Magnesium in PDB 5s4x: Tubulin-Z2856434917-Complex

The structure of Tubulin-Z2856434917-Complex, PDB code: 5s4x 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)	72.84 / 2.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.11, 159.22, 180.52, 90, 90, 90
R / Rfree (%)	20.2 / 24.5

The structure of Tubulin-Z2856434917-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z2856434917-Complex (pdb code 5s4x). 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-Z2856434917-Complex, PDB code: 5s4x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z2856434917-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z2856434917-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:64.8 occ:1.00 O A:HOH619 2.0 71.2 1.0 O A:HOH609 2.0 64.3 1.0 O A:HOH613 2.1 66.0 1.0 O1B A:GTP501 2.2 65.8 1.0 O1G A:GTP501 2.3 61.0 1.0 O A:HOH602 2.5 73.6 1.0 PB A:GTP501 3.3 59.9 1.0 PG A:GTP501 3.4 64.9 1.0 OE1 A:GLU71 3.5 80.6 1.0 O3B A:GTP501 3.7 73.8 1.0 O3A A:GTP501 3.8 69.7 1.0 CB A:GLN11 3.9 63.1 1.0 O2G A:GTP501 4.0 65.0 1.0 NZ B:LYS254 4.0 70.6 1.0 NE2 A:GLN11 4.1 76.6 1.0 OD1 A:ASP69 4.2 69.7 1.0 N A:GLN11 4.3 68.1 1.0 OD2 A:ASP69 4.4 72.8 1.0 CB A:ASP98 4.5 70.9 1.0 O1A A:GTP501 4.5 70.1 1.0 O2B A:GTP501 4.6 71.7 1.0 O3G A:GTP501 4.7 64.3 1.0 CA A:GLN11 4.7 69.3 1.0 OD2 A:ASP98 4.7 76.0 1.0 PA A:GTP501 4.7 70.0 1.0 CD A:GLU71 4.8 81.1 1.0 CG A:ASP69 4.8 72.0 1.0 CD A:GLN11 4.9 75.5 1.0 CG A:GLN11 5.0 68.9 1.0 CG A:ASP98 5.0 73.6 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z2856434917-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z2856434917-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:60.6 occ:1.00 O B:HOH601 1.8 71.3 1.0 O B:HOH615 2.1 72.9 1.0 O C:HOH645 2.2 64.0 1.0 O1A B:GDP501 2.3 66.2 1.0 OE1 B:GLN11 2.6 72.7 1.0 O B:HOH614 2.7 73.7 1.0 PA B:GDP501 3.5 60.7 1.0 OD1 B:ASN101 3.6 71.9 1.0 OD2 B:ASP179 3.7 68.1 1.0 O3A B:GDP501 3.7 65.5 1.0 CD B:GLN11 3.8 69.4 1.0 C5' B:GDP501 4.3 63.6 1.0 O1B B:GDP501 4.3 63.5 1.0 O5' B:GDP501 4.3 60.6 1.0 OE1 C:GLU254 4.4 76.2 1.0 CG B:ASN101 4.4 65.7 1.0 ND2 B:ASN101 4.5 64.0 1.0 CB B:GLN11 4.5 59.7 1.0 PB B:GDP501 4.6 60.6 1.0 O2A B:GDP501 4.6 59.0 1.0 NE2 B:GLN11 4.7 77.1 1.0 CG B:ASP179 4.7 74.0 1.0 CG B:GLN11 4.7 63.8 1.0 OE2 C:GLU254 4.8 79.3 1.0 CD C:GLU254 5.0 75.7 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z2856434917-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z2856434917-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:72.4 occ:1.00 O C:HOH601 1.9 62.1 1.0 O C:HOH620 2.2 60.9 1.0 O1G C:GTP501 2.3 54.4 1.0 O C:HOH605 2.4 57.9 1.0 OD2 C:ASP98 3.1 70.4 1.0 NZ D:LYS254 3.1 76.4 1.0 O1B C:GTP501 3.1 61.8 1.0 OE2 C:GLU71 3.2 82.2 1.0 CG C:GLU71 3.7 68.8 1.0 PG C:GTP501 3.7 60.7 1.0 CG D:ASN249 3.8 138.5 1.0 CD C:GLU71 3.9 72.1 1.0 OD1 D:ASN249 3.9 141.4 1.0 CB D:ASN249 3.9 135.1 1.0 CG C:ASP98 4.0 66.0 1.0 CB C:ASP98 4.1 62.1 1.0 O2G C:GTP501 4.1 62.4 1.0 PB C:GTP501 4.3 57.2 1.0 ND2 D:ASN249 4.3 137.4 1.0 CE D:LYS254 4.4 61.0 1.0 O3B C:GTP501 4.4 69.2 1.0 OE1 C:GLN11 4.6 79.1 1.0 OD2 C:ASP69 4.7 64.4 1.0 O3A C:GTP501 4.7 65.2 1.0 OD1 C:ASP69 4.8 63.5 1.0 O3G C:GTP501 4.8 63.0 1.0 CB C:GLN11 4.9 56.8 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z2856434917-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z2856434917-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:89.4 occ:1.00 O D:HOH604 2.1 76.5 1.0 O1A D:GDP501 2.4 104.0 1.0 OE1 D:GLN11 2.4 98.1 1.0 CD D:GLN11 3.5 102.4 1.0 PA D:GDP501 3.7 89.0 1.0 O1B D:GDP501 3.8 94.4 1.0 CB D:GLN11 3.9 96.9 1.0 O2A D:GDP501 4.0 90.1 1.0 OD1 D:ASN101 4.1 87.3 1.0 CG D:GLN11 4.3 99.3 1.0 NE2 D:GLN11 4.4 102.4 1.0 PB D:GDP501 4.6 90.9 1.0 O3B D:GDP501 4.6 88.2 1.0 O3A D:GDP501 4.7 95.7 1.0 O D:HOH607 4.7 81.4 1.0 O5' D:GDP501 4.8 89.2 1.0 C5' D:GDP501 4.9 87.7 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z2856434917-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z2856434917-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:137.7 occ:1.00 O3G F:ACP401 2.2 153.3 1.0 OE2 F:GLU331 2.6 135.9 1.0 OD1 F:ASN333 2.6 128.7 1.0 O1B F:ACP401 2.8 161.1 1.0 CD F:GLU331 3.4 135.5 1.0 OE1 F:GLU331 3.5 138.5 1.0 PG F:ACP401 3.7 166.5 1.0 CG F:ASN333 3.7 122.2 1.0 PB F:ACP401 3.9 164.6 1.0 NZ F:LYS74 4.1 134.3 1.0 O1G F:ACP401 4.2 159.6 1.0 O2B F:ACP401 4.2 164.1 1.0 ND2 F:ASN333 4.3 119.8 1.0 C3B F:ACP401 4.5 165.2 1.0 O2G F:ACP401 4.8 151.4 1.0 CG F:GLU331 4.9 124.5 1.0 CB F:ASN333 5.0 106.5 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