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Magnesium 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:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism, PDB code: 3epl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3epl

Go back to Magnesium Binding Sites List in 3epl
Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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
E:Mg72

b:0.4
occ:1.00
 OP2 E:C56 3.0 0.8 1.0
C6 E:U55 3.1 0.1 1.0
OP2 E:G57 3.2 0.8 1.0
C5 E:U55 3.2 0.9 1.0
C3' E:U55 3.7 0.7 1.0
N1 E:U55 3.8 0.7 1.0
C4 E:U55 4.0 0.7 1.0
C5' E:U55 4.1 0.5 1.0
P E:G57 4.2 0.2 1.0
OP1 E:G57 4.3 0.8 1.0
P E:C56 4.3 0.1 1.0
C4' E:U55 4.3 0.5 1.0
C2' E:U55 4.4 0.4 1.0
OP2 E:U55 4.4 0.7 1.0
C1' E:U55 4.5 0.4 1.0
O3' E:U55 4.5 0.1 1.0
O4' E:U55 4.5 0.3 1.0
C2 E:U55 4.5 0.8 1.0
N3 E:U55 4.5 0.9 1.0
O4 E:U55 4.7 0.9 1.0
C5' E:C56 4.7 0.7 1.0
O5' E:C56 4.8 0.6 1.0

Magnesium binding site 2 out of 4 in 3epl

Go back to Magnesium Binding Sites List in 3epl
Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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:Mg2

b:0.3
occ:1.00
 O1 B:DMA422 2.6 0.8 1.0
ND2 B:ASN59 3.1 0.2 1.0
O3B B:DMA422 3.1 0.4 1.0
CB B:SER28 3.5 0.8 1.0
CG B:ASN59 3.6 0.1 1.0
OD1 B:ASN59 3.6 0.1 1.0
PA B:DMA422 3.6 0.8 1.0
N B:HIS61 3.8 0.3 1.0
O1A B:DMA422 3.9 0.3 1.0
PB B:DMA422 4.1 0.3 1.0
OG B:SER28 4.1 0.1 1.0
ND1 B:HIS61 4.1 0.3 1.0
N B:LYS60 4.3 0.5 1.0
O3A B:DMA422 4.3 0.6 1.0
O2B B:DMA422 4.3 0.7 1.0
CB B:HIS61 4.4 0.4 1.0
CA B:LYS60 4.4 0.4 1.0
CG B:HIS61 4.4 0.3 1.0
C B:LYS60 4.6 0.1 1.0
CA B:HIS61 4.6 0.2 1.0
O B:HOH460 4.7 86.3 1.0
CA B:SER28 4.7 0.8 1.0
C B:ASN59 4.8 0.9 1.0
CE1 B:HIS61 4.9 0.2 1.0
CB B:ASN59 4.9 0.2 1.0
N B:SER28 5.0 0.8 1.0

Magnesium binding site 3 out of 4 in 3epl

Go back to Magnesium Binding Sites List in 3epl
Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg binding site number 3 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
F:Mg72

b:0.1
occ:1.00
 O F:HOH100 2.6 76.2 1.0
OP2 F:C2 3.7 0.6 1.0
O F:HOH99 4.5 50.6 1.0
P F:C2 5.0 0.1 1.0

Magnesium binding site 4 out of 4 in 3epl

Go back to Magnesium Binding Sites List in 3epl
Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg binding site number 4 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
F:Mg73

b:1.0
occ:1.00
 OP2 F:A26 3.6 99.3 1.0
O6 F:G27 3.7 96.6 1.0
N7 F:G27 4.0 95.8 1.0
N7 F:A26 4.4 95.8 1.0
C6 F:G27 4.6 95.5 1.0
C8 F:A26 4.6 95.9 1.0
C5 F:G27 4.7 95.4 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 Aug 14 13:13:06 2024

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