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Magnesium in PDB 1ek0: Gppnhp-Bound YPT51 at 1.48 A Resolution

Protein crystallography data

The structure of Gppnhp-Bound YPT51 at 1.48 A Resolution, PDB code: 1ek0 was solved by H.Esters, A.J.Scheidig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.00 / 1.48
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 62.326, 62.326, 91.221, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 22.8

Other elements in 1ek0:

The structure of Gppnhp-Bound YPT51 at 1.48 A Resolution also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Gppnhp-Bound YPT51 at 1.48 A Resolution (pdb code 1ek0). 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 Gppnhp-Bound YPT51 at 1.48 A Resolution, PDB code: 1ek0:

Magnesium binding site 1 out of 1 in 1ek0

Go back to Magnesium Binding Sites List in 1ek0
Magnesium binding site 1 out of 1 in the Gppnhp-Bound YPT51 at 1.48 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gppnhp-Bound YPT51 at 1.48 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:13.0
occ:1.00
O2B A:GNP501 2.0 15.1 1.0
O1G A:GNP501 2.0 17.7 1.0
OG A:SER21 2.1 13.0 1.0
O A:HOH1002 2.1 15.0 1.0
O A:HOH1001 2.2 15.6 1.0
OG1 A:THR39 2.2 14.9 1.0
CB A:SER21 3.1 13.3 1.0
PG A:GNP501 3.2 15.8 1.0
PB A:GNP501 3.2 16.5 1.0
CB A:THR39 3.3 15.8 1.0
N3B A:GNP501 3.5 13.9 1.0
N A:THR39 3.7 16.8 1.0
N A:SER21 3.8 14.2 1.0
O2G A:GNP501 3.9 17.7 1.0
OD2 A:ASP62 4.0 15.9 1.0
CA A:SER21 4.0 14.3 1.0
CA A:THR39 4.1 16.2 1.0
O2A A:GNP501 4.1 19.1 1.0
O A:HOH1008 4.2 19.5 1.0
OD1 A:ASP62 4.2 14.7 1.0
O3A A:GNP501 4.3 49.0 1.0
O1B A:GNP501 4.3 15.4 1.0
CG2 A:THR39 4.4 17.6 1.0
O3G A:GNP501 4.5 19.3 1.0
CG A:ASP62 4.5 15.6 1.0
O A:THR63 4.5 15.2 1.0
PA A:GNP501 4.6 17.9 1.0
O1A A:GNP501 4.7 14.9 1.0
C A:PRO38 4.7 24.0 1.0
O A:GLU37 4.7 22.1 1.0
CB A:LYS20 4.9 11.7 1.0
C A:LYS20 4.9 16.2 1.0
CA A:PRO38 5.0 21.9 1.0

Reference:

H.Esters, K.Alexandrov, A.T.Constantinescu, R.S.Goody, A.J.Scheidig. High-Resolution Crystal Structure of S. Cerevisiae YPT51(DELTAC15)-Gppnhp, A Small Gtp-Binding Protein Involved in Regulation of Endocytosis. J.Mol.Biol. V. 298 111 2000.
ISSN: ISSN 0022-2836
PubMed: 10756108
DOI: 10.1006/JMBI.2000.3645
Page generated: Mon Dec 14 05:52:09 2020

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