Zinc in PDB 5k4m: Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-3

All present enzymatic activity of Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-3:
3.5.2.6;

The structure of Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-3, PDB code: 5k4m was solved by N.-S.Hong, C.J.Jackson, P.D.Carr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.13 / 1.98
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	37.820, 138.160, 78.200, 90.00, 90.00, 90.00
R / Rfree (%)	14.2 / 20.8

The structure of Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-3 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-3 (pdb code 5k4m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-3, PDB code: 5k4m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:15.5 occ:1.00 OAC A:SV7308 2.0 23.5 1.0 ND1 A:HIS122 2.0 13.5 1.0 NE2 A:HIS189 2.1 12.1 1.0 NE2 A:HIS120 2.1 12.9 1.0 CD2 A:HIS189 3.0 11.2 1.0 CG A:HIS122 3.0 13.6 1.0 CE1 A:HIS122 3.0 14.7 1.0 CD2 A:HIS120 3.1 11.7 1.0 CE1 A:HIS120 3.1 13.9 1.0 CE1 A:HIS189 3.1 11.5 1.0 PAB A:SV7308 3.2 29.4 1.0 CB A:HIS122 3.4 12.9 1.0 OAA A:SV7308 3.7 28.7 1.0 OAD A:SV7308 4.1 18.4 1.0 OD1 A:ASP124 4.1 13.7 1.0 NE2 A:HIS122 4.1 15.9 1.0 CD2 A:HIS122 4.1 14.1 1.0 CG2 A:THR190 4.1 9.7 1.0 CG A:HIS189 4.1 10.7 1.0 ND1 A:HIS120 4.2 12.4 1.0 ND1 A:HIS189 4.2 10.9 1.0 CG A:HIS120 4.2 10.6 1.0 ZN A:ZN302 4.4 15.8 1.0 SG A:CYS208 4.5 11.2 1.0 CB A:CYS208 4.6 10.9 1.0 CAE A:SV7308 4.6 29.7 1.0 O A:HOH552 4.6 39.2 1.0 O A:HOH547 4.7 32.2 1.0 CAF A:SV7308 4.8 33.5 1.0 CA A:HIS122 4.8 12.8 1.0 CG A:ASP124 5.0 13.8 1.0

Zinc binding site 2 out of 2 in the Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:15.8 occ:1.00 OAD A:SV7308 1.9 18.4 1.0 OD2 A:ASP124 2.0 12.9 1.0 NE2 A:HIS250 2.1 13.9 1.0 SG A:CYS208 2.3 11.2 1.0 CG A:ASP124 3.0 13.8 1.0 OAC A:SV7308 3.1 23.5 1.0 CE1 A:HIS250 3.1 13.4 1.0 PAB A:SV7308 3.1 29.4 1.0 CD2 A:HIS250 3.1 13.6 1.0 CB A:CYS208 3.3 10.9 1.0 OD1 A:ASP124 3.4 13.7 1.0 O A:HOH415 3.6 15.8 1.0 CAE A:SV7308 3.8 29.7 1.0 CAJ A:SV7308 3.8 29.5 1.0 CB A:SER249 4.1 10.3 1.0 ND1 A:HIS250 4.2 13.1 1.0 CG A:HIS250 4.2 12.8 1.0 CB A:ASP124 4.3 14.1 1.0 OAA A:SV7308 4.4 28.7 1.0 ZN A:ZN301 4.4 15.5 1.0 OG A:SER249 4.4 11.2 1.0 CA A:CYS208 4.5 10.7 1.0 NE2 A:HIS189 4.6 12.1 1.0 CE1 A:HIS120 4.7 13.9 1.0 O A:HOH441 4.8 12.8 1.0 CAF A:SV7308 4.8 33.5 1.0 CE1 A:HIS189 4.8 11.5 1.0 CE A:LYS125 4.9 13.9 1.0 CAI A:SV7308 4.9 31.2 1.0 NE2 A:HIS120 5.0 12.9 1.0

F.Baier, N.-S.Hong, G.Yang, P.D.Carr, C.Jackson, N.Tokuriki. Enzyme Evolvability Is Contingent on the Initial Sequence Background To Be Published.