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Magnesium in PDB 1a2k: Gdpran-NTF2 Complex

Protein crystallography data

The structure of Gdpran-NTF2 Complex, PDB code: 1a2k was solved by M.Stewart, H.M.Kent, A.J.Mccoy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 155.150, 120.540, 108.920, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 27.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Gdpran-NTF2 Complex (pdb code 1a2k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Gdpran-NTF2 Complex, PDB code: 1a2k:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1a2k

Go back to Magnesium Binding Sites List in 1a2k
Magnesium binding site 1 out of 3 in the Gdpran-NTF2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gdpran-NTF2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg221

b:22.6
occ:1.00
O C:HOH248 2.0 19.9 1.0
O1B C:GDP220 2.0 26.6 1.0
O C:HOH247 2.1 19.0 1.0
O C:HOH246 2.1 29.8 1.0
O C:HOH249 2.2 13.7 1.0
OG1 C:THR24 2.6 22.6 1.0
PB C:GDP220 3.1 29.6 1.0
O3A C:GDP220 3.3 33.3 1.0
O2B C:GDP220 3.4 36.4 1.0
CB C:THR24 3.4 24.2 1.0
N C:THR24 4.1 27.4 1.0
OG1 C:THR66 4.3 17.6 1.0
O C:THR66 4.3 30.2 1.0
CG2 C:THR24 4.4 17.9 1.0
O3B C:GDP220 4.4 30.0 1.0
CA C:THR24 4.4 28.9 1.0
OE2 C:GLU70 4.4 25.0 1.0
OD1 C:ASP65 4.5 17.2 1.0
OD2 C:ASP65 4.5 18.3 1.0
PA C:GDP220 4.6 33.4 1.0
O1A C:GDP220 4.9 35.2 1.0
O2A C:GDP220 4.9 40.0 1.0
CG C:ASP65 4.9 13.2 1.0
N C:GLY68 5.0 28.0 1.0
CA C:GLY68 5.0 25.2 1.0

Magnesium binding site 2 out of 3 in 1a2k

Go back to Magnesium Binding Sites List in 1a2k
Magnesium binding site 2 out of 3 in the Gdpran-NTF2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gdpran-NTF2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg221

b:26.5
occ:1.00
O D:HOH349 2.0 16.5 1.0
O D:HOH347 2.1 22.4 1.0
O D:HOH348 2.1 18.7 1.0
O1B D:GDP220 2.1 30.9 1.0
O D:HOH346 2.2 29.0 1.0
OG1 D:THR24 2.5 27.5 1.0
PB D:GDP220 3.2 32.3 1.0
O3A D:GDP220 3.4 33.4 1.0
CB D:THR24 3.4 31.2 1.0
O2B D:GDP220 3.5 35.9 1.0
N D:THR24 4.0 25.5 1.0
O D:THR66 4.1 21.4 1.0
CA D:THR24 4.3 27.2 1.0
CG2 D:THR24 4.4 21.4 1.0
OD1 A:ASP94 4.4 34.6 1.0
O3B D:GDP220 4.4 32.6 1.0
OD2 D:ASP65 4.5 29.6 1.0
OD1 D:ASP65 4.5 27.6 1.0
O D:HOH355 4.5 27.0 1.0
OG1 D:THR66 4.5 19.6 1.0
OE2 D:GLU70 4.6 17.1 1.0
PA D:GDP220 4.6 35.1 1.0
CB D:LYS23 4.9 15.2 1.0
CG D:ASP65 4.9 28.0 1.0
O1A D:GDP220 4.9 37.5 1.0
O2A D:GDP220 5.0 42.3 1.0
NZ D:LYS23 5.0 21.7 1.0

Magnesium binding site 3 out of 3 in 1a2k

Go back to Magnesium Binding Sites List in 1a2k
Magnesium binding site 3 out of 3 in the Gdpran-NTF2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Gdpran-NTF2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg221

b:25.3
occ:1.00
O E:HOH447 2.0 27.1 1.0
O1B E:GDP220 2.1 31.7 1.0
O E:HOH448 2.1 28.1 1.0
O E:HOH449 2.2 35.1 1.0
O E:HOH446 2.3 22.3 1.0
OG1 E:THR24 2.4 24.5 1.0
PB E:GDP220 3.1 33.0 1.0
O3A E:GDP220 3.2 38.4 1.0
O2B E:GDP220 3.2 33.5 1.0
CB E:THR24 3.5 28.3 1.0
O E:HOH459 4.1 39.8 1.0
N E:THR24 4.1 26.9 1.0
CA E:THR24 4.3 28.9 1.0
O3B E:GDP220 4.3 28.1 1.0
OE2 E:GLU70 4.3 20.6 1.0
O E:THR66 4.4 28.5 1.0
OG1 E:THR66 4.4 26.6 1.0
OD2 E:ASP65 4.4 38.6 1.0
CG2 E:THR24 4.5 27.1 1.0
PA E:GDP220 4.6 32.5 1.0
OD1 E:ASP65 4.6 28.9 1.0
O2A E:GDP220 4.7 38.3 1.0
N E:GLY68 4.9 34.9 1.0
NZ E:LYS23 4.9 15.9 1.0
CB E:LYS23 4.9 25.4 1.0
CG E:ASP65 5.0 31.8 1.0

Reference:

M.Stewart, H.M.Kent, A.J.Mccoy. Structural Basis For Molecular Recognition Between Nuclear Transport Factor 2 (NTF2) and the Gdp-Bound Form of the Ras-Family Gtpase Ran. J.Mol.Biol. V. 277 635 1998.
ISSN: ISSN 0022-2836
PubMed: 9533885
DOI: 10.1006/JMBI.1997.1602
Page generated: Mon Dec 14 03:26:35 2020

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