Magnesium in PDB 5s53: Tubulin-Z1349163663-Complex

The structure of Tubulin-Z1349163663-Complex, PDB code: 5s53 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)	68.19 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.32, 159.31, 178.96, 90, 90, 90
R / Rfree (%)	21.8 / 26.7

The structure of Tubulin-Z1349163663-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z1349163663-Complex (pdb code 5s53). 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-Z1349163663-Complex, PDB code: 5s53:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z1349163663-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z1349163663-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:71.3 occ:1.00 O1G A:GTP501 1.9 69.2 1.0 O A:HOH603 2.0 65.6 1.0 O A:HOH602 2.0 70.5 1.0 O A:HOH605 2.2 70.1 1.0 O1B A:GTP501 2.3 70.9 1.0 PG A:GTP501 3.1 70.3 1.0 OE1 A:GLU71 3.2 87.3 1.0 PB A:GTP501 3.3 67.5 1.0 O3B A:GTP501 3.5 82.1 1.0 O2G A:GTP501 3.7 66.1 1.0 O3A A:GTP501 3.8 68.9 1.0 NZ B:LYS254 3.9 73.2 1.0 CB A:GLN11 4.0 71.3 1.0 OD1 A:ASP69 4.2 69.4 1.0 NE2 A:GLN11 4.2 80.2 1.0 CD A:GLU71 4.3 87.7 1.0 O3G A:GTP501 4.3 69.2 1.0 N A:GLN11 4.4 69.2 1.0 CB A:ASP98 4.4 77.5 1.0 OD2 A:ASP69 4.5 79.4 1.0 O2B A:GTP501 4.6 78.1 1.0 O1A A:GTP501 4.6 68.2 1.0 OD2 A:ASP98 4.7 86.2 1.0 PA A:GTP501 4.7 66.6 1.0 CG A:ASP98 4.8 79.2 1.0 CG A:ASP69 4.8 75.1 1.0 OE2 A:GLU71 4.8 89.4 1.0 CA A:GLN11 4.8 72.3 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z1349163663-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z1349163663-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:70.1 occ:1.00 O B:HOH602 1.9 76.6 1.0 O B:HOH606 1.9 66.0 1.0 O C:HOH617 1.9 71.4 1.0 OE1 B:GLN11 2.0 71.5 1.0 O B:HOH603 2.0 70.9 1.0 O1A B:GDP501 2.4 75.6 1.0 CD B:GLN11 3.2 69.3 1.0 PA B:GDP501 3.9 64.3 1.0 OD2 B:ASP179 4.0 66.5 1.0 CB B:GLN11 4.1 63.7 1.0 NE2 B:GLN11 4.1 74.2 1.0 CG B:GLN11 4.2 67.7 1.0 OE1 C:GLU254 4.3 77.1 1.0 O2A B:GDP501 4.3 64.2 1.0 O3B B:GDP501 4.5 64.4 1.0 ND2 B:ASN101 4.6 75.5 1.0 OD1 B:ASN101 4.8 72.4 1.0 C5' B:GDP501 4.8 69.2 1.0 O1B B:GDP501 4.8 65.0 1.0 O5' B:GDP501 4.8 66.1 1.0 O3A B:GDP501 4.9 65.0 1.0 OE2 C:GLU254 5.0 67.4 1.0 PB B:GDP501 5.0 67.3 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z1349163663-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z1349163663-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:71.0 occ:1.00 O C:HOH602 1.8 66.9 1.0 O1G C:GTP501 2.0 68.2 1.0 O C:HOH603 2.4 67.9 1.0 O1B C:GTP501 2.6 74.7 1.0 O C:HOH604 2.7 59.2 1.0 NZ D:LYS254 3.1 71.6 1.0 PG C:GTP501 3.4 78.1 1.0 OD2 C:ASP98 3.4 71.7 1.0 OE2 C:GLU71 3.6 81.7 1.0 PB C:GTP501 3.7 64.9 1.0 CG C:GLU71 4.0 81.7 1.0 O3B C:GTP501 4.0 78.4 1.0 O3A C:GTP501 4.1 63.3 1.0 O2G C:GTP501 4.1 60.1 1.0 CB C:ASP98 4.2 65.3 1.0 CE D:LYS254 4.2 70.2 1.0 CD C:GLU71 4.2 82.4 1.0 CG C:ASP98 4.2 73.5 1.0 O3G C:GTP501 4.4 59.8 1.0 O C:HOH631 4.4 85.3 1.0 OE1 C:GLN11 4.6 80.7 1.0 CB C:GLN11 4.8 66.3 1.0 OD1 C:ASP69 5.0 66.2 1.0 O1A C:GTP501 5.0 76.6 1.0 OE1 D:GLN247 5.0 119.1 1.0 O2B C:GTP501 5.0 64.8 1.0 OD2 C:ASP69 5.0 75.2 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z1349163663-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z1349163663-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:88.2 occ:1.00 O D:HOH603 2.2 90.1 1.0 OE1 D:GLN11 2.3 97.8 1.0 O1A D:GDP501 2.7 102.3 1.0 CD D:GLN11 3.2 97.5 1.0 CB D:GLN11 3.5 97.2 1.0 O1B D:GDP501 3.8 89.1 1.0 CG D:GLN11 3.9 98.6 1.0 PA D:GDP501 3.9 92.7 1.0 O2A D:GDP501 4.1 88.9 1.0 NE2 D:GLN11 4.2 103.0 1.0 O3B D:GDP501 4.4 99.6 1.0 PB D:GDP501 4.5 96.3 1.0 OD1 D:ASN101 4.7 112.1 1.0 O3A D:GDP501 4.7 93.9 1.0 CA D:GLN11 4.8 91.1 1.0 OE2 D:GLU71 4.9 137.2 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z1349163663-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z1349163663-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:140.9 occ:1.00 OE2 F:GLU331 2.6 158.3 1.0 O1B F:ACP401 2.7 155.1 1.0 O3G F:ACP401 2.8 151.9 1.0 CD F:GLU331 3.4 158.2 1.0 OE1 F:GLU331 3.4 161.9 1.0 OD1 F:ASN333 3.5 150.2 1.0 NZ F:LYS74 3.6 145.9 1.0 PB F:ACP401 3.9 157.3 1.0 O2B F:ACP401 3.9 156.7 1.0 PG F:ACP401 4.4 158.5 1.0 CG F:ASN333 4.5 144.5 1.0 C3B F:ACP401 4.8 155.9 1.0 CG F:GLU331 4.9 151.2 1.0 CE F:LYS74 4.9 143.9 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