Magnesium in PDB 5s50: Tubulin-Z57299526-Complex

The structure of Tubulin-Z57299526-Complex, PDB code: 5s50 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)	79.01 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.03, 158.02, 180.88, 90, 90, 90
R / Rfree (%)	20.8 / 27

The structure of Tubulin-Z57299526-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z57299526-Complex (pdb code 5s50). 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-Z57299526-Complex, PDB code: 5s50:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z57299526-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z57299526-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:110.4 occ:1.00 O A:HOH601 1.8 103.0 1.0 O A:HOH603 1.8 105.3 1.0 O1G A:GTP501 2.4 100.6 1.0 OE1 A:GLU71 2.5 134.7 1.0 O1B A:GTP501 2.9 102.8 1.0 NZ B:LYS254 3.8 113.1 1.0 CD A:GLU71 3.8 138.0 1.0 PG A:GTP501 3.8 99.5 1.0 NE2 A:GLN11 3.9 123.9 1.0 OD2 A:ASP69 4.1 109.6 1.0 OD1 A:ASP69 4.1 113.0 1.0 CB A:ASP98 4.1 112.4 1.0 OD2 A:ASP98 4.1 112.5 1.0 PB A:GTP501 4.1 103.7 1.0 CB A:GLU71 4.2 122.5 1.0 CB A:GLN11 4.3 108.0 1.0 O2G A:GTP501 4.4 104.4 1.0 O3B A:GTP501 4.4 115.4 1.0 CG A:ASP98 4.5 108.5 1.0 CG A:ASP69 4.5 109.4 1.0 OE2 A:GLU71 4.6 151.9 1.0 CG A:GLU71 4.6 131.1 1.0 O3A A:GTP501 4.6 110.8 1.0 CG2 A:VAL74 4.8 131.0 1.0 N A:GLN11 4.9 103.4 1.0 CE B:LYS254 4.9 108.8 1.0 O3G A:GTP501 4.9 94.1 1.0 CD A:GLN11 5.0 112.7 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z57299526-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z57299526-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:129.3 occ:1.00 O B:HOH602 2.0 118.9 1.0 O B:HOH604 2.1 155.5 1.0 O B:HOH601 2.3 101.1 1.0 OE1 B:GLN11 2.7 107.7 1.0 O1A B:GDP501 3.4 109.8 1.0 CD B:GLN11 3.7 103.9 1.0 OE1 C:GLU254 4.0 167.6 1.0 OD1 B:ASN101 4.1 117.6 1.0 NE2 B:GLN11 4.4 111.0 1.0 OE2 B:GLU71 4.4 133.2 1.0 ND2 B:ASN101 4.7 118.0 1.0 CB B:GLN11 4.7 99.7 1.0 OD2 B:ASP179 4.8 102.7 1.0 CG B:GLN11 4.8 96.7 1.0 CG B:ASN101 4.8 111.6 1.0 PA B:GDP501 4.9 104.4 1.0 CD C:GLU254 5.0 167.3 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z57299526-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z57299526-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:92.6 occ:1.00 O C:HOH605 2.0 88.5 1.0 O1G C:GTP501 2.1 96.8 1.0 O1B C:GTP501 2.4 90.5 1.0 O C:HOH602 2.7 83.9 1.0 NZ D:LYS254 3.2 113.8 1.0 PG C:GTP501 3.5 85.2 1.0 PB C:GTP501 3.5 88.4 1.0 OD2 C:ASP98 3.8 116.3 1.0 O3A C:GTP501 3.8 94.4 1.0 OE2 C:GLU71 3.8 120.3 1.0 OE1 C:GLN11 3.9 103.1 1.0 O3B C:GTP501 4.0 93.3 1.0 O2G C:GTP501 4.1 98.1 1.0 CB D:ASN249 4.2 141.5 1.0 CB C:GLN11 4.3 89.4 1.0 CE D:LYS254 4.3 97.1 1.0 CB C:ASP98 4.4 112.5 1.0 CG C:GLU71 4.5 105.0 1.0 CG D:ASN249 4.5 139.0 1.0 O1A C:GTP501 4.5 93.7 1.0 CG C:ASP98 4.6 119.0 1.0 O3G C:GTP501 4.6 83.0 1.0 CD C:GLU71 4.6 114.0 1.0 ND2 D:ASN249 4.8 141.2 1.0 PA C:GTP501 4.8 94.2 1.0 O2B C:GTP501 4.8 92.8 1.0 N C:GLN11 4.9 85.5 1.0 OD2 C:ASP69 4.9 94.3 1.0 CD C:GLN11 4.9 103.3 1.0 OD1 C:ASP69 4.9 88.9 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z57299526-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z57299526-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:164.5 occ:1.00 O D:HOH601 2.3 144.0 1.0 OE1 D:GLN11 2.5 173.7 1.0 CD D:GLN11 3.1 175.2 1.0 O1A D:GDP502 3.2 156.0 1.0 CB D:GLN11 3.4 170.0 1.0 NE2 D:GLN11 3.7 186.9 1.0 O1B D:GDP502 3.8 155.1 1.0 CG D:GLN11 3.8 170.2 1.0 OE2 D:GLU71 4.1 188.5 1.0 PA D:GDP502 4.4 133.2 1.0 O2A D:GDP502 4.6 133.1 1.0 PB D:GDP502 4.8 156.4 1.0 CA D:GLN11 4.8 169.6 1.0 O3B D:GDP502 4.8 156.2 1.0 OG1 D:THR74 5.0 191.6 1.0 CD D:GLU71 5.0 182.9 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z57299526-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z57299526-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:164.9 occ:1.00 O1B F:ACP401 2.6 185.6 1.0 OE2 F:GLU331 2.9 172.6 1.0 O3G F:ACP401 3.0 178.7 1.0 OD1 F:ASN333 3.2 193.2 1.0 OE1 F:GLU331 3.4 169.3 1.0 CD F:GLU331 3.5 167.7 1.0 NZ F:LYS74 3.7 183.4 1.0 PB F:ACP401 3.8 190.6 1.0 O2B F:ACP401 4.0 182.2 1.0 CG F:ASN333 4.3 189.2 1.0 PG F:ACP401 4.5 190.2 1.0 CE F:LYS74 4.9 176.5 1.0 C3B F:ACP401 4.9 188.5 1.0 ND2 F:ASN333 5.0 186.9 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