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Magnesium in PDB 3oij: Crystal Structure of Saccharomyces Cerevisiae NEP1/EMG1 Bound to S- Adenosylhomocysteine and 2 Molecules of Cognate Rna

Protein crystallography data

The structure of Crystal Structure of Saccharomyces Cerevisiae NEP1/EMG1 Bound to S- Adenosylhomocysteine and 2 Molecules of Cognate Rna, PDB code: 3oij was solved by S.R.Thomas, N.Laronde-Leblanc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.89 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.377, 91.860, 96.931, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 26

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Saccharomyces Cerevisiae NEP1/EMG1 Bound to S- Adenosylhomocysteine and 2 Molecules of Cognate Rna (pdb code 3oij). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Saccharomyces Cerevisiae NEP1/EMG1 Bound to S- Adenosylhomocysteine and 2 Molecules of Cognate Rna, PDB code: 3oij:

Magnesium binding site 1 out of 1 in 3oij

Go back to Magnesium Binding Sites List in 3oij
Magnesium binding site 1 out of 1 in the Crystal Structure of Saccharomyces Cerevisiae NEP1/EMG1 Bound to S- Adenosylhomocysteine and 2 Molecules of Cognate Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Saccharomyces Cerevisiae NEP1/EMG1 Bound to S- Adenosylhomocysteine and 2 Molecules of Cognate Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg15

b:86.2
occ:1.00
O6 D:G3 3.0 88.5 1.0
OP1 D:A9 4.0 62.1 1.0
C6 D:G3 4.1 82.2 1.0
N4 D:C4 4.2 78.4 1.0
OP2 D:A9 4.3 69.5 1.0
N7 D:G3 4.3 80.9 1.0
C5 D:G3 4.6 81.4 1.0
P D:A9 4.6 67.3 1.0
O6 D:G11 4.6 76.8 1.0
N4 D:C12 4.8 86.4 1.0
O6 D:G2 4.9 84.8 1.0

Reference:

S.R.Thomas, C.A.Keller, A.Szyk, J.R.Cannon, N.A.Laronde-Leblanc. Structural Insight Into the Functional Mechanism of NEP1/EMG1 N1-Specific Pseudouridine Methyltransferase in Ribosome Biogenesis. Nucleic Acids Res. V. 39 2445 2011.
ISSN: ISSN 0305-1048
PubMed: 21087996
DOI: 10.1093/NAR/GKQ1131
Page generated: Mon Dec 14 08:36:06 2020

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