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Nickel 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:

Magnesium (Mg) 1 atom

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total only one binding site of Nickel was determined in the Gppnhp-Bound YPT51 at 1.48 A Resolution, PDB code: 1ek0:

Nickel binding site 1 out of 1 in 1ek0

Go back to Nickel Binding Sites List in 1ek0
Nickel 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 Nickel with other atoms in the Ni 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:Ni602

b:19.9
occ:1.00
N7 A:GDP502 2.0 17.6 1.0
NE2 A:HIS54 2.1 19.3 1.0
O A:HOH1016 2.1 23.8 1.0
O A:HOH1156 2.1 22.8 1.0
O A:HOH1155 2.1 27.6 1.0
O A:HOH1154 2.1 24.2 1.0
C8 A:GDP502 2.9 17.8 1.0
CE1 A:HIS54 2.9 21.5 1.0
CD2 A:HIS54 3.2 15.0 1.0
C5 A:GDP502 3.2 14.9 1.0
O6 A:GDP502 3.8 18.1 1.0
C6 A:GDP502 3.9 16.9 1.0
OE2 A:GLU53 3.9 27.3 1.0
OE1 A:GLU53 4.1 21.1 1.0
ND1 A:HIS54 4.1 19.9 1.0
N9 A:GDP502 4.1 19.3 1.0
CG A:HIS54 4.2 17.5 1.0
C4 A:GDP502 4.3 16.8 1.0
O1A A:GDP502 4.3 32.2 1.0
CD A:GLU53 4.4 21.1 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: Wed Dec 16 01:11:47 2020

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