Magnesium in PDB 5s56: Tubulin-Z2856434783-Complex

The structure of Tubulin-Z2856434783-Complex, PDB code: 5s56 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)	62.66 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.56, 158.3, 180.09, 90, 90, 90
R / Rfree (%)	20.4 / 23.9

The structure of Tubulin-Z2856434783-Complex also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Fluorine	(F)	2 atoms

The binding sites of Magnesium atom in the Tubulin-Z2856434783-Complex (pdb code 5s56). 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-Z2856434783-Complex, PDB code: 5s56:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z2856434783-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z2856434783-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:61.8 occ:1.00 O A:HOH603 1.8 71.0 1.0 O1B A:GTP501 2.0 52.8 1.0 O A:HOH609 2.1 57.0 1.0 O A:HOH613 2.1 57.6 1.0 O1G A:GTP501 2.2 53.4 1.0 O A:HOH612 2.2 57.8 1.0 PB A:GTP501 3.2 55.6 1.0 PG A:GTP501 3.3 58.0 1.0 O3B A:GTP501 3.6 59.5 1.0 O3A A:GTP501 3.6 57.2 1.0 CB A:GLN11 3.7 52.8 1.0 O2G A:GTP501 4.0 58.4 1.0 N A:GLN11 4.0 57.0 1.0 NE2 A:GLN11 4.0 70.8 1.0 NZ B:LYS254 4.0 83.2 1.0 OD1 A:ASP69 4.1 62.7 1.0 OE1 A:GLU71 4.1 79.3 1.0 OD2 A:ASP69 4.1 66.1 1.0 O1A A:GTP501 4.4 52.4 1.0 CA A:GLN11 4.4 58.1 1.0 O2B A:GTP501 4.4 58.2 1.0 PA A:GTP501 4.5 57.8 1.0 CG A:ASP69 4.5 65.4 1.0 CB A:ASP98 4.5 65.8 1.0 O3G A:GTP501 4.6 57.1 1.0 OD2 A:ASP98 4.6 78.6 1.0 CG A:GLN11 4.9 60.2 1.0 CD A:GLN11 4.9 65.1 1.0 O2A A:GTP501 5.0 55.8 1.0 CE B:LYS254 5.0 75.4 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z2856434783-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z2856434783-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:40.6 occ:1.00 O B:HOH643 2.0 56.8 1.0 OE1 B:GLN11 2.1 57.1 1.0 O B:HOH636 2.1 51.8 1.0 O1A B:GDP501 2.3 49.9 1.0 O B:HOH614 2.5 53.3 1.0 O B:HOH627 2.6 50.0 1.0 CD B:GLN11 3.3 57.3 1.0 PA B:GDP501 3.6 47.4 1.0 O3A B:GDP501 4.0 50.5 1.0 OD2 B:ASP179 4.0 55.0 1.0 CB B:GLN11 4.0 50.0 1.0 CG B:GLN11 4.1 54.9 1.0 NE2 B:GLN11 4.2 65.0 1.0 OD1 B:ASN101 4.3 52.8 1.0 O1B B:GDP501 4.4 47.6 1.0 C5' B:GDP501 4.4 48.8 1.0 O C:HOH633 4.4 58.6 1.0 O5' B:GDP501 4.5 51.4 1.0 OE1 C:GLU254 4.6 64.7 1.0 O2A B:GDP501 4.6 45.3 1.0 PB B:GDP501 4.8 39.0 1.0 CG B:ASP179 4.9 57.4 1.0 C8 B:GDP501 5.0 54.2 1.0 ND2 B:ASN101 5.0 54.2 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z2856434783-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z2856434783-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:49.1 occ:1.00 O1G C:GTP501 1.8 47.1 1.0 O1B C:GTP501 2.0 49.9 1.0 O C:HOH654 2.0 52.8 1.0 O C:HOH696 2.1 48.6 1.0 O C:HOH634 2.2 51.1 1.0 O C:HOH632 2.2 53.3 1.0 PG C:GTP501 3.0 45.7 1.0 PB C:GTP501 3.0 43.6 1.0 O3B C:GTP501 3.4 55.0 1.0 O2G C:GTP501 3.5 48.8 1.0 O3A C:GTP501 3.6 55.2 1.0 NZ D:LYS254 3.8 61.7 1.0 OD1 C:ASP69 4.0 53.1 1.0 OD2 C:ASP98 4.2 58.8 1.0 CB C:GLN11 4.2 51.3 1.0 O3G C:GTP501 4.3 47.7 1.0 OD2 C:ASP69 4.3 51.7 1.0 O2B C:GTP501 4.3 52.1 1.0 N C:GLN11 4.4 45.5 1.0 CB C:ASP98 4.4 55.3 1.0 OE2 C:GLU71 4.4 63.0 1.0 CG C:GLU71 4.4 61.4 1.0 O1A C:GTP501 4.5 51.8 1.0 CG C:ASP69 4.6 54.2 1.0 PA C:GTP501 4.6 43.5 1.0 CG C:ASP98 4.7 56.1 1.0 O C:HOH620 4.8 72.5 1.0 CE D:LYS254 4.9 59.6 1.0 OE1 C:GLN11 4.9 62.3 1.0 CA C:GLN11 4.9 50.6 1.0 CD C:GLU71 4.9 59.3 1.0 OG1 C:THR145 4.9 51.6 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z2856434783-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z2856434783-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:83.6 occ:1.00 O D:HOH602 1.9 77.2 1.0 OE1 D:GLN11 2.0 84.1 1.0 O1A D:GDP501 2.4 93.3 1.0 CD D:GLN11 3.1 83.9 1.0 PA D:GDP501 3.7 79.5 1.0 CB D:GLN11 3.7 80.0 1.0 O1B D:GDP501 3.9 79.9 1.0 O2A D:GDP501 3.9 78.8 1.0 CG D:GLN11 4.0 81.2 1.0 NE2 D:GLN11 4.0 85.3 1.0 O D:HOH621 4.2 83.6 1.0 OD1 D:ASN101 4.6 85.7 1.0 PB D:GDP501 4.7 72.9 1.0 O3A D:GDP501 4.8 88.1 1.0 O5' D:GDP501 4.8 82.6 1.0 C5' D:GDP501 4.8 80.9 1.0 O3B D:GDP501 4.9 81.8 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z2856434783-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z2856434783-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:109.5 occ:1.00 O1B F:ACP401 2.1 118.5 1.0 O3G F:ACP401 2.4 112.5 1.0 OE2 F:GLU331 2.5 106.5 1.0 OE1 F:GLU331 2.7 107.0 1.0 OD1 F:ASN333 2.9 106.8 1.0 CD F:GLU331 3.0 103.3 1.0 NZ F:LYS74 3.4 113.8 1.0 PB F:ACP401 3.5 123.2 1.0 PG F:ACP401 3.9 129.8 1.0 O2B F:ACP401 3.9 125.4 1.0 CG F:ASN333 4.0 100.4 1.0 C3B F:ACP401 4.3 121.9 1.0 CG F:GLU331 4.5 92.9 1.0 ND2 F:ASN333 4.5 97.7 1.0 O1G F:ACP401 4.6 121.5 1.0 CE F:LYS74 4.6 109.9 1.0 O3A F:ACP401 4.6 120.9 1.0 O1A F:ACP401 4.6 112.7 1.0 O2G F:ACP401 4.9 113.9 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