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Zinc in PDB 3eph: 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: 3eph 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 / 2.95
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 162.463, 211.596, 125.518, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.6

Other elements in 3eph:

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) 10 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 3eph). 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: 3eph:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3eph

Go back to Zinc Binding Sites List in 3eph
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:79.4
occ:1.00
 ND1 A:HIS403 1.9 77.4 1.0
SG A:CYS375 2.2 71.2 1.0
SG A:CYS378 2.4 86.4 1.0
NE2 A:HIS397 2.5 73.7 1.0
CE1 A:HIS403 2.8 76.0 1.0
CE1 A:HIS397 2.8 73.5 1.0
CG A:HIS403 2.9 77.8 1.0
CB A:CYS378 3.0 87.6 1.0
CB A:HIS403 3.3 78.9 1.0
CB A:CYS375 3.4 76.9 1.0
CD2 A:HIS397 3.6 71.8 1.0
CA A:HIS403 3.8 82.1 1.0
N A:CYS378 3.9 89.2 1.0
NE2 A:HIS403 3.9 76.8 1.0
ND1 A:HIS397 4.0 69.9 1.0
CD2 A:HIS403 4.0 77.2 1.0
CA A:CYS378 4.1 89.0 1.0
CG A:HIS397 4.4 70.1 1.0
O A:HOH506 4.6 88.5 1.0
N A:HIS403 4.7 83.7 1.0
CA A:CYS375 4.8 79.9 1.0
C A:HIS403 4.8 84.1 1.0
C A:VAL377 4.9 88.4 1.0
CB A:VAL377 4.9 85.9 1.0
O A:HIS403 4.9 84.5 1.0

Zinc binding site 2 out of 2 in 3eph

Go back to Zinc Binding Sites List in 3eph
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:72.9
occ:1.00
 ND1 B:HIS403 2.0 82.6 1.0
SG B:CYS375 2.2 74.6 1.0
SG B:CYS378 2.4 87.0 1.0
NE2 B:HIS397 2.5 78.7 1.0
CE1 B:HIS397 2.9 78.3 1.0
CB B:CYS378 2.9 84.5 1.0
CE1 B:HIS403 3.0 82.2 1.0
CG B:HIS403 3.1 83.5 1.0
CB B:CYS375 3.3 78.9 1.0
CB B:HIS403 3.4 85.8 1.0
CD2 B:HIS397 3.7 78.2 1.0
N B:CYS378 3.7 86.1 1.0
CA B:HIS403 3.8 87.3 1.0
CA B:CYS378 3.9 85.4 1.0
ND1 B:HIS397 4.1 77.6 1.0
NE2 B:HIS403 4.1 82.6 1.0
CD2 B:HIS403 4.2 81.7 1.0
CG B:HIS397 4.5 76.7 1.0
CA B:CYS375 4.7 80.8 1.0
C B:VAL377 4.7 85.9 1.0
N B:HIS403 4.8 87.9 1.0
CB B:VAL377 4.8 84.3 1.0
C B:HIS403 4.9 88.3 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: Thu Oct 24 12:53:13 2024

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