Magnesium in PDB 5s5k: Tubulin-Z2472938267-Complex

The structure of Tubulin-Z2472938267-Complex, PDB code: 5s5k 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)	73.28 / 2.41
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.46, 160.78, 178.27, 90, 90, 90
R / Rfree (%)	21.4 / 24.8

The structure of Tubulin-Z2472938267-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z2472938267-Complex (pdb code 5s5k). 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-Z2472938267-Complex, PDB code: 5s5k:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z2472938267-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z2472938267-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:68.9 occ:1.00 O A:HOH610 1.9 63.0 1.0 O1G A:GTP501 2.0 63.0 1.0 O A:HOH601 2.0 65.6 1.0 O A:HOH605 2.1 68.0 1.0 O1B A:GTP501 2.2 63.0 1.0 O A:HOH609 2.3 71.2 1.0 PG A:GTP501 3.1 67.5 1.0 PB A:GTP501 3.3 62.9 1.0 OE1 A:GLU71 3.4 80.4 1.0 O2G A:GTP501 3.5 61.8 1.0 O3B A:GTP501 3.6 69.4 1.0 OD1 A:ASP69 4.0 70.6 1.0 NZ B:LYS254 4.0 72.3 1.0 O3A A:GTP501 4.0 64.9 1.0 CB A:ASP98 4.2 72.6 1.0 CB A:GLN11 4.2 64.8 1.0 OD2 A:ASP69 4.3 78.4 1.0 O3G A:GTP501 4.4 64.3 1.0 N A:GLN11 4.5 63.8 1.0 NE2 A:GLN11 4.5 68.1 1.0 O2B A:GTP501 4.6 62.3 1.0 CG A:ASP69 4.6 73.5 1.0 CG A:ASP98 4.6 74.3 1.0 CD A:GLU71 4.7 87.1 1.0 O1A A:GTP501 4.7 63.6 1.0 OD2 A:ASP98 4.7 82.2 1.0 PA A:GTP501 4.9 64.5 1.0 CA A:GLN11 5.0 64.1 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z2472938267-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z2472938267-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:49.0 occ:1.00 OE1 B:GLN11 2.0 61.8 1.0 O C:HOH615 2.1 50.5 1.0 O B:HOH612 2.2 58.2 1.0 O B:HOH602 2.2 63.1 1.0 O1A B:GDP501 2.3 54.5 1.0 O B:HOH613 2.4 53.9 1.0 CD B:GLN11 3.2 60.3 1.0 PA B:GDP501 3.6 49.9 1.0 O3A B:GDP501 3.9 52.7 1.0 CB B:GLN11 3.9 56.5 1.0 OD2 B:ASP179 4.1 58.4 1.0 CG B:GLN11 4.1 57.6 1.0 NE2 B:GLN11 4.1 62.5 1.0 O1B B:GDP501 4.3 51.3 1.0 OD1 B:ASN101 4.3 51.9 1.0 OE1 C:GLU254 4.4 63.9 1.0 C5' B:GDP501 4.5 56.8 1.0 O5' B:GDP501 4.6 55.8 1.0 O2A B:GDP501 4.6 53.6 1.0 PB B:GDP501 4.7 49.6 1.0 ND2 B:ASN101 4.9 51.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z2472938267-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z2472938267-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:59.5 occ:1.00 O C:HOH611 1.9 57.2 1.0 O C:HOH617 2.0 58.8 1.0 O1G C:GTP501 2.1 57.0 1.0 O C:HOH604 2.1 56.8 1.0 O C:HOH605 2.1 53.2 1.0 O1B C:GTP501 2.3 55.0 1.0 PG C:GTP501 3.2 60.7 1.0 PB C:GTP501 3.4 55.1 1.0 O2G C:GTP501 3.6 56.7 1.0 O3B C:GTP501 3.7 58.3 1.0 NZ D:LYS254 3.7 61.3 1.0 OE2 C:GLU71 3.9 67.8 1.0 O3A C:GTP501 3.9 56.2 1.0 CG C:GLU71 4.1 65.6 1.0 OD1 C:ASP69 4.2 57.3 1.0 OD2 C:ASP98 4.2 65.0 1.0 OD2 C:ASP69 4.3 57.2 1.0 CB C:GLN11 4.3 54.8 1.0 CB C:ASP98 4.4 60.1 1.0 CD C:GLU71 4.5 66.1 1.0 CG C:ASP98 4.5 60.5 1.0 O3G C:GTP501 4.5 55.7 1.0 N C:GLN11 4.6 54.0 1.0 OE1 C:GLN11 4.6 67.4 1.0 O2B C:GTP501 4.7 57.3 1.0 CG C:ASP69 4.7 61.0 1.0 O1A C:GTP501 4.7 59.9 1.0 PA C:GTP501 4.9 58.8 1.0 CE D:LYS254 4.9 60.2 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z2472938267-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z2472938267-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:86.9 occ:1.00 O D:HOH602 1.9 87.3 1.0 OE1 D:GLN11 2.1 90.8 1.0 O1A D:GDP501 2.3 97.1 1.0 CD D:GLN11 3.2 93.0 1.0 PA D:GDP501 3.7 85.9 1.0 CB D:GLN11 3.8 89.5 1.0 O D:HOH608 4.0 86.4 1.0 O1B D:GDP501 4.0 83.1 1.0 CG D:GLN11 4.1 92.8 1.0 NE2 D:GLN11 4.2 98.6 1.0 OD1 D:ASN101 4.2 90.0 1.0 O2A D:GDP501 4.3 84.4 1.0 O3B D:GDP501 4.4 95.2 1.0 PB D:GDP501 4.6 86.8 1.0 O3A D:GDP501 4.6 89.8 1.0 C5' D:GDP501 4.8 89.4 1.0 O5' D:GDP501 4.8 88.2 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z2472938267-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z2472938267-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:114.8 occ:1.00 O3G F:ACP401 2.6 124.0 1.0 O1B F:ACP401 2.9 127.0 1.0 OE2 F:GLU331 2.9 119.9 1.0 OD1 F:ASN333 2.9 114.8 1.0 OE1 F:GLU331 3.6 121.5 1.0 CD F:GLU331 3.6 119.3 1.0 PB F:ACP401 3.9 128.7 1.0 O2B F:ACP401 4.0 130.4 1.0 CG F:ASN333 4.1 111.4 1.0 PG F:ACP401 4.1 130.8 1.0 NZ F:LYS74 4.2 122.9 1.0 C3B F:ACP401 4.7 127.8 1.0 ND2 F:ASN333 4.7 110.4 1.0 O1G F:ACP401 4.8 126.3 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