0.4 CG A:HIS230 4.3 58.0 1.0 O A:HOH2621 4.3 40.8 1.0 NE2 A:HIS55 4.4 21.3 1.0 CE1 A:HIS55 4.5 18.2 1.0 CD1 A:TRP131 4.5 21.9 1.0 OD2 A:ASP301 4.5 27.6 1.0 CA A:HIS201 4.6 28.2 1.0 C1 A:CAC2403 4.7 48.7 0.7 NE A:ARG254 4.7 38.9 0.4 CE A:KCX169 4.7 22.8 1.0 C2 A:CAC2403 4.9 35.3 0.7

Zinc binding site 3 out of 4 in the Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn402 b:18.9 occ:0.67 O1 G:CAC401 1.9 31.2 0.7 NE2 G:HIS57 2.1 15.7 1.0 OQ2 G:KCX169 2.2 30.4 1.0 OD1 G:ASP301 2.2 21.4 1.0 NE2 G:HIS55 2.2 21.8 1.0 CE1 G:HIS57 3.1 22.9 1.0 CG G:ASP301 3.1 22.2 1.0 CD2 G:HIS55 3.1 21.6 1.0 CD2 G:HIS57 3.1 21.8 1.0 CX G:KCX169 3.2 39.6 1.0 CE1 G:HIS55 3.2 19.9 1.0 AS G:CAC401 3.4 39.1 0.7 OD2 G:ASP301 3.4 22.1 1.0 OQ1 G:KCX169 3.7 31.0 1.0 ZN G:ZN403 3.8 20.5 0.4 CE1 G:HIS230 4.0 24.3 1.0 C2 G:CAC401 4.1 30.0 0.7 O2 G:CAC401 4.1 28.3 0.7 CG2 G:VAL101 4.2 18.0 1.0 ND1 G:HIS57 4.2 18.4 1.0 NZ G:KCX169 4.2 32.8 1.0 NE2 G:HIS230 4.2 27.4 1.0 CG G:HIS57 4.2 20.1 1.0 CG G:HIS55 4.3 20.0 1.0 ND1 G:HIS55 4.3 20.8 1.0 CB G:ASP301 4.4 15.0 1.0 C1 G:CAC401 4.9 41.9 0.7 CA G:ASP301 4.9 14.9 1.0

Zinc binding site 4 out of 4 in the Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn403 b:20.5 occ:0.44 OQ1 G:KCX169 2.0 31.0 1.0 NE2 G:HIS230 2.1 27.4 1.0 ND1 G:HIS201 2.1 30.8 1.0 O2 G:CAC401 2.2 28.3 0.7 O1 G:CAC401 2.9 31.2 0.7 CD2 G:HIS230 2.9 27.9 1.0 CX G:KCX169 3.0 39.6 1.0 CE1 G:HIS201 3.0 34.1 1.0 CG G:HIS201 3.1 28.4 1.0 CE1 G:HIS230 3.2 24.3 1.0 AS G:CAC401 3.2 39.1 0.7 OQ2 G:KCX169 3.2 30.4 1.0 NH2 G:ARG254 3.3 28.1 0.4 CB G:HIS201 3.5 27.1 1.0 ZN G:ZN402 3.8 18.9 0.7 NE2 G:HIS201 4.1 46.3 1.0 NE1 G:TRP131 4.1 24.7 1.0 CG G:HIS230 4.1 23.8 1.0 CZ G:ARG254 4.2 25.6 0.4 NZ G:KCX169 4.2 32.8 1.0 CD2 G:HIS201 4.2 41.6 1.0 ND1 G:HIS230 4.2 26.4 1.0 CE1 G:HIS55 4.3 19.9 1.0 NE2 G:HIS55 4.3 21.8 1.0 C1 G:CAC401 4.4 41.9 0.7 NE G:ARG254 4.6 27.1 0.4 OD2 G:ASP301 4.6 22.1 1.0 CA G:HIS201 4.6 24.6 1.0 CE G:KCX169 4.7 26.4 1.0 CD1 G:TRP131 4.7 20.8 1.0 C2 G:CAC401 4.8 30.0 0.7

E.Campbell, M.Kaltenbach, G.J.Correy, P.D.Carr, B.T.Porebski, E.K.Livingstone, L.Afriat-Jurnou, A.M.Buckle, M.Weik, F.Hollfelder, N.Tokuriki, C.J.Jackson. The Role of Protein Dynamics in the Evolution of New Enzyme Function. Nat.Chem.Biol. V. 12 944 2016.
ISSN: ESSN 1552-4469
PubMed: 27618189
DOI: 10.1038/NCHEMBIO.2175