Zinc in PDB 6eok: Crystal Structure of E. Coli L-Asparaginase II

All present enzymatic activity of Crystal Structure of E. Coli L-Asparaginase II:
3.5.1.1;

The structure of Crystal Structure of E. Coli L-Asparaginase II, PDB code: 6eok was solved by L.Cerofolini, S.Giuntini, A.Carlon, E.Ravera, V.Calderone, M.Fragai, G.Parigi, C.Luchinat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.50 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.330, 121.230, 126.560, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 25.2

The binding sites of Zinc atom in the Crystal Structure of E. Coli L-Asparaginase II (pdb code 6eok). 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 E. Coli L-Asparaginase II, PDB code: 6eok:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of E. Coli L-Asparaginase II


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 E. Coli L-Asparaginase II within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:53.6 occ:1.00 OD2 A:ASP100 2.0 50.2 1.0 CG A:ASP100 3.0 46.7 1.0 O A:HOH519 3.1 14.4 1.0 ND1 A:HIS197 3.2 19.1 1.0 OD1 A:ASP100 3.3 49.6 1.0 CB A:HIS197 3.8 18.0 1.0 CB A:ARG158 3.9 19.2 1.0 CG A:HIS197 3.9 19.7 1.0 N A:ARG158 3.9 21.8 1.0 OD2 A:ASP156 4.1 22.9 1.0 CB A:ASP156 4.2 20.4 1.0 N A:GLY157 4.2 19.0 1.0 CE1 A:HIS197 4.2 19.7 1.0 O A:HOH522 4.3 10.8 1.0 CB A:ASP100 4.3 37.0 1.0 CG A:PRO193 4.4 24.0 1.0 CA A:ARG158 4.6 21.0 1.0 CG A:ASP156 4.6 22.2 1.0 C A:ASP156 4.7 18.2 1.0 O A:ARG144 4.7 26.4 1.0 CB A:PRO193 4.8 23.8 1.0 CA A:ASP156 4.8 18.7 1.0 CA A:GLY145 4.8 23.5 1.0 C A:GLY157 4.8 21.3 1.0 O A:VAL146 4.8 19.1 1.0 CA A:GLY157 4.9 19.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of E. Coli L-Asparaginase II


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 E. Coli L-Asparaginase II within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:37.3 occ:1.00 OD1 B:ASP100 2.3 13.5 1.0 ND1 B:HIS197 2.9 26.6 1.0 CG B:ASP100 3.0 13.3 1.0 OD2 B:ASP100 3.0 13.7 1.0 O B:HOH542 3.3 11.5 1.0 CB B:HIS197 3.4 25.6 1.0 O B:HOH570 3.5 11.3 1.0 CG B:HIS197 3.6 23.3 1.0 CE1 B:HIS197 4.1 24.8 1.0 CB B:ARG158 4.2 10.4 1.0 CB B:ASP100 4.4 13.1 1.0 CB B:PRO193 4.5 18.9 1.0 N B:ARG158 4.6 11.8 1.0 OD1 B:ASP156 4.7 14.9 1.0 CG B:PRO193 4.8 18.8 1.0 O B:ARG195 4.8 23.4 1.0 CA B:HIS197 4.8 24.3 1.0 CD2 B:HIS197 4.8 27.2 1.0 CA B:GLY145 4.9 22.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of E. Coli L-Asparaginase II


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 E. Coli L-Asparaginase II within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:40.4 occ:1.00 O C:HOH541 2.1 40.3 1.0 OD2 C:ASP100 2.2 9.9 1.0 O C:HOH582 2.4 28.5 1.0 ND1 C:HIS197 2.8 19.6 1.0 CG C:ASP100 2.9 9.2 1.0 OD1 C:ASP100 3.0 9.4 1.0 CB C:HIS197 3.1 19.7 1.0 CG C:HIS197 3.3 20.4 1.0 O C:HOH552 3.6 21.0 1.0 O C:HOH503 3.9 16.9 1.0 CE1 C:HIS197 4.0 20.2 1.0 CB C:ASP100 4.3 8.8 1.0 CG C:PRO193 4.3 19.9 1.0 CB C:ARG158 4.4 12.5 1.0 CA C:HIS197 4.5 20.8 1.0 O C:ARG195 4.5 19.6 1.0 CB C:PRO193 4.6 19.5 1.0 CD2 C:HIS197 4.6 20.3 1.0 OD2 C:ASP156 4.6 13.3 1.0 O C:ARG144 4.6 18.4 1.0 CA C:GLY145 4.7 16.8 1.0 N C:ARG158 4.8 13.3 1.0 NE2 C:HIS197 4.9 20.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of E. Coli L-Asparaginase II


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 E. Coli L-Asparaginase II within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:41.0 occ:1.00 OD2 D:ASP100 2.1 40.8 1.0 ND1 D:HIS197 2.9 29.2 1.0 CG D:ASP100 3.0 40.0 1.0 OD1 D:ASP100 3.2 41.3 1.0 O D:HOH544 3.4 12.7 1.0 CB D:HIS197 3.4 30.5 1.0 CG D:HIS197 3.5 36.1 1.0 O D:HOH535 3.8 12.4 1.0 CE1 D:HIS197 4.0 29.4 1.0 CB D:ARG158 4.3 13.0 1.0 CB D:ASP100 4.4 35.4 1.0 CG D:PRO193 4.5 22.7 1.0 OD2 D:ASP156 4.5 22.3 1.0 N D:ARG158 4.6 16.0 1.0 CB D:PRO193 4.7 22.8 1.0 O D:ARG195 4.7 30.4 1.0 CD2 D:HIS197 4.7 30.4 1.0 CA D:HIS197 4.8 34.4 1.0 O D:ARG144 4.8 29.8 1.0 CA D:GLY145 4.9 26.5 1.0 NE2 D:HIS197 4.9 30.0 1.0

L.Cerofolini, S.Giuntini, A.Carlon, E.Ravera, V.Calderone, M.Fragai, G.Parigi, C.Luchinat. Characterization of Pegylated Asparaginase: New Opportunities From uc(Nmr) Analysis of Large Pegylated Therapeutics. Chemistry V. 25 1984 2019.
ISSN: ISSN 1521-3765
PubMed: 30462348
DOI: 10.1002/CHEM.201804488