Magnesium in PDB 5s5z: Tubulin-Z2856434944-Complex

The structure of Tubulin-Z2856434944-Complex, PDB code: 5s5z 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)	91.08 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.18, 158.03, 182.1, 90, 90, 90
R / Rfree (%)	20.9 / 25.3

The structure of Tubulin-Z2856434944-Complex also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Calcium	(Ca)	4 atoms

The binding sites of Magnesium atom in the Tubulin-Z2856434944-Complex (pdb code 5s5z). 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-Z2856434944-Complex, PDB code: 5s5z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z2856434944-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z2856434944-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:63.0 occ:1.00 O A:HOH617 2.0 73.1 1.0 O A:HOH612 2.0 60.9 1.0 O A:HOH607 2.1 65.8 1.0 O1B A:GTP501 2.1 60.8 1.0 O A:HOH606 2.2 64.7 1.0 O1G A:GTP501 2.3 59.5 1.0 PG A:GTP501 3.3 62.8 1.0 PB A:GTP501 3.3 59.6 1.0 O3B A:GTP501 3.5 68.5 1.0 O2G A:GTP501 3.7 68.4 1.0 OE1 A:GLU71 3.9 82.4 1.0 O3A A:GTP501 3.9 62.7 1.0 CB A:GLN11 4.0 62.8 1.0 NZ B:LYS254 4.1 68.2 1.0 OD1 A:ASP69 4.2 71.6 1.0 NE2 A:GLN11 4.2 68.8 1.0 N A:GLN11 4.3 63.4 1.0 O1A A:GTP501 4.4 59.9 1.0 OD2 A:ASP69 4.5 76.3 1.0 O2B A:GTP501 4.5 66.7 1.0 CB A:ASP98 4.6 73.6 1.0 O3G A:GTP501 4.6 59.8 1.0 PA A:GTP501 4.7 57.0 1.0 CA A:GLN11 4.7 66.3 1.0 CG A:ASP69 4.8 73.8 1.0 CG A:ASP98 4.8 72.4 1.0 OD2 A:ASP98 4.8 81.4 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z2856434944-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z2856434944-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:89.6 occ:1.00 O B:HOH605 2.0 61.8 1.0 OE1 B:GLN11 2.0 81.6 1.0 O B:HOH623 2.5 66.6 1.0 O1A B:GDP501 2.6 61.1 1.0 CD B:GLN11 3.1 81.7 1.0 NE2 B:GLN11 3.9 86.6 1.0 PA B:GDP501 4.1 52.2 1.0 CB B:GLN11 4.1 63.8 1.0 CG B:GLN11 4.2 66.0 1.0 OD1 B:ASN101 4.5 59.1 1.0 O3A B:GDP501 4.6 54.7 1.0 O1B B:GDP501 4.6 57.3 1.0 C5' B:GDP501 4.8 50.8 1.0 O5' B:GDP501 4.9 48.8 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z2856434944-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z2856434944-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:55.9 occ:1.00 O C:HOH634 1.9 55.1 1.0 O1B C:GTP501 2.0 52.7 1.0 O C:HOH647 2.0 48.2 1.0 O C:HOH610 2.0 56.1 1.0 O C:HOH622 2.1 48.6 1.0 O1G C:GTP501 2.1 49.4 1.0 PB C:GTP501 3.2 45.1 1.0 PG C:GTP501 3.2 56.0 1.0 O3B C:GTP501 3.6 59.2 1.0 O2G C:GTP501 3.7 56.6 1.0 OE2 C:GLU71 3.8 64.1 1.0 O3A C:GTP501 3.9 55.5 1.0 NZ D:LYS254 3.9 67.7 1.0 OD1 C:ASP69 4.1 55.9 1.0 OD2 C:ASP69 4.2 56.8 1.0 CB C:GLN11 4.2 52.4 1.0 OD2 C:ASP98 4.2 68.4 1.0 CG C:GLU71 4.4 60.8 1.0 N C:GLN11 4.4 51.0 1.0 O2B C:GTP501 4.4 54.0 1.0 O3G C:GTP501 4.5 58.9 1.0 CD C:GLU71 4.6 63.5 1.0 CB C:ASP98 4.6 60.8 1.0 CG C:ASP69 4.6 56.0 1.0 O1A C:GTP501 4.6 53.8 1.0 OE1 C:GLN11 4.8 66.2 1.0 PA C:GTP501 4.8 55.1 1.0 CG C:ASP98 4.8 66.3 1.0 CA C:GLN11 4.9 55.5 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z2856434944-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z2856434944-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:92.2 occ:1.00 O1A D:GDP501 2.3 102.8 1.0 OE1 D:GLN11 2.3 100.1 1.0 CD D:GLN11 3.5 99.9 1.0 PA D:GDP501 3.7 90.1 1.0 CB D:GLN11 4.1 91.3 1.0 OD1 D:ASN101 4.1 97.5 1.0 O3B D:GDP501 4.2 103.9 1.0 O2A D:GDP501 4.2 84.8 1.0 O1B D:GDP501 4.3 93.7 1.0 CG D:GLN11 4.4 97.4 1.0 NE2 D:GLN11 4.4 99.4 1.0 PB D:GDP501 4.6 91.6 1.0 O3A D:GDP501 4.6 97.9 1.0 C5' D:GDP501 4.7 88.7 1.0 O5' D:GDP501 4.8 88.2 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z2856434944-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z2856434944-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:120.7 occ:1.00 O1B F:ACP401 2.2 128.0 1.0 O3G F:ACP401 2.5 118.0 1.0 OE2 F:GLU331 2.9 113.8 1.0 OD1 F:ASN333 3.3 105.5 1.0 OE1 F:GLU331 3.4 117.0 1.0 CD F:GLU331 3.5 112.4 1.0 PB F:ACP401 3.5 132.5 1.0 NZ F:LYS74 3.7 132.9 1.0 O2B F:ACP401 3.9 127.8 1.0 PG F:ACP401 3.9 136.4 1.0 C3B F:ACP401 4.4 127.6 1.0 CG F:ASN333 4.5 99.3 1.0 O1G F:ACP401 4.5 130.8 1.0 O3A F:ACP401 4.8 135.6 1.0 O1A F:ACP401 4.9 124.5 1.0 CE F:LYS74 5.0 124.4 1.0 CG F:GLU331 5.0 99.6 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