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Zinc in PDB 3epl: Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism

Enzymatic activity of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism

All present enzymatic activity of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism:
2.5.1.8;

Protein crystallography data

The structure of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism, PDB code: 3epl was solved by R.H.Huang, C.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 164.074, 209.850, 127.318, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 26.6

Other elements in 3epl:

The structure of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism (pdb code 3epl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism, PDB code: 3epl:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3epl

Go back to Zinc Binding Sites List in 3epl
Zinc binding site 1 out of 2 in the Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:96.1
occ:1.00
ND1 A:HIS403 1.8 97.5 1.0
SG A:CYS378 2.0 0.6 1.0
SG A:CYS375 2.1 0.9 1.0
NE2 A:HIS397 2.4 86.3 1.0
CE1 A:HIS403 2.6 96.6 1.0
CE1 A:HIS397 2.9 86.9 1.0
CG A:HIS403 3.0 97.8 1.0
CB A:CYS378 3.1 0.7 1.0
CB A:CYS375 3.4 0.1 1.0
CD2 A:HIS397 3.4 85.7 1.0
CB A:HIS403 3.6 0.5 1.0
NE2 A:HIS403 3.7 96.8 1.0
CA A:HIS403 3.9 0.0 1.0
CD2 A:HIS403 3.9 96.8 1.0
ND1 A:HIS397 4.0 86.2 1.0
N A:CYS378 4.1 0.0 1.0
CA A:CYS378 4.2 0.2 1.0
CG A:HIS397 4.3 86.3 1.0
C A:VAL377 4.4 0.2 1.0
CA A:CYS375 4.7 0.1 1.0
O A:VAL377 4.8 0.8 1.0
CB A:VAL377 4.8 0.9 1.0
N A:HIS403 4.8 0.9 1.0
N A:VAL377 5.0 0.4 1.0
CA A:VAL377 5.0 0.1 1.0
C A:HIS403 5.0 0.1 1.0

Zinc binding site 2 out of 2 in 3epl

Go back to Zinc Binding Sites List in 3epl
Zinc binding site 2 out of 2 in the Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:98.3
occ:1.00
ND1 B:HIS403 2.0 99.3 1.0
NE2 B:HIS397 2.1 91.1 1.0
SG B:CYS378 2.1 0.3 1.0
CE1 B:HIS397 2.5 92.8 1.0
SG B:CYS375 2.6 96.3 1.0
CE1 B:HIS403 2.9 0.3 1.0
CG B:HIS403 2.9 98.5 1.0
CB B:CYS378 3.0 0.7 1.0
CD2 B:HIS397 3.2 90.3 1.0
CB B:HIS403 3.3 96.7 1.0
ND1 B:HIS397 3.6 91.7 1.0
CB B:CYS375 3.7 99.6 1.0
CA B:HIS403 3.7 97.8 1.0
CG B:HIS397 4.0 89.7 1.0
NE2 B:HIS403 4.0 0.4 1.0
CD2 B:HIS403 4.0 99.6 1.0
CA B:CYS378 4.3 0.1 1.0
N B:CYS378 4.4 0.0 1.0
N B:HIS403 4.4 99.4 1.0
C B:VAL377 4.7 0.6 1.0
CG2 B:VAL386 4.8 91.3 1.0
C B:HIS403 4.9 97.5 1.0
O B:HIS397 4.9 88.5 1.0
O B:VAL377 5.0 0.9 1.0

Reference:

C.Zhou, R.H.Huang. Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism. Proc.Natl.Acad.Sci.Usa V. 105 16142 2008.
ISSN: ISSN 0027-8424
PubMed: 18852462
DOI: 10.1073/PNAS.0805680105
Page generated: Wed Dec 16 04:16:43 2020

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