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

Enzymatic activity of 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;

Protein crystallography data

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

Zinc Binding Sites:

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 6eok

Go back to Zinc Binding Sites List in 6eok
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 6eok

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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 6eok

Go back to Zinc Binding Sites List in 6eok
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 6eok

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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

Reference:

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
Page generated: Wed Dec 16 11:43:45 2020

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