Sodium in PDB 7evi: Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 79% Gtp, 21% Gdp, Na+, MG2+

The structure of Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 79% Gtp, 21% Gdp, Na+, MG2+, PDB code: 7evi 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)	26.10 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.335, 92.22, 102.958, 90, 90, 90
R / Rfree (%)	14.9 / 17

The structure of Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 79% Gtp, 21% Gdp, Na+, MG2+ also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 79% Gtp, 21% Gdp, Na+, MG2+ (pdb code 7evi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 79% Gtp, 21% Gdp, Na+, MG2+, PDB code: 7evi:

Sodium binding site 1 out of 1 in the Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 79% Gtp, 21% Gdp, Na+, MG2+


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 79% Gtp, 21% Gdp, Na+, MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:13.4 occ:0.96 O B:HOH701 2.4 15.0 1.0 O B:HOH809 2.5 13.6 1.0 O2G B:GTP501 2.5 14.8 0.8 MG B:MG503 3.3 12.3 1.0 PG B:GTP501 4.0 13.4 0.8 ND2 B:ASN102 4.0 9.5 1.0 O2A B:GTP501 4.1 10.7 0.8 O1G B:GTP501 4.4 12.4 0.8 O3A B:GDP502 4.4 11.2 0.2 O2A B:GDP502 4.5 11.3 0.2 O3A B:GTP501 4.5 9.2 0.8 OE1 B:GLN13 4.5 13.6 1.0 O2B B:GTP501 4.6 11.1 0.8 O1B B:GDP502 4.8 11.9 0.2 O3B B:GTP501 4.8 11.6 0.8 PB B:GTP501 5.0 11.2 0.8 PA B:GTP501 5.0 10.6 0.8 O B:HOH741 5.0 12.0 1.0

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