Magnesium in PDB 5s4w: Tubulin-Z1416571195-Complex

The structure of Tubulin-Z1416571195-Complex, PDB code: 5s4w 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)	62.66 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.13, 160.08, 178.76, 90, 90, 90
R / Rfree (%)	22.1 / 26.8

The structure of Tubulin-Z1416571195-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z1416571195-Complex (pdb code 5s4w). 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-Z1416571195-Complex, PDB code: 5s4w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z1416571195-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z1416571195-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:86.8 occ:1.00 O1G A:GTP501 1.9 82.7 1.0 O A:HOH605 2.0 79.7 1.0 O A:HOH607 2.1 84.0 1.0 O1B A:GTP501 2.1 86.8 1.0 O A:HOH603 2.2 89.1 1.0 PG A:GTP501 3.2 81.4 1.0 OE1 A:GLU71 3.2 104.5 1.0 PB A:GTP501 3.3 82.2 1.0 O3B A:GTP501 3.5 90.4 1.0 NZ B:LYS254 3.8 92.4 1.0 O2G A:GTP501 3.8 79.5 1.0 O3A A:GTP501 3.9 86.7 1.0 CB A:GLN11 4.1 87.4 1.0 NE2 A:GLN11 4.2 96.4 1.0 CB A:ASP98 4.2 91.1 1.0 OD1 A:ASP69 4.2 91.8 1.0 O3G A:GTP501 4.4 77.4 1.0 CD A:GLU71 4.4 110.4 1.0 OD2 A:ASP98 4.5 94.5 1.0 O2B A:GTP501 4.5 84.7 1.0 N A:GLN11 4.5 88.5 1.0 OD2 A:ASP69 4.5 91.4 1.0 CG A:ASP98 4.6 88.8 1.0 O1A A:GTP501 4.7 80.3 1.0 CG A:ASP69 4.8 93.8 1.0 CA A:GLN11 4.8 88.7 1.0 PA A:GTP501 4.9 79.8 1.0 OE2 A:GLU71 4.9 123.0 1.0 CE B:LYS254 5.0 86.0 1.0 CD A:GLN11 5.0 100.0 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z1416571195-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z1416571195-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:96.0 occ:1.00 OE1 B:GLN11 1.9 95.5 1.0 O B:HOH614 1.9 85.0 1.0 O B:HOH615 2.0 85.2 1.0 O1A B:GDP501 2.1 89.3 1.0 O B:HOH620 2.4 77.7 1.0 CD B:GLN11 3.1 94.2 1.0 PA B:GDP501 3.6 77.6 1.0 OD2 B:ASP179 3.6 88.8 1.0 CB B:GLN11 3.9 86.1 1.0 NE2 B:GLN11 4.0 97.8 1.0 CG B:GLN11 4.0 89.0 1.0 O1B B:GDP501 4.0 88.1 1.0 O2A B:GDP501 4.1 76.4 1.0 C5' B:GDP501 4.4 85.7 1.0 OD1 B:ASN101 4.4 94.4 1.0 O5' B:GDP501 4.5 86.9 1.0 O3A B:GDP501 4.5 77.8 1.0 OE1 C:GLU254 4.6 89.2 1.0 ND2 B:ASN101 4.6 83.5 1.0 CG B:ASP179 4.7 88.2 1.0 PB B:GDP501 4.8 76.8 1.0 C8 B:GDP501 4.8 84.8 1.0 CG B:ASN101 5.0 85.3 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z1416571195-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z1416571195-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:87.9 occ:1.00 O C:HOH601 1.8 81.2 1.0 O1G C:GTP501 1.9 76.4 1.0 O1B C:GTP501 2.5 85.7 1.0 O C:HOH607 2.5 76.7 1.0 O C:HOH602 2.8 74.2 1.0 NZ D:LYS254 3.1 78.2 1.0 OD2 C:ASP98 3.1 84.0 1.0 PG C:GTP501 3.3 78.9 1.0 PB C:GTP501 3.6 83.1 1.0 OE2 C:GLU71 3.7 96.7 1.0 O2G C:GTP501 3.8 77.5 1.0 O3B C:GTP501 3.9 92.1 1.0 CG C:GLU71 3.9 97.0 1.0 CG C:ASP98 3.9 87.1 1.0 CB C:ASP98 4.0 82.8 1.0 O3A C:GTP501 4.1 80.3 1.0 CE D:LYS254 4.2 77.8 1.0 CD C:GLU71 4.3 96.3 1.0 O3G C:GTP501 4.4 80.8 1.0 OD2 C:ASP69 4.7 83.5 1.0 OD1 C:ASP69 4.7 81.3 1.0 OE1 C:GLN11 4.7 108.1 1.0 CB C:GLN11 4.8 82.5 1.0 O2B C:GTP501 4.9 75.3 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z1416571195-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z1416571195-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:114.2 occ:1.00 O D:HOH603 2.1 116.3 1.0 OE1 D:GLN11 2.2 114.0 1.0 O1A D:GDP501 2.8 121.1 1.0 CD D:GLN11 3.2 113.8 1.0 CB D:GLN11 3.7 120.9 1.0 PA D:GDP501 4.0 110.6 1.0 CG D:GLN11 4.0 116.0 1.0 NE2 D:GLN11 4.1 121.4 1.0 O2A D:GDP501 4.2 105.8 1.0 O1B D:GDP501 4.3 112.1 1.0 O3B D:GDP501 4.5 116.8 1.0 OD1 D:ASN101 4.6 124.2 1.0 PB D:GDP501 4.8 113.6 1.0 O3A D:GDP501 5.0 118.7 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z1416571195-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z1416571195-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:141.6 occ:1.00 O1B F:ACP401 2.4 160.3 1.0 O3G F:ACP401 2.5 155.5 1.0 OE2 F:GLU331 2.6 156.7 1.0 OD1 F:ASN333 3.1 146.0 1.0 CD F:GLU331 3.5 154.8 1.0 PB F:ACP401 3.5 166.0 1.0 O2B F:ACP401 3.6 165.9 1.0 NZ F:LYS74 3.7 154.2 1.0 OE1 F:GLU331 3.7 156.9 1.0 PG F:ACP401 4.0 162.6 1.0 CG F:ASN333 4.2 140.1 1.0 C3B F:ACP401 4.5 162.7 1.0 O1G F:ACP401 4.8 160.8 1.0 CG F:GLU331 4.8 148.6 1.0 O3A F:ACP401 4.9 160.9 1.0 ND2 F:ASN333 4.9 137.5 1.0 O2G F:ACP401 5.0 150.3 1.0 CE F:LYS74 5.0 155.7 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