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Sodium in PDB 7eve: Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 100% Gdp and 2 Na+

Protein crystallography data

The structure of Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 100% Gdp and 2 Na+, PDB code: 7eve was solved by R.C.Robinson, C.Akil, L.T.Tran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.50 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.13, 88.421, 95.47, 90, 90, 90
R / Rfree (%) 21.1 / 25.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 100% Gdp and 2 Na+ (pdb code 7eve). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 100% Gdp and 2 Na+, PDB code: 7eve:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7eve

Go back to Sodium Binding Sites List in 7eve
Sodium binding site 1 out of 2 in the Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 100% Gdp and 2 Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 100% Gdp and 2 Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:20.2
occ:1.00
O B:HOH626 2.3 31.6 1.0
O B:HOH647 2.4 23.9 1.0
O B:HOH690 2.8 24.4 1.0
NA B:NA503 3.1 34.8 1.0
OD1 B:ASN102 4.1 26.2 1.0
O1A B:GDP501 4.2 25.9 1.0
OE1 B:GLN13 4.2 17.6 1.0
O3A B:GDP501 4.4 18.4 1.0
PA B:GDP501 5.0 28.7 1.0

Sodium binding site 2 out of 2 in 7eve

Go back to Sodium Binding Sites List in 7eve
Sodium binding site 2 out of 2 in the Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 100% Gdp and 2 Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 100% Gdp and 2 Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:34.8
occ:1.00
O B:HOH647 2.0 23.9 1.0
O B:HOH673 2.3 32.1 1.0
O B:HOH626 2.3 31.6 1.0
O1B B:GDP501 2.6 12.6 1.0
O B:HOH628 2.7 22.2 1.0
NA B:NA502 3.1 20.2 1.0
PB B:GDP501 3.5 18.1 1.0
O3A B:GDP501 3.6 18.4 1.0
O3B B:GDP501 3.8 22.8 1.0
CB B:GLN13 4.1 16.7 1.0
OE1 B:GLN13 4.1 17.6 1.0
O B:HOH622 4.1 16.7 1.0
O1A B:GDP501 4.4 25.9 1.0
CG B:GLU71 4.5 30.9 1.0
N B:GLN13 4.5 18.5 1.0
PA B:GDP501 4.6 28.7 1.0
O B:HOH630 4.6 20.7 1.0
OE1 B:GLU71 4.6 32.4 1.0
O B:HOH690 4.9 24.4 1.0
OD1 B:ASP69 4.9 20.3 1.0
O2B B:GDP501 4.9 19.3 1.0
CA B:GLN13 4.9 14.7 1.0
OD2 B:ASP69 5.0 22.8 1.0
CD B:GLU71 5.0 33.2 1.0

Reference:

C.Akil, S.Ali, L.T.Tran, J.Gaillard, W.Li, K.Hayashida, M.Hirose, T.Kato, A.Oshima, K.Fujishima, L.Blanchoin, A.Narita, R.C.Robinson. Structure and Dynamics of Odinarchaeota Tubulin and the Implications For Eukaryotic Microtubule Evolution. Sci Adv V. 8 M2225 2022.
ISSN: ESSN 2375-2548
PubMed: 35333570
DOI: 10.1126/SCIADV.ABM2225
Page generated: Mon Aug 18 09:45:56 2025

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