Magnesium in PDB 5s5r: Tubulin-Z33452106-Complex

The structure of Tubulin-Z33452106-Complex, PDB code: 5s5r 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)	72.81 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.24, 159.48, 178.6, 90, 90, 90
R / Rfree (%)	20.7 / 24.4

The structure of Tubulin-Z33452106-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z33452106-Complex (pdb code 5s5r). 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-Z33452106-Complex, PDB code: 5s5r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z33452106-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z33452106-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:54.0 occ:1.00 O A:HOH609 1.9 61.9 1.0 O A:HOH603 1.9 49.3 1.0 O A:HOH633 2.0 52.4 1.0 O A:HOH636 2.2 55.3 1.0 O1G A:GTP501 2.2 47.3 1.0 O1B A:GTP501 2.3 49.4 1.0 PG A:GTP501 3.3 57.3 1.0 PB A:GTP501 3.4 50.4 1.0 OE1 A:GLU71 3.5 66.4 1.0 O3B A:GTP501 3.6 60.2 1.0 O2G A:GTP501 3.8 54.8 1.0 OD1 A:ASP69 3.9 58.2 1.0 O3A A:GTP501 3.9 53.6 1.0 CB A:GLN11 4.1 50.1 1.0 OD2 A:ASP69 4.1 56.7 1.0 NZ B:LYS254 4.1 67.6 1.0 CB A:ASP98 4.2 59.2 1.0 N A:GLN11 4.3 52.2 1.0 NE2 A:GLN11 4.3 64.5 1.0 OD2 A:ASP98 4.4 69.0 1.0 CG A:ASP69 4.4 60.0 1.0 O3G A:GTP501 4.6 52.4 1.0 CG A:ASP98 4.6 66.2 1.0 O2B A:GTP501 4.7 55.3 1.0 O1A A:GTP501 4.7 54.9 1.0 CD A:GLU71 4.7 73.2 1.0 CA A:GLN11 4.7 53.5 1.0 PA A:GTP501 4.9 53.2 1.0 OG1 A:THR145 5.0 54.8 1.0 CE B:LYS254 5.0 63.8 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z33452106-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z33452106-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:43.2 occ:1.00 O C:HOH677 2.0 50.0 1.0 OE1 B:GLN11 2.1 60.1 1.0 O B:HOH636 2.1 59.2 1.0 O1A B:GDP501 2.2 50.6 1.0 O B:HOH607 2.2 59.5 1.0 O B:HOH655 2.4 50.9 1.0 CD B:GLN11 3.3 58.9 1.0 PA B:GDP501 3.5 48.6 1.0 O3A B:GDP501 3.9 51.3 1.0 OD2 B:ASP179 3.9 57.2 1.0 CB B:GLN11 4.1 52.1 1.0 NE2 B:GLN11 4.2 66.6 1.0 CG B:GLN11 4.2 56.2 1.0 OD1 B:ASN101 4.3 50.4 1.0 OE1 C:GLU254 4.4 59.1 1.0 O1B B:GDP501 4.4 47.0 1.0 C5' B:GDP501 4.5 51.2 1.0 O C:HOH624 4.5 55.1 1.0 O5' B:GDP501 4.5 49.2 1.0 O2A B:GDP501 4.5 46.3 1.0 PB B:GDP501 4.8 47.8 1.0 CG B:ASP179 4.9 57.4 1.0 ND2 B:ASN101 4.9 51.0 1.0 C8 B:GDP501 5.0 54.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z33452106-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z33452106-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:58.4 occ:1.00 O C:HOH605 1.7 46.0 1.0 O1G C:GTP501 1.9 50.2 1.0 O C:HOH635 2.2 50.8 1.0 O1B C:GTP501 2.4 43.9 1.0 O C:HOH622 2.7 51.9 1.0 NZ D:LYS254 3.2 55.6 1.0 PB C:GTP501 3.3 45.8 1.0 PG C:GTP501 3.3 52.1 1.0 O3A C:GTP501 3.4 49.7 1.0 O C:HOH602 3.5 56.2 1.0 O3B C:GTP501 3.7 56.9 1.0 O1A C:GTP501 4.0 50.1 1.0 CB C:GLN11 4.1 50.0 1.0 O2G C:GTP501 4.1 53.0 1.0 OE1 C:GLN11 4.2 63.5 1.0 OD2 C:ASP98 4.3 59.0 1.0 PA C:GTP501 4.3 43.2 1.0 OE2 C:GLU71 4.3 63.0 1.0 O3G C:GTP501 4.3 47.4 1.0 CE D:LYS254 4.5 59.8 1.0 O D:HOH609 4.6 57.6 1.0 N C:GLN11 4.7 49.9 1.0 O2B C:GTP501 4.7 53.5 1.0 CG C:GLU71 4.8 61.1 1.0 O C:HOH659 4.8 70.2 1.0 CG C:ASP98 4.9 58.7 1.0 CD C:GLN11 5.0 57.4 1.0 CB C:ASP98 5.0 56.2 1.0 OD2 C:ASP69 5.0 49.8 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z33452106-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z33452106-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:80.0 occ:1.00 OE1 D:GLN11 2.1 83.8 1.0 O D:HOH604 2.2 75.2 1.0 O1A D:GDP502 2.3 93.2 1.0 CD D:GLN11 3.3 83.5 1.0 PA D:GDP502 3.7 75.8 1.0 CB D:GLN11 3.9 79.0 1.0 O2A D:GDP502 4.1 76.8 1.0 CG D:GLN11 4.2 79.6 1.0 NE2 D:GLN11 4.2 83.7 1.0 O D:HOH621 4.2 81.2 1.0 O1B D:GDP502 4.4 77.3 1.0 C5' D:GDP502 4.6 80.8 1.0 OD1 D:ASN101 4.6 85.1 1.0 O5' D:GDP502 4.6 78.7 1.0 O3A D:GDP502 4.8 85.5 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z33452106-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z33452106-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:99.7 occ:1.00 OE2 F:GLU331 2.1 109.2 1.0 O3G F:ACP401 2.3 109.4 1.0 O1B F:ACP401 2.5 116.3 1.0 CD F:GLU331 3.0 107.5 1.0 OD1 F:ASN333 3.0 102.2 1.0 OE1 F:GLU331 3.1 112.5 1.0 PB F:ACP401 3.7 117.5 1.0 PG F:ACP401 3.9 122.8 1.0 O2B F:ACP401 3.9 124.4 1.0 NZ F:LYS74 4.0 118.0 1.0 CG F:ASN333 4.0 96.4 1.0 CG F:GLU331 4.4 97.9 1.0 C3B F:ACP401 4.5 115.6 1.0 ND2 F:ASN333 4.6 92.2 1.0 O1G F:ACP401 4.7 117.7 1.0 O2G F:ACP401 4.8 107.1 1.0 O3A F:ACP401 4.9 117.9 1.0 O1A F:ACP401 5.0 111.6 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