Magnesium in PDB 5s65: Tubulin-Z1354416068-Complex

The structure of Tubulin-Z1354416068-Complex, PDB code: 5s65 was solved by T.Muehlethaler, D.Gioia, A.E.Prota, M.E.Sharpe, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.70 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.19, 158.92, 179.34, 90, 90, 90
R / Rfree (%)	20.5 / 23.4

The structure of Tubulin-Z1354416068-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z1354416068-Complex (pdb code 5s65). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Tubulin-Z1354416068-Complex, PDB code: 5s65:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z1354416068-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z1354416068-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:40.3 occ:1.00 O1G A:GTP501 2.1 38.7 1.0 O A:HOH619 2.1 47.5 1.0 O A:HOH622 2.1 43.6 1.0 O A:HOH638 2.2 41.9 1.0 O1B A:GTP501 2.2 38.0 1.0 O A:HOH605 2.2 41.4 1.0 PG A:GTP501 3.2 47.1 1.0 PB A:GTP501 3.3 42.0 1.0 O2G A:GTP501 3.6 42.1 1.0 O3B A:GTP501 3.6 45.1 1.0 OE1 A:GLU71 3.7 58.3 1.0 NZ B:LYS254 3.8 56.1 1.0 O3A A:GTP501 3.9 44.5 1.0 OD1 A:ASP69 4.0 48.7 1.0 OD2 A:ASP69 4.2 52.4 1.0 CB A:GLN11 4.2 44.7 1.0 CB A:ASP98 4.2 50.0 1.0 N A:GLN11 4.4 41.8 1.0 OD2 A:ASP98 4.4 60.3 1.0 O3G A:GTP501 4.5 43.8 1.0 CG A:ASP69 4.5 51.8 1.0 NE2 A:GLN11 4.6 51.1 1.0 O2B A:GTP501 4.6 42.0 1.0 CG A:ASP98 4.7 50.9 1.0 O1A A:GTP501 4.7 40.8 1.0 O B:HOH601 4.7 57.6 1.0 CD A:GLU71 4.8 63.6 1.0 CE B:LYS254 4.9 54.0 1.0 CA A:GLN11 4.9 43.1 1.0 PA A:GTP501 4.9 46.8 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z1354416068-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z1354416068-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:34.7 occ:1.00 O B:HOH635 2.1 42.3 1.0 OE1 B:GLN11 2.2 46.4 1.0 O C:HOH672 2.2 44.2 1.0 O1A B:GDP501 2.3 37.0 1.0 O B:HOH618 2.3 46.5 1.0 O B:HOH642 2.5 38.1 1.0 CD B:GLN11 3.4 45.5 1.0 PA B:GDP501 3.6 38.2 1.0 O3A B:GDP501 3.9 38.7 1.0 OD2 B:ASP179 4.0 44.4 1.0 CB B:GLN11 4.1 39.8 1.0 CG B:GLN11 4.2 42.9 1.0 O C:HOH643 4.4 50.1 1.0 NE2 B:GLN11 4.4 49.9 1.0 O1B B:GDP501 4.4 37.6 1.0 C5' B:GDP501 4.5 42.9 1.0 O5' B:GDP501 4.5 41.9 1.0 OD1 B:ASN101 4.5 42.3 1.0 OE1 C:GLU254 4.5 51.5 1.0 O2A B:GDP501 4.6 39.9 1.0 PB B:GDP501 4.8 38.2 1.0 ND2 B:ASN101 5.0 40.9 1.0 CG B:ASP179 5.0 45.6 1.0 C8 B:GDP501 5.0 43.9 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z1354416068-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z1354416068-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:38.0 occ:1.00 O C:HOH628 2.0 39.1 1.0 O C:HOH621 2.0 37.0 1.0 O1G C:GTP501 2.1 34.7 1.0 O C:HOH675 2.1 39.9 1.0 O1B C:GTP501 2.1 36.7 1.0 O C:HOH642 2.2 39.3 1.0 PG C:GTP501 3.1 36.8 1.0 PB C:GTP501 3.2 35.0 1.0 O2G C:GTP501 3.5 36.6 1.0 O3B C:GTP501 3.5 39.8 1.0 O3A C:GTP501 3.8 37.2 1.0 OD1 C:ASP69 3.9 38.9 1.0 OD2 C:ASP69 4.1 33.4 1.0 NZ D:LYS254 4.1 40.1 1.0 CG C:GLU71 4.2 44.7 1.0 OE2 C:GLU71 4.2 47.2 1.0 CB C:GLN11 4.3 37.9 1.0 OD2 C:ASP98 4.3 45.0 1.0 CB C:ASP98 4.3 40.0 1.0 N C:GLN11 4.3 32.2 1.0 CG C:ASP69 4.4 37.1 1.0 O3G C:GTP501 4.4 38.1 1.0 O2B C:GTP501 4.5 37.5 1.0 CG C:ASP98 4.7 42.0 1.0 O C:HOH717 4.7 62.5 1.0 CD C:GLU71 4.7 47.0 1.0 O1A C:GTP501 4.7 36.2 1.0 PA C:GTP501 4.8 35.0 1.0 OG1 C:THR145 4.9 38.6 1.0 OE1 C:GLN11 4.9 49.0 1.0 CA C:GLN11 4.9 35.1 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z1354416068-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z1354416068-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:55.6 occ:1.00 O D:HOH606 1.9 60.4 1.0 OE1 D:GLN11 2.0 62.8 1.0 O1A D:GDP501 2.2 67.6 1.0 CD D:GLN11 3.3 65.3 1.0 PA D:GDP501 3.6 61.9 1.0 CB D:GLN11 3.9 61.4 1.0 CG D:GLN11 4.1 61.9 1.0 NE2 D:GLN11 4.2 64.1 1.0 O1B D:GDP501 4.2 63.0 1.0 O3A D:GDP501 4.3 59.9 1.0 O2A D:GDP501 4.4 63.1 1.0 O D:HOH629 4.6 68.1 1.0 C5' D:GDP501 4.6 62.1 1.0 O5' D:GDP501 4.6 61.7 1.0 OD1 D:ASN101 4.7 66.8 1.0 PB D:GDP501 4.8 59.2 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z1354416068-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z1354416068-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:79.3 occ:1.00 O3G F:ACP401 2.2 89.0 1.0 OE2 F:GLU331 2.3 86.8 1.0 O1B F:ACP401 2.5 96.7 1.0 OD1 F:ASN333 2.7 79.2 1.0 CD F:GLU331 3.1 84.5 1.0 OE1 F:GLU331 3.2 90.5 1.0 PB F:ACP401 3.8 100.2 1.0 CG F:ASN333 3.8 73.7 1.0 PG F:ACP401 3.8 106.5 1.0 NZ F:LYS74 3.9 98.0 1.0 O2B F:ACP401 4.1 105.2 1.0 ND2 F:ASN333 4.4 70.2 1.0 C3B F:ACP401 4.5 99.5 1.0 CG F:GLU331 4.5 69.9 1.0 O1G F:ACP401 4.6 97.7 1.0 O2G F:ACP401 4.7 85.6 1.0 CB F:ASN333 5.0 67.8 1.0

T.Muhlethaler, D.Gioia, A.E.Prota, M.E.Sharpe, A.Cavalli, M.O.Steinmetz. Comprehensive Analysis of Binding Sites in Tubulin. Angew.Chem.Int.Ed.Engl. V. 60 13331 2021.
ISSN: ESSN 1521-3773
PubMed: 33951246
DOI: 10.1002/ANIE.202100273