Magnesium in PDB 5s5u: Tubulin-Z1124201124-Complex

The structure of Tubulin-Z1124201124-Complex, PDB code: 5s5u 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)	79.33 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.78, 158.65, 178.88, 90, 90, 90
R / Rfree (%)	21 / 25.6

The structure of Tubulin-Z1124201124-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z1124201124-Complex (pdb code 5s5u). 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-Z1124201124-Complex, PDB code: 5s5u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z1124201124-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z1124201124-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:59.0 occ:1.00 O A:HOH611 1.9 62.8 1.0 O A:HOH605 2.1 69.4 1.0 O1G A:GTP501 2.1 56.8 1.0 O A:HOH616 2.2 57.9 1.0 O1B A:GTP501 2.2 55.0 1.0 O A:HOH630 2.2 57.9 1.0 PB A:GTP501 3.4 57.0 1.0 PG A:GTP501 3.4 63.6 1.0 OE1 A:GLU71 3.5 76.9 1.0 O3B A:GTP501 3.7 70.4 1.0 CB A:GLN11 3.9 64.4 1.0 NZ B:LYS254 3.9 75.8 1.0 O3A A:GTP501 4.0 62.2 1.0 O2G A:GTP501 4.0 59.4 1.0 OD2 A:ASP69 4.0 67.6 1.0 OD1 A:ASP69 4.0 67.3 1.0 NE2 A:GLN11 4.2 71.0 1.0 N A:GLN11 4.3 58.3 1.0 CB A:ASP98 4.4 69.1 1.0 CG A:ASP69 4.5 69.3 1.0 O1A A:GTP501 4.5 61.9 1.0 OD2 A:ASP98 4.5 75.2 1.0 O3G A:GTP501 4.6 61.2 1.0 O2B A:GTP501 4.6 63.3 1.0 CA A:GLN11 4.6 61.8 1.0 CD A:GLU71 4.7 84.2 1.0 PA A:GTP501 4.8 62.1 1.0 CG A:ASP98 4.8 72.3 1.0 CG A:GLN11 4.9 65.7 1.0 CD A:GLN11 4.9 69.3 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z1124201124-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z1124201124-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:56.7 occ:1.00 O B:HOH633 1.9 66.0 1.0 OE1 B:GLN11 1.9 72.6 1.0 O C:HOH637 2.3 50.2 1.0 O B:HOH643 2.3 57.6 1.0 O1A B:GDP501 2.4 58.7 1.0 CD B:GLN11 3.1 70.6 1.0 PA B:GDP501 3.8 52.7 1.0 CB B:GLN11 4.0 61.4 1.0 OD2 B:ASP179 4.0 63.9 1.0 CG B:GLN11 4.1 64.7 1.0 NE2 B:GLN11 4.1 74.1 1.0 O3A B:GDP501 4.3 56.4 1.0 O C:HOH611 4.3 61.9 1.0 OD1 B:ASN101 4.4 57.5 1.0 OE1 C:GLU254 4.5 64.3 1.0 C5' B:GDP501 4.6 58.5 1.0 O1B B:GDP501 4.7 54.5 1.0 O5' B:GDP501 4.7 57.4 1.0 O2A B:GDP501 4.7 51.5 1.0 C8 B:GDP501 4.9 57.6 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z1124201124-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z1124201124-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:59.4 occ:1.00 O C:HOH620 2.0 59.4 1.0 O C:HOH654 2.0 61.0 1.0 O1B C:GTP501 2.0 54.9 1.0 O C:HOH615 2.1 58.6 1.0 O C:HOH616 2.1 58.8 1.0 O1G C:GTP501 2.2 50.8 1.0 PB C:GTP501 3.3 54.5 1.0 PG C:GTP501 3.4 59.2 1.0 O3B C:GTP501 3.7 65.5 1.0 NZ D:LYS254 3.8 62.8 1.0 O3A C:GTP501 3.8 61.4 1.0 O2G C:GTP501 3.9 58.0 1.0 OD1 C:ASP69 4.0 61.6 1.0 OE2 C:GLU71 4.0 72.3 1.0 OD2 C:ASP69 4.1 61.8 1.0 CB C:GLN11 4.1 57.5 1.0 CG C:GLU71 4.1 68.9 1.0 OD2 C:ASP98 4.2 66.4 1.0 N C:GLN11 4.3 57.3 1.0 O C:HOH659 4.5 77.6 1.0 O2B C:GTP501 4.5 58.0 1.0 CG C:ASP69 4.5 61.5 1.0 CB C:ASP98 4.5 59.1 1.0 OE1 C:GLN11 4.6 68.5 1.0 CD C:GLU71 4.6 68.4 1.0 O1A C:GTP501 4.6 60.7 1.0 O3G C:GTP501 4.7 57.6 1.0 PA C:GTP501 4.8 50.9 1.0 CG C:ASP98 4.8 61.8 1.0 CA C:GLN11 4.8 57.9 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z1124201124-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z1124201124-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:91.2 occ:1.00 OE1 D:GLN11 2.3 93.6 1.0 O1A D:GDP501 2.3 98.2 1.0 CD D:GLN11 3.3 96.2 1.0 PA D:GDP501 3.7 86.0 1.0 CB D:GLN11 3.9 93.2 1.0 O2A D:GDP501 4.0 83.2 1.0 NE2 D:GLN11 4.2 102.0 1.0 CG D:GLN11 4.2 93.5 1.0 O1B D:GDP501 4.2 90.5 1.0 OD1 D:ASN101 4.3 89.1 1.0 O D:HOH608 4.7 85.7 1.0 C5' D:GDP501 4.7 86.4 1.0 O5' D:GDP501 4.7 88.3 1.0 O3A D:GDP501 4.7 93.9 1.0 O3B D:GDP501 4.7 92.0 1.0 PB D:GDP501 4.8 91.5 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z1124201124-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z1124201124-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:114.9 occ:1.00 OE2 F:GLU331 2.2 124.7 1.0 O1B F:ACP401 2.4 132.3 1.0 O3G F:ACP401 2.6 126.4 1.0 CD F:GLU331 3.0 124.6 1.0 OE1 F:GLU331 3.1 130.3 1.0 OD1 F:ASN333 3.3 118.0 1.0 PB F:ACP401 3.6 134.4 1.0 O2B F:ACP401 3.9 136.2 1.0 NZ F:LYS74 3.9 137.7 1.0 PG F:ACP401 4.1 138.5 1.0 CG F:ASN333 4.4 110.8 1.0 CG F:GLU331 4.5 114.6 1.0 C3B F:ACP401 4.6 134.3 1.0 O1A F:ACP401 4.8 128.2 1.0 O3A F:ACP401 4.9 133.2 1.0 O1G F:ACP401 4.9 134.3 1.0 ND2 F:ASN333 5.0 109.5 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