Magnesium in PDB 5s58: Tubulin-Z2856434826-Complex

The structure of Tubulin-Z2856434826-Complex, PDB code: 5s58 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)	72.14 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.28, 157.51, 179.79, 90, 90, 90
R / Rfree (%)	20.9 / 24.6

The structure of Tubulin-Z2856434826-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z2856434826-Complex (pdb code 5s58). 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-Z2856434826-Complex, PDB code: 5s58:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z2856434826-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z2856434826-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:51.1 occ:1.00 O A:HOH619 1.9 47.8 1.0 O1G A:GTP501 2.1 45.0 1.0 O A:HOH618 2.1 49.7 1.0 O A:HOH642 2.1 57.3 1.0 O A:HOH614 2.2 49.7 1.0 O1B A:GTP501 2.3 45.6 1.0 PG A:GTP501 3.3 58.2 1.0 PB A:GTP501 3.4 52.5 1.0 O3B A:GTP501 3.7 54.2 1.0 O2G A:GTP501 3.8 51.2 1.0 OE1 A:GLU71 3.8 66.7 1.0 O3A A:GTP501 3.8 53.1 1.0 CB A:GLN11 3.9 46.9 1.0 NZ B:LYS254 4.0 66.0 1.0 OD1 A:ASP69 4.0 54.2 1.0 NE2 A:GLN11 4.0 59.5 1.0 OD2 A:ASP69 4.2 57.0 1.0 N A:GLN11 4.3 50.6 1.0 CB A:ASP98 4.3 54.5 1.0 OD2 A:ASP98 4.5 62.3 1.0 O3G A:GTP501 4.5 48.4 1.0 CG A:ASP69 4.6 58.1 1.0 O2B A:GTP501 4.7 51.3 1.0 O1A A:GTP501 4.7 47.4 1.0 CG A:ASP98 4.7 56.2 1.0 CA A:GLN11 4.7 49.2 1.0 PA A:GTP501 4.8 46.9 1.0 CD A:GLU71 4.9 69.5 1.0 CD A:GLN11 5.0 59.4 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z2856434826-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z2856434826-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:41.7 occ:1.00 O B:HOH645 1.9 58.4 1.0 OE1 B:GLN11 2.1 53.7 1.0 O C:HOH682 2.2 51.2 1.0 O1A B:GDP501 2.2 44.9 1.0 O B:HOH635 2.3 46.1 1.0 O B:HOH610 2.5 50.5 1.0 CD B:GLN11 3.4 51.9 1.0 PA B:GDP501 3.5 44.7 1.0 O3A B:GDP501 3.9 47.0 1.0 CB B:GLN11 4.0 48.6 1.0 OD2 B:ASP179 4.0 52.5 1.0 OD1 B:ASN101 4.1 52.5 1.0 CG B:GLN11 4.2 48.4 1.0 O1B B:GDP501 4.3 43.4 1.0 NE2 B:GLN11 4.3 61.4 1.0 C5' B:GDP501 4.4 47.2 1.0 O C:HOH616 4.4 54.1 1.0 O5' B:GDP501 4.4 44.9 1.0 OE1 C:GLU254 4.5 57.2 1.0 O2A B:GDP501 4.6 43.5 1.0 PB B:GDP501 4.7 42.8 1.0 ND2 B:ASN101 4.8 47.5 1.0 CG B:ASN101 4.9 53.5 1.0 C8 B:GDP501 4.9 47.4 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z2856434826-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z2856434826-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:42.2 occ:1.00 O1G C:GTP501 1.8 48.6 1.0 O1B C:GTP501 2.0 50.4 1.0 O C:HOH698 2.0 46.5 1.0 O C:HOH609 2.1 44.9 1.0 O C:HOH691 2.1 49.4 1.0 O C:HOH685 2.2 47.1 1.0 PG C:GTP501 2.9 35.1 1.0 PB C:GTP501 3.0 34.0 1.0 O3B C:GTP501 3.4 53.2 1.0 O2G C:GTP501 3.4 39.4 1.0 O3A C:GTP501 3.4 47.3 1.0 NZ D:LYS254 3.8 43.6 1.0 OE2 C:GLU71 4.1 55.5 1.0 OD1 C:ASP69 4.2 47.7 1.0 OD2 C:ASP98 4.2 53.9 1.0 O3G C:GTP501 4.3 39.2 1.0 CB C:GLN11 4.3 43.2 1.0 O2B C:GTP501 4.3 49.4 1.0 CG C:GLU71 4.4 54.6 1.0 N C:GLN11 4.4 40.7 1.0 CB C:ASP98 4.5 46.0 1.0 OD2 C:ASP69 4.5 43.4 1.0 O1A C:GTP501 4.6 47.4 1.0 PA C:GTP501 4.6 40.8 1.0 CG C:ASP98 4.7 48.8 1.0 CD C:GLU71 4.8 54.3 1.0 OE1 C:GLN11 4.8 54.5 1.0 CG C:ASP69 4.8 45.0 1.0 CE D:LYS254 4.9 46.6 1.0 CA C:GLN11 5.0 44.5 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z2856434826-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z2856434826-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:68.8 occ:1.00 O D:HOH602 1.9 60.3 1.0 OE1 D:GLN11 2.0 75.5 1.0 O1A D:GDP501 2.2 83.7 1.0 CD D:GLN11 3.1 77.5 1.0 PA D:GDP501 3.5 68.1 1.0 CB D:GLN11 3.9 71.4 1.0 O2A D:GDP501 3.9 65.1 1.0 CG D:GLN11 4.1 74.1 1.0 NE2 D:GLN11 4.1 77.4 1.0 O1B D:GDP501 4.2 68.0 1.0 O D:HOH620 4.4 71.8 1.0 O3A D:GDP501 4.5 66.6 1.0 OD1 D:ASN101 4.6 66.9 1.0 C5' D:GDP501 4.6 72.2 1.0 O5' D:GDP501 4.6 68.0 1.0 PB D:GDP501 4.8 66.0 1.0 C8 D:GDP501 4.9 66.3 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z2856434826-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z2856434826-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:100.2 occ:1.00 O1B F:ACP401 2.2 106.0 1.0 O3G F:ACP401 2.4 99.2 1.0 OE2 F:GLU331 2.6 94.7 1.0 OE1 F:GLU331 2.7 93.8 1.0 OD1 F:ASN333 2.8 86.1 1.0 CD F:GLU331 3.0 90.3 1.0 PB F:ACP401 3.5 112.3 1.0 NZ F:LYS74 3.6 103.7 1.0 PG F:ACP401 3.9 119.6 1.0 CG F:ASN333 4.0 83.2 1.0 O2B F:ACP401 4.0 110.3 1.0 C3B F:ACP401 4.4 114.2 1.0 CG F:GLU331 4.5 82.6 1.0 O1A F:ACP401 4.6 107.3 1.0 ND2 F:ASN333 4.6 83.6 1.0 O1G F:ACP401 4.7 108.8 1.0 CE F:LYS74 4.7 99.2 1.0 O3A F:ACP401 4.7 115.8 1.0 O2G F:ACP401 4.8 103.2 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