Magnesium in PDB 5s57: Tubulin-Z2856434883-Complex

The structure of Tubulin-Z2856434883-Complex, PDB code: 5s57 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)	63.38 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.68, 159.27, 180.71, 90, 90, 90
R / Rfree (%)	20.7 / 24.5

The structure of Tubulin-Z2856434883-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z2856434883-Complex (pdb code 5s57). 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-Z2856434883-Complex, PDB code: 5s57:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z2856434883-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z2856434883-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:69.6 occ:1.00 O A:HOH608 2.0 71.7 1.0 O A:HOH606 2.0 68.8 1.0 O A:HOH626 2.0 62.8 1.0 O1G A:GTP501 2.1 64.0 1.0 O1B A:GTP501 2.1 63.5 1.0 PB A:GTP501 3.3 58.7 1.0 PG A:GTP501 3.3 63.9 1.0 OE1 A:GLU71 3.6 97.7 1.0 O3B A:GTP501 3.6 75.9 1.0 O3A A:GTP501 3.8 65.7 1.0 CB A:GLN11 3.9 64.0 1.0 O2G A:GTP501 4.0 66.7 1.0 NZ B:LYS254 4.1 80.3 1.0 OD1 A:ASP69 4.2 72.5 1.0 OE1 A:GLN11 4.3 76.2 1.0 N A:GLN11 4.3 64.4 1.0 OD2 A:ASP98 4.4 83.1 1.0 O1A A:GTP501 4.4 60.0 1.0 OD2 A:ASP69 4.4 83.7 1.0 O3G A:GTP501 4.5 66.5 1.0 O2B A:GTP501 4.5 66.7 1.0 CB A:ASP98 4.6 79.0 1.0 PA A:GTP501 4.7 62.6 1.0 CA A:GLN11 4.7 66.8 1.0 CD A:GLU71 4.7 102.9 1.0 CG A:ASP69 4.8 80.4 1.0 CG A:ASP98 4.8 77.2 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z2856434883-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z2856434883-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:55.9 occ:1.00 O B:HOH601 1.8 64.6 1.0 O C:HOH669 2.1 59.1 1.0 O B:HOH610 2.3 58.4 1.0 O1A B:GDP501 2.4 64.5 1.0 OE1 B:GLN11 2.6 69.2 1.0 OD2 B:ASP179 3.4 69.3 1.0 OD1 B:ASN101 3.4 72.0 1.0 PA B:GDP501 3.8 61.4 1.0 CD B:GLN11 3.8 68.4 1.0 OE1 C:GLU254 4.2 69.2 1.0 C5' B:GDP501 4.3 62.0 1.0 CG B:ASN101 4.3 66.1 1.0 O3A B:GDP501 4.3 63.1 1.0 ND2 B:ASN101 4.4 61.1 1.0 CG B:ASP179 4.4 69.6 1.0 O5' B:GDP501 4.5 55.6 1.0 O1B B:GDP501 4.5 57.3 1.0 NE2 B:GLN11 4.6 67.2 1.0 CB B:GLN11 4.7 51.9 1.0 OE2 C:GLU254 4.7 70.9 1.0 CD C:GLU254 4.8 67.7 1.0 CG B:GLN11 4.8 58.2 1.0 CB B:ASP179 4.8 68.9 1.0 O2A B:GDP501 4.8 55.9 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z2856434883-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z2856434883-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:57.2 occ:1.00 O C:HOH661 2.0 54.3 1.0 O C:HOH624 2.0 51.0 1.0 O C:HOH611 2.0 51.1 1.0 O C:HOH629 2.0 55.1 1.0 O1G C:GTP501 2.1 50.5 1.0 O1B C:GTP501 2.1 56.8 1.0 PB C:GTP501 3.3 50.3 1.0 PG C:GTP501 3.3 58.4 1.0 O3B C:GTP501 3.7 60.0 1.0 O3A C:GTP501 3.7 61.0 1.0 O2G C:GTP501 3.8 60.4 1.0 NZ D:LYS254 4.0 63.5 1.0 OE2 C:GLU71 4.0 69.0 1.0 CB C:GLN11 4.1 50.7 1.0 OD1 C:ASP69 4.1 57.2 1.0 OD2 C:ASP69 4.2 59.6 1.0 CG C:GLU71 4.3 61.5 1.0 NE2 C:GLN11 4.4 70.0 1.0 N C:GLN11 4.4 55.2 1.0 OD2 C:ASP98 4.5 61.3 1.0 O2B C:GTP501 4.5 59.4 1.0 O3G C:GTP501 4.5 61.8 1.0 O1A C:GTP501 4.6 57.4 1.0 CB C:ASP98 4.6 58.8 1.0 CG C:ASP69 4.6 59.5 1.0 CD C:GLU71 4.7 64.8 1.0 PA C:GTP501 4.7 53.4 1.0 CG C:ASP98 4.8 60.4 1.0 CA C:GLN11 4.8 55.8 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z2856434883-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z2856434883-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:87.2 occ:1.00 O D:HOH602 1.9 82.8 1.0 OE1 D:GLN11 2.0 87.6 1.0 O1A D:GDP501 2.7 98.9 1.0 CD D:GLN11 3.2 90.8 1.0 PA D:GDP501 4.0 85.4 1.0 NE2 D:GLN11 4.0 89.7 1.0 O2A D:GDP501 4.1 78.8 1.0 CG D:GLN11 4.2 92.1 1.0 CB D:GLN11 4.3 87.4 1.0 C5' D:GDP501 4.5 82.7 1.0 C8 D:GDP501 4.6 78.1 1.0 O5' D:GDP501 4.8 87.0 1.0 OD1 D:ASN101 4.9 88.1 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z2856434883-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z2856434883-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:125.4 occ:1.00 O3G F:ACP401 2.0 131.0 1.0 OE2 F:GLU331 2.1 119.1 1.0 O1B F:ACP401 2.4 135.0 1.0 OD1 F:ASN333 2.6 121.6 1.0 CD F:GLU331 3.0 118.6 1.0 OE1 F:GLU331 3.2 121.0 1.0 PG F:ACP401 3.5 145.9 1.0 CG F:ASN333 3.5 115.3 1.0 PB F:ACP401 3.7 147.0 1.0 ND2 F:ASN333 3.8 113.5 1.0 NZ F:LYS74 4.2 131.4 1.0 O1G F:ACP401 4.2 141.1 1.0 C3B F:ACP401 4.3 142.6 1.0 O2B F:ACP401 4.3 135.0 1.0 CG F:GLU331 4.4 106.7 1.0 O2G F:ACP401 4.5 126.2 1.0 O1A F:ACP401 4.7 127.5 1.0 CB F:ASN333 4.8 102.6 1.0 O3A F:ACP401 4.9 143.4 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