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Sodium in PDB 7evk: Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 78% Gtp, 22% Gdp, Na+

Protein crystallography data

The structure of Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 78% Gtp, 22% Gdp, Na+, PDB code: 7evk 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) 26.20 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.364, 92.731, 103.112, 90, 90, 90
R / Rfree (%) 15.4 / 18.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 78% Gtp, 22% Gdp, Na+ (pdb code 7evk). 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 78% Gtp, 22% Gdp, Na+, PDB code: 7evk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7evk

Go back to Sodium Binding Sites List in 7evk
Sodium binding site 1 out of 2 in the Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 78% Gtp, 22% Gdp, 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 78% Gtp, 22% Gdp, Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:19.6
occ:1.00
O B:HOH678 2.2 19.1 1.0
O B:HOH668 2.3 21.8 1.0
O B:HOH689 2.3 20.3 1.0
O2B B:GTP501 2.3 15.3 0.8
O2G B:GTP501 2.4 20.1 0.8
O1B B:GDP502 2.4 16.1 0.2
NA B:NA504 3.4 18.1 1.0
PG B:GTP501 3.4 22.0 0.8
PB B:GTP501 3.5 16.7 0.8
PB B:GDP502 3.6 16.9 0.2
O3G B:GTP501 3.7 18.1 0.8
O3B B:GTP501 3.8 19.1 0.8
O3B B:GDP502 3.8 19.0 0.2
CB B:GLN13 3.9 16.7 1.0
O3A B:GDP502 3.9 16.7 0.2
O3A B:GTP501 4.0 16.6 0.8
CG B:GLU71 4.0 26.3 1.0
N B:GLN13 4.2 17.2 1.0
OE1 B:GLU71 4.2 23.6 1.0
OE1 B:GLN13 4.3 18.3 1.0
OD1 B:ASP69 4.4 20.1 1.0
O2A B:GTP501 4.4 17.8 0.8
OD2 B:ASP69 4.5 22.0 1.0
CD B:GLU71 4.5 24.7 1.0
CA B:GLN13 4.6 17.5 1.0
PA B:GTP501 4.7 16.8 0.8
O1G B:GTP501 4.7 19.5 0.8
O1B B:GTP501 4.8 17.6 0.8
O2A B:GDP502 4.8 17.4 0.2
O2B B:GDP502 4.9 17.4 0.2
PA B:GDP502 4.9 17.1 0.2
CG B:ASP69 4.9 22.3 1.0
O B:HOH798 5.0 20.6 1.0

Sodium binding site 2 out of 2 in 7evk

Go back to Sodium Binding Sites List in 7evk
Sodium binding site 2 out of 2 in the Odinarchaeota Tubulin (Odintubulin) H393D Mutant, in A Protofilament Arrangement, Bound to 78% Gtp, 22% Gdp, 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 78% Gtp, 22% Gdp, Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na504

b:18.1
occ:1.00
O B:HOH668 2.5 21.8 1.0
O2G B:GTP501 2.6 20.1 0.8
O B:HOH798 2.6 20.6 1.0
NA B:NA503 3.4 19.6 1.0
OD1 B:ASN102 4.0 17.4 1.0
PG B:GTP501 4.0 22.0 0.8
O2A B:GTP501 4.1 17.8 0.8
O3A B:GDP502 4.4 16.7 0.2
O1G B:GTP501 4.4 19.5 0.8
O3A B:GTP501 4.4 16.6 0.8
OE1 B:GLN13 4.5 18.3 1.0
O2A B:GDP502 4.6 17.4 0.2
O2B B:GTP501 4.8 15.3 0.8
O1B B:GDP502 4.8 16.1 0.2
O3B B:GTP501 4.9 19.1 0.8
CG B:ASN102 5.0 19.5 1.0
PA B:GTP501 5.0 16.8 0.8
O3G B:GTP501 5.0 18.1 0.8

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: Tue Oct 8 16:45:24 2024

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