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Zinc in PDB 1z3a: Crystal Structure of Trna Adenosine Deaminase Tada From Escherichia Coli

Protein crystallography data

The structure of Crystal Structure of Trna Adenosine Deaminase Tada From Escherichia Coli, PDB code: 1z3a was solved by V.Malashkevich, J.Kim, M.Lisbin, S.C.Almo, S.K.Burley, New Yorksgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.95 / 2.03
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 100.232, 100.232, 159.576, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Trna Adenosine Deaminase Tada From Escherichia Coli (pdb code 1z3a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Trna Adenosine Deaminase Tada From Escherichia Coli, PDB code: 1z3a:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1z3a

Go back to Zinc Binding Sites List in 1z3a
Zinc binding site 1 out of 2 in the Crystal Structure of Trna Adenosine Deaminase Tada From Escherichia Coli


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 Trna Adenosine Deaminase Tada From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:21.9
occ:1.00
ND1 A:HIS68 2.0 21.2 1.0
O A:HOH416 2.1 21.2 1.0
SG A:CYS98 2.2 19.6 1.0
SG A:CYS101 2.3 22.3 1.0
CE1 A:HIS68 2.9 22.1 1.0
CG A:HIS68 3.1 20.7 1.0
CB A:CYS101 3.3 17.1 1.0
CB A:CYS98 3.5 20.2 1.0
CB A:HIS68 3.5 19.3 1.0
N A:CYS98 3.8 19.8 1.0
N A:CYS101 3.9 19.1 1.0
OE2 A:GLU70 3.9 22.0 1.0
CE A:MET100 3.9 17.2 1.0
O A:HOH377 4.0 44.4 1.0
NE2 A:HIS68 4.0 24.3 1.0
OE1 A:GLU70 4.1 21.9 1.0
CD2 A:HIS68 4.2 22.8 1.0
CA A:CYS101 4.2 18.8 1.0
CA A:CYS98 4.2 19.3 1.0
CD A:GLU70 4.2 25.6 1.0
NE2 B:HIS107 4.6 28.2 1.0
C A:CYS98 4.7 19.5 1.0
CB A:MET100 4.8 18.5 1.0
O A:HOH322 4.8 34.9 1.0
O A:CYS98 4.8 18.5 1.0
C A:PRO97 4.9 23.0 1.0
C A:MET100 5.0 19.5 1.0

Zinc binding site 2 out of 2 in 1z3a

Go back to Zinc Binding Sites List in 1z3a
Zinc binding site 2 out of 2 in the Crystal Structure of Trna Adenosine Deaminase Tada From Escherichia Coli


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 Trna Adenosine Deaminase Tada From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:21.0
occ:1.00
O B:HOH413 2.0 19.4 1.0
ND1 B:HIS68 2.0 25.2 1.0
SG B:CYS101 2.2 19.5 1.0
SG B:CYS98 2.4 22.0 1.0
CE1 B:HIS68 2.9 26.5 1.0
CG B:HIS68 3.0 26.0 1.0
CB B:CYS101 3.2 17.8 1.0
CB B:HIS68 3.4 23.1 1.0
CB B:CYS98 3.6 22.3 1.0
CE B:MET100 3.9 17.4 1.0
OE2 B:GLU70 3.9 19.7 1.0
N B:CYS98 3.9 19.7 1.0
N B:CYS101 3.9 18.5 1.0
NE2 B:HIS68 4.1 24.0 1.0
OE1 B:GLU70 4.1 20.4 1.0
CD2 B:HIS68 4.1 26.4 1.0
CA B:CYS101 4.2 19.0 1.0
O B:HOH360 4.2 45.3 1.0
CD B:GLU70 4.2 21.1 1.0
CA B:CYS98 4.3 21.5 1.0
NE2 A:HIS107 4.6 29.6 1.0
O B:HOH319 4.7 33.2 1.0
C B:CYS98 4.8 21.0 1.0
O B:CYS98 4.8 18.8 1.0
CB B:MET100 4.9 17.4 1.0
CA B:HIS68 5.0 16.4 1.0
C B:MET100 5.0 18.7 1.0

Reference:

J.Kim, V.Malashkevich, S.Roday, M.Lisbin, V.L.Schramm, S.C.Almo. Structural and Kinetic Characterization of Escherichia Coli Tada, the Wobble-Specific Trna Deaminase. Biochemistry V. 45 6407 2006.
ISSN: ISSN 0006-2960
PubMed: 16700551
DOI: 10.1021/BI0522394
Page generated: Wed Dec 16 03:15:14 2020

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