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Magnesium in PDB 3pey: S. Cerevisiae DBP5 Bound to Rna and Adp BEF3

Enzymatic activity of S. Cerevisiae DBP5 Bound to Rna and Adp BEF3

All present enzymatic activity of S. Cerevisiae DBP5 Bound to Rna and Adp BEF3:
3.6.4.13;

Protein crystallography data

The structure of S. Cerevisiae DBP5 Bound to Rna and Adp BEF3, PDB code: 3pey was solved by B.Montpetit, N.D.Thomsen, K.J.Helmke, M.A.Seeliger, J.M.Berger, K.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.47 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.136, 92.206, 104.524, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 18

Other elements in 3pey:

The structure of S. Cerevisiae DBP5 Bound to Rna and Adp BEF3 also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S. Cerevisiae DBP5 Bound to Rna and Adp BEF3 (pdb code 3pey). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the S. Cerevisiae DBP5 Bound to Rna and Adp BEF3, PDB code: 3pey:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3pey

Go back to Magnesium Binding Sites List in 3pey
Magnesium binding site 1 out of 4 in the S. Cerevisiae DBP5 Bound to Rna and Adp BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S. Cerevisiae DBP5 Bound to Rna and Adp BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:7.1
occ:1.00
F3 A:BEF1002 2.0 7.0 1.0
O2B A:ADP1000 2.0 7.0 1.0
O A:HOH1095 2.1 7.2 1.0
O A:HOH1096 2.1 6.6 1.0
O A:HOH1481 2.1 6.5 1.0
O A:HOH1010 2.2 7.4 1.0
BE A:BEF1002 3.3 6.9 1.0
PB A:ADP1000 3.3 7.0 1.0
O1B A:ADP1000 3.5 6.9 1.0
OD2 A:ASP239 3.9 6.2 1.0
OG1 A:THR145 3.9 6.4 1.0
OE2 A:GLU240 3.9 7.8 1.0
OD1 A:ASP239 4.0 6.8 1.0
F2 A:BEF1002 4.0 6.9 1.0
CA A:GLY393 4.1 5.9 1.0
O3A A:ADP1000 4.3 6.9 1.0
O2A A:ADP1000 4.3 7.3 1.0
F1 A:BEF1002 4.3 7.1 1.0
CG A:ASP239 4.4 6.7 1.0
O3B A:ADP1000 4.4 6.9 1.0
O A:GLY393 4.4 6.8 1.0
O A:HOH1012 4.4 7.1 1.0
PA A:ADP1000 4.5 7.0 1.0
CE A:LYS144 4.5 6.0 1.0
O1A A:ADP1000 4.6 7.0 1.0
CB A:LYS144 4.7 6.4 1.0
C A:GLY393 4.8 6.1 1.0
N A:THR145 4.9 5.8 1.0
NH2 A:ARG429 4.9 6.7 1.0
O A:HOH1011 4.9 7.7 1.0
CD A:GLU240 4.9 8.8 1.0

Magnesium binding site 2 out of 4 in 3pey

Go back to Magnesium Binding Sites List in 3pey
Magnesium binding site 2 out of 4 in the S. Cerevisiae DBP5 Bound to Rna and Adp BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S. Cerevisiae DBP5 Bound to Rna and Adp BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:11.8
occ:0.51
MG A:MG1003 0.0 11.8 0.5
MG A:MG1003 1.6 14.6 0.5
O A:HOH1125 1.8 14.2 0.8
O A:HOH1117 1.9 21.8 1.0
O A:HOH1147 1.9 15.3 0.6
O A:HOH1228 2.0 25.1 0.8
O A:HOH1234 2.1 15.5 0.6
OD1 A:ASP264 2.4 17.1 1.0
O A:HOH1148 2.6 15.7 0.4
CG A:ASP264 3.3 14.4 1.0
OD2 A:ASP264 3.4 12.9 1.0
O A:HOH1320 3.4 21.3 0.6
O A:HOH1356 3.6 26.2 0.8
O A:HOH1077 4.0 15.7 1.0
O A:HOH1140 4.1 20.3 1.0
O A:HOH1249 4.4 26.4 1.0
O A:HOH1185 4.4 18.9 1.0
CB A:ASP264 4.7 12.2 1.0
O A:HOH1063 4.7 14.6 1.0

Magnesium binding site 3 out of 4 in 3pey

Go back to Magnesium Binding Sites List in 3pey
Magnesium binding site 3 out of 4 in the S. Cerevisiae DBP5 Bound to Rna and Adp BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of S. Cerevisiae DBP5 Bound to Rna and Adp BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:14.6
occ:0.49
MG A:MG1003 0.0 14.6 0.5
O A:HOH1147 1.4 15.3 0.6
MG A:MG1003 1.6 11.8 0.5
OD1 A:ASP264 2.0 17.1 1.0
O A:HOH1117 2.0 21.8 1.0
O A:HOH1148 2.1 15.7 0.4
O A:HOH1356 2.2 26.2 0.8
O A:HOH1320 2.3 21.3 0.6
O A:HOH1125 2.8 14.2 0.8
CG A:ASP264 3.0 14.4 1.0
O A:HOH1234 3.3 15.5 0.6
O A:HOH1228 3.4 25.1 0.8
OD2 A:ASP264 3.5 12.9 1.0
O A:HOH1185 3.5 18.9 1.0
O A:HOH1358 4.1 37.7 1.0
CB A:ASP264 4.2 12.2 1.0
O A:HOH1063 4.4 14.6 1.0
O A:HOH1077 4.5 15.7 1.0
NZ A:LYS234 4.9 16.8 0.6
O A:HOH1140 5.0 20.3 1.0

Magnesium binding site 4 out of 4 in 3pey

Go back to Magnesium Binding Sites List in 3pey
Magnesium binding site 4 out of 4 in the S. Cerevisiae DBP5 Bound to Rna and Adp BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of S. Cerevisiae DBP5 Bound to Rna and Adp BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:28.7
occ:1.00
O A:HOH1403 1.9 27.2 1.0
O A:HOH1200 2.0 28.3 1.0
O A:HOH1215 2.0 22.8 1.0
O A:HOH1349 2.0 37.7 1.0
O A:HOH1483 2.1 30.4 1.0
O A:HOH1477 2.3 45.0 1.0
OD2 A:ASP95 4.0 21.4 1.0
O A:HOH1299 4.2 31.9 1.0
CB A:ASP95 4.3 14.3 1.0
CG A:ASP95 4.5 18.0 1.0
O A:HOH1390 4.5 38.8 1.0
OE2 A:GLU96 4.5 45.8 1.0

Reference:

B.Montpetit, N.D.Thomsen, K.J.Helmke, M.A.Seeliger, J.M.Berger, K.Weis. A Conserved Mechanism of Dead-Box Atpase Activation By Nucleoporins and Insp(6) in Mrna Export. Nature V. 472 238 2011.
ISSN: ISSN 0028-0836
PubMed: 21441902
DOI: 10.1038/NATURE09862
Page generated: Mon Dec 14 08:39:02 2020

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