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Magnesium in PDB 3a6p: Crystal Structure of Exportin-5:Rangtp:Pre-Mirna Complex

Protein crystallography data

The structure of Crystal Structure of Exportin-5:Rangtp:Pre-Mirna Complex, PDB code: 3a6p was solved by C.Okada, E.Yamashita, S.J.Lee, S.Shibata, J.Katahira, A.Nakagawa, Y.Yoneda, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.84 / 2.92
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.157, 304.667, 89.230, 90.00, 110.79, 90.00
R / Rfree (%) 24.7 / 31.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Exportin-5:Rangtp:Pre-Mirna Complex (pdb code 3a6p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Exportin-5:Rangtp:Pre-Mirna Complex, PDB code: 3a6p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3a6p

Go back to Magnesium Binding Sites List in 3a6p
Magnesium binding site 1 out of 2 in the Crystal Structure of Exportin-5:Rangtp:Pre-Mirna Complex


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 Exportin-5:Rangtp:Pre-Mirna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1178

b:85.8
occ:1.00
OG1 C:THR24 2.0 94.7 1.0
O1G C:GTP1177 2.2 0.8 1.0
O2B C:GTP1177 2.3 0.4 1.0
OG1 C:THR42 2.4 98.4 1.0
OD1 C:ASP65 3.2 0.3 1.0
CB C:THR42 3.3 99.0 1.0
OD2 C:ASP65 3.3 98.2 1.0
CB C:THR24 3.4 94.1 1.0
PB C:GTP1177 3.4 99.3 1.0
N C:THR24 3.5 92.6 1.0
CG C:ASP65 3.6 95.6 1.0
PG C:GTP1177 3.6 0.7 1.0
O1B C:GTP1177 3.6 96.5 1.0
CG2 C:THR42 3.8 98.3 1.0
CA C:THR24 3.9 93.8 1.0
O3B C:GTP1177 4.0 1.0 1.0
CB C:LYS23 4.0 92.1 1.0
O2G C:GTP1177 4.2 0.9 1.0
CG2 C:THR24 4.3 95.9 1.0
CE C:LYS23 4.3 92.6 1.0
C C:LYS23 4.4 92.2 1.0
O C:THR66 4.5 94.9 1.0
NZ C:LYS23 4.6 93.7 1.0
CA C:THR42 4.6 98.8 1.0
O3G C:GTP1177 4.6 98.9 1.0
CA C:LYS23 4.6 92.1 1.0
CA C:ALA67 4.7 97.3 1.0
O C:ASP65 4.8 91.7 1.0
O3A C:GTP1177 4.8 0.3 1.0
N C:LYS23 4.8 91.4 1.0
C C:THR66 4.9 94.7 1.0
N C:THR42 4.9 0.9 1.0
O1A C:GTP1177 4.9 0.3 1.0

Magnesium binding site 2 out of 2 in 3a6p

Go back to Magnesium Binding Sites List in 3a6p
Magnesium binding site 2 out of 2 in the Crystal Structure of Exportin-5:Rangtp:Pre-Mirna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Exportin-5:Rangtp:Pre-Mirna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1178

b:74.9
occ:1.00
O2B H:GTP1177 2.0 96.3 1.0
OG1 H:THR42 2.1 0.3 1.0
O3G H:GTP1177 2.3 98.5 1.0
OG1 H:THR24 2.6 80.2 1.0
O3B H:GTP1177 2.7 97.9 1.0
PB H:GTP1177 2.8 95.3 1.0
PG H:GTP1177 3.0 98.7 1.0
CB H:THR42 3.2 1.0 1.0
O3A H:GTP1177 3.3 95.2 1.0
N H:THR42 3.6 0.4 1.0
CB H:THR24 3.6 82.3 1.0
O2A H:GTP1177 3.7 95.2 1.0
PA H:GTP1177 3.8 94.7 1.0
O2G H:GTP1177 3.9 0.6 1.0
CA H:THR42 4.0 0.7 1.0
O1A H:GTP1177 4.1 95.3 1.0
O1B H:GTP1177 4.2 92.2 1.0
O H:VAL40 4.2 0.0 1.0
O1G H:GTP1177 4.3 99.8 1.0
N H:THR24 4.3 80.8 1.0
CG2 H:THR42 4.4 0.3 1.0
CE1 H:TYR39 4.5 0.9 1.0
C H:ALA41 4.6 0.1 1.0
CA H:THR24 4.6 82.3 1.0
CG2 H:THR24 4.7 82.1 1.0
CA H:ALA41 4.8 0.4 1.0
OD2 H:ASP65 4.9 95.7 1.0
CD1 H:TYR39 5.0 0.5 1.0

Reference:

C.Okada, E.Yamashita, S.J.Lee, S.Shibata, J.Katahira, A.Nakagawa, Y.Yoneda, T.Tsukihara. A High-Resolution Structure of the Pre-Microrna Nuclear Export Machinery Science V. 326 1275 2009.
ISSN: ISSN 0036-8075
PubMed: 19965479
DOI: 10.1126/SCIENCE.1178705
Page generated: Mon Dec 14 07:52:35 2020

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