Magnesium in PDB 5s64: Tubulin-Z28870646-Complex

The structure of Tubulin-Z28870646-Complex, PDB code: 5s64 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)	87.30 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.62, 158.42, 179.97, 90, 90, 90
R / Rfree (%)	21.4 / 26.2

The structure of Tubulin-Z28870646-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z28870646-Complex (pdb code 5s64). 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-Z28870646-Complex, PDB code: 5s64:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z28870646-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z28870646-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:76.4 occ:1.00 O A:HOH606 1.9 70.2 1.0 O A:HOH603 2.0 68.4 1.0 O A:HOH602 2.0 78.8 1.0 O1G A:GTP501 2.0 67.8 1.0 O1B A:GTP501 2.4 71.2 1.0 OE1 A:GLU71 3.1 92.8 1.0 PG A:GTP501 3.3 71.9 1.0 PB A:GTP501 3.6 66.9 1.0 NZ B:LYS254 3.7 87.5 1.0 O3B A:GTP501 3.8 74.4 1.0 O2G A:GTP501 3.8 70.1 1.0 CB A:ASP98 4.1 75.2 1.0 OD1 A:ASP69 4.2 74.7 1.0 NE2 A:GLN11 4.3 84.8 1.0 CD A:GLU71 4.3 99.5 1.0 O3A A:GTP501 4.4 71.5 1.0 CB A:GLN11 4.4 70.5 1.0 OD2 A:ASP69 4.4 74.4 1.0 O3G A:GTP501 4.5 70.7 1.0 CG A:ASP98 4.6 80.6 1.0 OD2 A:ASP98 4.6 86.7 1.0 CG A:ASP69 4.7 75.1 1.0 CB A:GLU71 4.7 85.9 1.0 N A:GLN11 4.7 69.4 1.0 O2B A:GTP501 4.7 70.4 1.0 O1A A:GTP501 4.7 66.0 1.0 CE B:LYS254 4.9 79.2 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z28870646-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z28870646-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:70.0 occ:1.00 O B:HOH605 2.1 73.3 1.0 OE1 B:GLN11 2.1 80.4 1.0 O C:HOH613 2.2 73.8 1.0 O1A B:GDP501 2.2 71.7 1.0 O B:HOH610 2.3 76.8 1.0 O B:HOH603 2.5 73.9 1.0 CD B:GLN11 3.3 75.2 1.0 PA B:GDP501 3.6 62.5 1.0 OD1 B:ASN101 3.9 69.9 1.0 OD2 B:ASP179 3.9 63.4 1.0 O1B B:GDP501 4.0 70.0 1.0 CB B:GLN11 4.0 66.1 1.0 O2A B:GDP501 4.1 65.9 1.0 NE2 B:GLN11 4.1 78.3 1.0 OE1 C:GLU254 4.2 85.1 1.0 CG B:GLN11 4.2 71.3 1.0 ND2 B:ASN101 4.6 83.6 1.0 CG B:ASN101 4.7 70.5 1.0 C5' B:GDP501 4.7 63.0 1.0 O5' B:GDP501 4.7 70.1 1.0 O3A B:GDP501 4.7 70.4 1.0 PB B:GDP501 4.8 64.1 1.0 CD C:GLU254 5.0 80.3 1.0 OE2 C:GLU254 5.0 72.9 1.0 O3B B:GDP501 5.0 61.7 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z28870646-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z28870646-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:67.8 occ:1.00 O C:HOH601 1.8 60.9 1.0 O C:HOH606 2.1 54.8 1.0 O1G C:GTP501 2.3 57.7 1.0 O C:HOH605 2.4 63.4 1.0 O1B C:GTP501 2.8 64.2 1.0 OE2 C:GLU71 3.1 66.3 1.0 OD2 C:ASP98 3.5 63.5 1.0 CG C:GLU71 3.6 66.8 1.0 NZ D:LYS254 3.6 70.3 1.0 PG C:GTP501 3.7 64.0 1.0 CD C:GLU71 3.8 70.7 1.0 PB C:GTP501 4.1 56.6 1.0 O2G C:GTP501 4.1 57.6 1.0 CB C:ASP98 4.3 66.0 1.0 CG C:ASP98 4.3 69.8 1.0 O3B C:GTP501 4.3 67.5 1.0 OE1 C:GLN11 4.4 79.2 1.0 OD2 C:ASP69 4.5 62.1 1.0 O3A C:GTP501 4.6 64.6 1.0 OD1 C:ASP69 4.6 62.8 1.0 CB C:GLN11 4.7 64.4 1.0 CE D:LYS254 4.7 66.6 1.0 O3G C:GTP501 4.8 67.8 1.0 CG C:ASP69 5.0 64.0 1.0 OE1 C:GLU71 5.0 69.2 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z28870646-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z28870646-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:89.9 occ:1.00 O1A D:GDP501 2.4 101.8 1.0 OE1 D:GLN11 2.4 102.7 1.0 CD D:GLN11 3.7 102.2 1.0 PA D:GDP501 3.8 98.6 1.0 OD1 D:ASN101 4.0 103.0 1.0 O2A D:GDP501 4.3 90.1 1.0 C5' D:GDP501 4.3 91.7 1.0 NE2 D:GLN11 4.4 106.7 1.0 CB D:GLN11 4.6 98.4 1.0 O5' D:GDP501 4.6 93.3 1.0 CG D:GLN11 4.7 96.8 1.0 CG D:ASN101 4.9 110.9 1.0 O3B D:GDP501 5.0 99.3 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z28870646-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z28870646-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:125.4 occ:1.00 O1B F:ACP401 2.3 133.5 1.0 O3G F:ACP401 2.8 128.7 1.0 OE2 F:GLU331 2.9 122.9 1.0 PB F:ACP401 3.4 141.0 1.0 O2B F:ACP401 3.4 142.9 1.0 OD1 F:ASN333 3.4 123.8 1.0 NZ F:LYS74 3.5 134.3 1.0 OE1 F:GLU331 3.5 122.0 1.0 CD F:GLU331 3.6 120.7 1.0 PG F:ACP401 4.2 142.3 1.0 C3B F:ACP401 4.4 140.6 1.0 CG F:ASN333 4.5 120.4 1.0 O3A F:ACP401 4.7 135.9 1.0 CE F:LYS74 4.8 132.6 1.0 O1G F:ACP401 4.8 136.4 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