Magnesium in PDB 5s4y: Tubulin-Z2856434857-Complex

The structure of Tubulin-Z2856434857-Complex, PDB code: 5s4y 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)	78.89 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.14, 157.78, 178.7, 90, 90, 90
R / Rfree (%)	20 / 23.8

The structure of Tubulin-Z2856434857-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z2856434857-Complex (pdb code 5s4y). 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-Z2856434857-Complex, PDB code: 5s4y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z2856434857-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z2856434857-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:59.4 occ:1.00 O A:HOH616 1.9 62.7 1.0 O A:HOH611 2.1 61.6 1.0 O1G A:GTP501 2.1 50.9 1.0 O A:HOH607 2.1 63.1 1.0 O A:HOH628 2.2 58.5 1.0 O1B A:GTP501 2.3 54.5 1.0 PG A:GTP501 3.3 60.8 1.0 PB A:GTP501 3.4 57.0 1.0 OE1 A:GLU71 3.7 74.4 1.0 O3B A:GTP501 3.7 67.1 1.0 O2G A:GTP501 3.8 60.6 1.0 O3A A:GTP501 3.9 59.3 1.0 CB A:GLN11 4.0 56.8 1.0 NZ B:LYS254 4.0 69.7 1.0 OD1 A:ASP69 4.1 67.9 1.0 OD2 A:ASP69 4.1 62.6 1.0 CB A:ASP98 4.2 65.3 1.0 NE2 A:GLN11 4.2 70.1 1.0 OD2 A:ASP98 4.2 72.4 1.0 N A:GLN11 4.4 59.5 1.0 CG A:ASP69 4.5 67.2 1.0 O3G A:GTP501 4.6 54.7 1.0 CG A:ASP98 4.6 67.9 1.0 O1A A:GTP501 4.7 59.3 1.0 O2B A:GTP501 4.7 61.0 1.0 CA A:GLN11 4.8 61.0 1.0 CD A:GLU71 4.9 78.9 1.0 PA A:GTP501 4.9 59.3 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z2856434857-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z2856434857-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:57.9 occ:1.00 O B:HOH610 2.0 73.6 1.0 O1A B:GDP501 2.2 61.9 1.0 O B:HOH626 2.3 64.5 1.0 OE1 B:GLN11 2.3 74.2 1.0 O C:HOH652 2.4 53.4 1.0 CD B:GLN11 3.5 61.7 1.0 PA B:GDP501 3.5 59.0 1.0 OD2 B:ASP179 3.9 71.6 1.0 O3A B:GDP501 3.9 60.8 1.0 OD1 B:ASN101 4.1 65.7 1.0 CB B:GLN11 4.1 54.0 1.0 C5' B:GDP501 4.3 64.8 1.0 CG B:GLN11 4.3 59.1 1.0 O1B B:GDP501 4.3 54.7 1.0 O5' B:GDP501 4.4 55.8 1.0 NE2 B:GLN11 4.5 73.7 1.0 OE1 C:GLU254 4.6 80.6 1.0 O2A B:GDP501 4.6 57.1 1.0 PB B:GDP501 4.8 56.7 1.0 C8 B:GDP501 4.9 60.0 1.0 ND2 B:ASN101 4.9 65.7 1.0 CG B:ASN101 4.9 63.1 1.0 CG B:ASP179 4.9 73.8 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z2856434857-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z2856434857-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:61.2 occ:1.00 O1G C:GTP501 1.9 53.8 1.0 O C:HOH635 2.0 54.3 1.0 O C:HOH644 2.0 58.1 1.0 O C:HOH655 2.0 55.3 1.0 O C:HOH619 2.0 55.6 1.0 O1B C:GTP501 2.1 56.7 1.0 PG C:GTP501 3.1 56.8 1.0 PB C:GTP501 3.2 56.2 1.0 O3B C:GTP501 3.5 61.9 1.0 O2G C:GTP501 3.6 55.1 1.0 O3A C:GTP501 3.7 60.5 1.0 NZ D:LYS254 3.8 62.9 1.0 OD2 C:ASP98 4.1 69.6 1.0 OD1 C:ASP69 4.1 63.6 1.0 OE2 C:GLU71 4.2 67.3 1.0 CB C:GLN11 4.2 53.5 1.0 CG C:GLU71 4.3 65.4 1.0 OD2 C:ASP69 4.3 58.7 1.0 CB C:ASP98 4.3 58.3 1.0 O3G C:GTP501 4.4 50.0 1.0 O2B C:GTP501 4.5 60.5 1.0 N C:GLN11 4.5 53.1 1.0 O1A C:GTP501 4.6 58.1 1.0 CG C:ASP98 4.7 61.5 1.0 CG C:ASP69 4.7 63.9 1.0 OE1 C:GLN11 4.7 70.5 1.0 PA C:GTP501 4.7 54.9 1.0 CD C:GLU71 4.8 64.3 1.0 CE D:LYS254 4.9 61.6 1.0 CA C:GLN11 5.0 55.4 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z2856434857-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z2856434857-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:77.3 occ:1.00 OE1 D:GLN11 2.0 84.0 1.0 O D:HOH601 2.0 80.0 1.0 O1A D:GDP501 2.4 103.5 1.0 CD D:GLN11 3.2 88.0 1.0 PA D:GDP501 3.7 80.4 1.0 NE2 D:GLN11 4.0 88.6 1.0 O2A D:GDP501 4.0 77.6 1.0 CB D:GLN11 4.2 78.8 1.0 CG D:GLN11 4.2 78.7 1.0 C5' D:GDP501 4.3 81.9 1.0 O5' D:GDP501 4.5 81.8 1.0 OD1 D:ASN101 4.6 92.5 1.0 C8 D:GDP501 4.7 78.3 1.0 O1B D:GDP501 4.8 77.0 1.0 O3A D:GDP501 5.0 89.1 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z2856434857-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z2856434857-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:92.4 occ:1.00 O3G F:ACP401 2.0 106.0 1.0 O1B F:ACP401 2.2 120.5 1.0 OE2 F:GLU331 2.3 104.9 1.0 OD1 F:ASN333 2.5 105.0 1.0 OE1 F:GLU331 2.8 106.3 1.0 CD F:GLU331 2.9 100.8 1.0 PB F:ACP401 3.5 119.9 1.0 PG F:ACP401 3.5 131.5 1.0 CG F:ASN333 3.5 98.0 1.0 NZ F:LYS74 3.9 107.5 1.0 ND2 F:ASN333 4.1 97.6 1.0 O2B F:ACP401 4.1 121.7 1.0 C3B F:ACP401 4.2 119.0 1.0 CG F:GLU331 4.4 90.6 1.0 O1G F:ACP401 4.4 116.5 1.0 O2G F:ACP401 4.5 106.7 1.0 O1A F:ACP401 4.5 111.6 1.0 O3A F:ACP401 4.8 117.5 1.0 CB F:ASN333 4.8 89.1 1.0 CE F:LYS74 4.9 106.2 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