Magnesium in PDB 5s5n: Tubulin-Z165170770-Complex

The structure of Tubulin-Z165170770-Complex, PDB code: 5s5n 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)	63.62 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.61, 159.43, 179.48, 90, 90, 90
R / Rfree (%)	22.2 / 27.4

The structure of Tubulin-Z165170770-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z165170770-Complex (pdb code 5s5n). 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-Z165170770-Complex, PDB code: 5s5n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z165170770-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z165170770-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:81.3 occ:1.00 O A:HOH601 1.9 69.9 1.0 O A:HOH607 2.4 69.8 1.0 O1B A:GTP501 2.4 76.9 1.0 O1G A:GTP501 2.5 67.0 1.0 O A:HOH602 3.2 78.9 1.0 NE2 A:GLN11 3.3 80.8 1.0 NZ B:LYS254 3.4 82.2 1.0 PB A:GTP501 3.5 79.5 1.0 O3A A:GTP501 3.6 80.0 1.0 CB A:GLN11 3.8 74.5 1.0 PG A:GTP501 3.8 75.6 1.0 OE1 A:GLU71 4.0 91.8 1.0 O1A A:GTP501 4.0 72.2 1.0 O3B A:GTP501 4.1 86.8 1.0 PA A:GTP501 4.3 75.8 1.0 CD A:GLN11 4.4 80.8 1.0 CE B:LYS254 4.5 83.3 1.0 OD2 A:ASP98 4.6 82.3 1.0 CG A:GLN11 4.6 77.4 1.0 O2G A:GTP501 4.7 79.4 1.0 N A:GLN11 4.7 71.2 1.0 O2B A:GTP501 4.8 78.5 1.0 O3G A:GTP501 4.8 79.8 1.0 CA A:GLN11 4.8 72.9 1.0 O2A A:GTP501 4.8 76.7 1.0 OD2 A:ASP69 5.0 74.7 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z165170770-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z165170770-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:75.6 occ:1.00 O B:HOH601 2.0 66.7 1.0 OE1 B:GLN11 2.1 77.3 1.0 O B:HOH607 2.2 67.3 1.0 CD B:GLN11 2.3 75.5 1.0 O1A B:GDP501 2.4 78.9 1.0 O B:HOH602 2.7 72.5 1.0 NE2 B:GLN11 2.9 78.7 1.0 O2A B:GDP501 2.9 68.2 1.0 O C:HOH606 3.0 70.8 1.0 CG B:GLN11 3.2 79.4 1.0 CB B:GLN11 3.2 72.9 1.0 PA B:GDP501 3.2 63.0 1.0 OD2 B:ASP179 3.9 75.4 1.0 O3B B:GDP501 3.9 72.8 1.0 C8 B:GDP501 4.2 72.8 1.0 O5' B:GDP501 4.3 72.3 1.0 O3A B:GDP501 4.4 71.9 1.0 C5' B:GDP501 4.4 73.3 1.0 CA B:GLN11 4.6 68.9 1.0 N7 B:GDP501 4.6 75.3 1.0 PB B:GDP501 4.7 72.0 1.0 N B:CYS12 4.7 72.4 1.0 OD1 B:ASN101 4.8 78.8 1.0 O1B B:GDP501 5.0 69.9 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z165170770-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z165170770-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:61.4 occ:1.00 O C:HOH607 1.8 68.1 1.0 O1G C:GTP501 2.0 62.0 1.0 O C:HOH608 2.1 64.7 1.0 O1B C:GTP501 2.2 67.8 1.0 O C:HOH601 2.7 59.9 1.0 PG C:GTP501 3.1 68.7 1.0 PB C:GTP501 3.4 70.6 1.0 OD2 C:ASP98 3.5 68.2 1.0 OE2 C:GLU71 3.5 80.8 1.0 O3B C:GTP501 3.5 70.3 1.0 NZ D:LYS254 3.6 64.8 1.0 O2G C:GTP501 3.6 64.8 1.0 CG C:GLU71 3.7 75.8 1.0 CB C:ASP98 3.8 65.4 1.0 OD1 C:ASP69 4.0 61.5 1.0 CG C:ASP98 4.0 69.4 1.0 CD C:GLU71 4.1 76.0 1.0 O3A C:GTP501 4.1 64.6 1.0 OD2 C:ASP69 4.2 72.0 1.0 O3G C:GTP501 4.4 61.5 1.0 CG C:ASP69 4.5 65.9 1.0 O2B C:GTP501 4.5 74.5 1.0 CE D:LYS254 4.6 63.6 1.0 OG1 C:THR145 4.8 63.9 1.0 CB C:GLN11 4.9 68.3 1.0 N C:GLN11 4.9 58.1 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z165170770-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z165170770-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:88.7 occ:1.00 O D:HOH601 2.2 89.6 1.0 OE1 D:GLN11 2.3 101.3 1.0 O1A D:GDP501 2.7 109.6 1.0 CD D:GLN11 3.5 99.7 1.0 CB D:GLN11 3.6 98.8 1.0 O1B D:GDP501 3.6 99.3 1.0 PA D:GDP501 3.9 97.3 1.0 O2A D:GDP501 4.0 91.8 1.0 OE2 D:GLU71 4.0 122.9 1.0 CG D:GLN11 4.1 101.3 1.0 O3B D:GDP501 4.4 99.2 1.0 PB D:GDP501 4.4 95.5 1.0 OD1 D:ASN101 4.5 112.9 1.0 NE2 D:GLN11 4.6 102.5 1.0 O3A D:GDP501 4.7 99.7 1.0 CA D:GLN11 4.9 92.7 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z165170770-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z165170770-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:125.2 occ:1.00 O1B F:ACP401 2.0 137.4 1.0 O3G F:ACP401 2.6 137.1 1.0 OE2 F:GLU331 2.7 129.3 1.0 PB F:ACP401 3.1 148.4 1.0 O2B F:ACP401 3.1 144.9 1.0 CD F:GLU331 3.5 127.9 1.0 OE1 F:GLU331 3.6 127.4 1.0 OD1 F:ASN333 3.7 140.1 1.0 NZ F:LYS74 3.7 130.4 1.0 PG F:ACP401 3.9 145.3 1.0 C3B F:ACP401 4.2 143.5 1.0 O3A F:ACP401 4.3 141.1 1.0 CG F:ASN333 4.5 137.4 1.0 O1G F:ACP401 4.6 143.4 1.0 ND2 F:ASN333 4.7 137.9 1.0 O1A F:ACP401 4.7 131.1 1.0 CG F:GLU331 4.8 120.1 1.0 CE F:LYS74 5.0 128.8 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