Magnesium in PDB 5s4n: Tubulin-Z285782452-Complex

The structure of Tubulin-Z285782452-Complex, PDB code: 5s4n 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)	90.81 / 2.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.26, 158.63, 179.55, 90, 90, 90
R / Rfree (%)	21.6 / 25.8

The structure of Tubulin-Z285782452-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z285782452-Complex (pdb code 5s4n). 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-Z285782452-Complex, PDB code: 5s4n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z285782452-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z285782452-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:69.2 occ:1.00 O A:HOH612 1.9 65.8 1.0 O1G A:GTP501 2.0 61.7 1.0 O A:HOH616 2.1 67.0 1.0 O A:HOH613 2.2 58.4 1.0 O1B A:GTP501 2.4 60.4 1.0 PG A:GTP501 3.3 64.1 1.0 OE1 A:GLU71 3.6 86.1 1.0 PB A:GTP501 3.6 62.7 1.0 O3B A:GTP501 3.8 70.2 1.0 O2G A:GTP501 3.8 61.6 1.0 NZ B:LYS254 3.9 75.2 1.0 OD1 A:ASP69 4.1 68.3 1.0 OD2 A:ASP69 4.2 68.2 1.0 CB A:ASP98 4.2 66.5 1.0 O3A A:GTP501 4.2 62.2 1.0 CB A:GLN11 4.3 59.8 1.0 OD2 A:ASP98 4.5 76.5 1.0 NE2 A:GLN11 4.5 80.2 1.0 O3G A:GTP501 4.5 62.3 1.0 CG A:ASP69 4.6 69.2 1.0 N A:GLN11 4.6 62.6 1.0 CG A:ASP98 4.6 69.2 1.0 CD A:GLU71 4.7 91.3 1.0 O2B A:GTP501 4.8 65.8 1.0 O1A A:GTP501 4.8 60.2 1.0 CB A:GLU71 4.9 75.9 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z285782452-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z285782452-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:61.1 occ:1.00 OE1 B:GLN11 1.9 71.2 1.0 O B:HOH616 2.1 66.8 1.0 O B:HOH609 2.2 56.0 1.0 O C:HOH616 2.2 62.1 1.0 O1A B:GDP501 2.3 67.5 1.0 CD B:GLN11 3.2 68.7 1.0 PA B:GDP501 3.6 54.1 1.0 O2A B:GDP501 3.9 58.3 1.0 CB B:GLN11 3.9 60.5 1.0 OD2 B:ASP179 4.0 62.8 1.0 NE2 B:GLN11 4.1 72.0 1.0 CG B:GLN11 4.1 62.7 1.0 OD1 B:ASN101 4.1 65.6 1.0 O1B B:GDP501 4.1 59.2 1.0 OE1 C:GLU254 4.3 68.0 1.0 O5' B:GDP501 4.7 60.8 1.0 C5' B:GDP501 4.7 61.9 1.0 O3A B:GDP501 4.7 62.4 1.0 PB B:GDP501 4.9 54.0 1.0 CG B:ASN101 5.0 65.7 1.0 ND2 B:ASN101 5.0 64.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z285782452-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z285782452-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:61.9 occ:1.00 O1G C:GTP501 1.9 54.8 1.0 O C:HOH608 2.0 57.2 1.0 O C:HOH629 2.0 60.8 1.0 O C:HOH610 2.1 56.6 1.0 O1B C:GTP501 2.1 57.8 1.0 O C:HOH626 2.3 61.3 1.0 PG C:GTP501 3.2 60.6 1.0 PB C:GTP501 3.3 54.6 1.0 O3B C:GTP501 3.6 61.5 1.0 NZ D:LYS254 3.7 60.1 1.0 O2G C:GTP501 3.8 56.9 1.0 O3A C:GTP501 3.8 64.0 1.0 OD2 C:ASP98 3.9 65.1 1.0 OE2 C:GLU71 4.0 66.2 1.0 CG C:GLU71 4.2 65.3 1.0 OD1 C:ASP69 4.2 60.5 1.0 CB C:ASP98 4.3 60.0 1.0 OD2 C:ASP69 4.3 58.6 1.0 O3G C:GTP501 4.4 57.6 1.0 O C:HOH620 4.4 69.7 1.0 CB C:GLN11 4.4 58.8 1.0 CG C:ASP98 4.5 63.9 1.0 O2B C:GTP501 4.6 61.3 1.0 CD C:GLU71 4.6 67.3 1.0 N C:GLN11 4.7 53.9 1.0 CG C:ASP69 4.7 58.7 1.0 NE2 C:GLN11 4.7 67.9 1.0 O1A C:GTP501 4.8 64.8 1.0 CE D:LYS254 4.9 58.8 1.0 PA C:GTP501 4.9 60.2 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z285782452-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z285782452-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:92.4 occ:1.00 O D:HOH602 2.0 83.9 1.0 O1A D:GDP501 2.3 97.7 1.0 OE1 D:GLN11 2.6 90.2 1.0 PA D:GDP501 3.7 88.8 1.0 CD D:GLN11 3.7 89.5 1.0 O1B D:GDP501 3.7 84.2 1.0 CB D:GLN11 3.9 88.3 1.0 O3B D:GDP501 4.0 91.9 1.0 O2A D:GDP501 4.0 84.0 1.0 OD1 D:ASN101 4.1 88.2 1.0 PB D:GDP501 4.3 86.9 1.0 CG D:GLN11 4.4 87.3 1.0 O3A D:GDP501 4.5 93.0 1.0 NE2 D:GLN11 4.7 92.5 1.0 OE2 D:GLU71 4.8 137.6 1.0 O5' D:GDP501 4.9 86.8 1.0 C5' D:GDP501 5.0 86.5 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z285782452-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z285782452-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:118.0 occ:1.00 O3G F:ACP401 1.9 123.5 1.0 OE2 F:GLU331 2.0 121.5 1.0 ND2 F:ASN333 2.2 123.8 1.0 O1B F:ACP401 2.5 130.3 1.0 CD F:GLU331 3.1 118.8 1.0 CG F:ASN333 3.3 121.5 1.0 OE1 F:GLU331 3.4 122.0 1.0 PG F:ACP401 3.4 133.9 1.0 OD1 F:ASN333 3.6 118.9 1.0 PB F:ACP401 3.7 134.9 1.0 O1G F:ACP401 4.0 129.4 1.0 O2B F:ACP401 4.1 138.6 1.0 C3B F:ACP401 4.2 134.6 1.0 CG F:GLU331 4.4 109.6 1.0 NZ F:LYS74 4.5 127.0 1.0 O2G F:ACP401 4.5 122.8 1.0 CB F:ASN333 4.6 112.3 1.0 O1A F:ACP401 4.8 125.5 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