Sodium in PDB 7evl: Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 64% Gtp/36% Gdp and 2 Na+ in A Small Unit Cell

The structure of Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 64% Gtp/36% Gdp and 2 Na+ in A Small Unit Cell, PDB code: 7evl 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)	20.00 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.166, 79.515, 90.892, 90, 90, 90
R / Rfree (%)	20.3 / 24.4

The binding sites of Sodium atom in the Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 64% Gtp/36% Gdp and 2 Na+ in A Small Unit Cell (pdb code 7evl). 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 64% Gtp/36% Gdp and 2 Na+ in A Small Unit Cell, PDB code: 7evl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 64% Gtp/36% Gdp and 2 Na+ in A Small Unit Cell


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 64% Gtp/36% Gdp and 2 Na+ in A Small Unit Cell within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:53.1 occ:1.00 O B:HOH607 2.4 65.3 1.0 O2B B:GTP501 2.5 40.0 0.6 O2G B:GTP501 2.5 31.2 0.6 O2B B:GDP502 2.5 41.1 0.4 O B:HOH619 2.6 59.3 1.0 O B:HOH602 2.9 52.2 1.0 O3G B:GTP501 3.1 36.8 0.6 PG B:GTP501 3.2 39.0 0.6 PB B:GTP501 3.5 36.1 0.6 NA B:NA504 3.6 47.7 1.0 PB B:GDP502 3.7 37.0 0.4 O3B B:GTP501 3.8 39.2 0.6 CG B:GLU71 3.8 61.6 1.0 O3A B:GTP501 3.9 40.2 0.6 OE1 B:GLU71 3.9 68.7 1.0 O3A B:GDP502 3.9 39.5 0.4 CB B:GLN13 4.1 39.0 1.0 O1B B:GDP502 4.1 39.3 0.4 CD B:GLU71 4.3 68.6 1.0 OE1 B:GLN13 4.3 59.2 1.0 N B:GLN13 4.5 47.4 1.0 OD1 B:ASP69 4.5 46.3 1.0 OD2 B:ASP69 4.6 51.8 1.0 O1G B:GTP501 4.6 26.2 0.6 O1B B:GTP501 4.8 39.9 0.6 CA B:GLN13 4.9 45.3 1.0 O2A B:GDP502 4.9 40.3 0.4 O3B B:GDP502 4.9 41.4 0.4 PA B:GTP501 4.9 34.4 0.6 O2A B:GTP501 4.9 40.5 0.6 OG1 B:THR143 5.0 41.1 1.0 PA B:GDP502 5.0 36.7 0.4 CG B:ASP69 5.0 47.3 1.0

Sodium binding site 2 out of 2 in the Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 64% Gtp/36% Gdp and 2 Na+ in A Small Unit Cell


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 64% Gtp/36% Gdp and 2 Na+ in A Small Unit Cell within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:47.7 occ:1.00 O B:HOH619 2.4 59.3 1.0 O2G B:GTP501 2.5 31.2 0.6 O B:HOH626 2.7 82.6 1.0 NA B:NA503 3.6 53.1 1.0 PG B:GTP501 4.0 39.0 0.6 OD1 B:ASN102 4.0 45.8 1.0 O3A B:GTP501 4.2 40.2 0.6 O3A B:GDP502 4.3 39.5 0.4 O1G B:GTP501 4.4 26.2 0.6 O2A B:GDP502 4.4 40.3 0.4 O2A B:GTP501 4.5 40.5 0.6 OE1 B:GLN13 4.6 59.2 1.0 O3G B:GTP501 4.7 36.8 0.6 CG B:ASN102 4.9 48.1 1.0 O3B B:GTP501 5.0 39.2 0.6 O2B B:GTP501 5.0 40.0 0.6

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