Magnesium in PDB 5s51: Tubulin-Z1251207602-Complex

The structure of Tubulin-Z1251207602-Complex, PDB code: 5s51 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)	78.73 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.42, 157.45, 179.36, 90, 90, 90
R / Rfree (%)	20.3 / 24.5

The structure of Tubulin-Z1251207602-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z1251207602-Complex (pdb code 5s51). 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-Z1251207602-Complex, PDB code: 5s51:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z1251207602-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z1251207602-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:59.3 occ:1.00 O A:HOH610 1.9 56.7 1.0 O A:HOH618 2.0 59.2 1.0 O A:HOH616 2.0 57.3 1.0 O1G A:GTP501 2.2 50.9 1.0 O1B A:GTP501 2.3 55.2 1.0 O A:HOH615 2.3 62.1 1.0 PG A:GTP501 3.3 58.3 1.0 PB A:GTP501 3.4 53.1 1.0 O3B A:GTP501 3.7 65.5 1.0 OE1 A:GLU71 3.8 69.4 1.0 O2G A:GTP501 3.8 56.3 1.0 O3A A:GTP501 3.8 56.9 1.0 CB A:GLN11 3.9 53.7 1.0 NE2 A:GLN11 3.9 63.9 1.0 NZ B:LYS254 4.0 65.7 1.0 OD1 A:ASP69 4.1 66.8 1.0 OD2 A:ASP69 4.2 63.2 1.0 CB A:ASP98 4.4 60.5 1.0 N A:GLN11 4.4 57.4 1.0 O1A A:GTP501 4.6 53.3 1.0 O3G A:GTP501 4.6 55.4 1.0 CG A:ASP69 4.6 66.1 1.0 O2B A:GTP501 4.7 58.0 1.0 CA A:GLN11 4.7 59.1 1.0 OD2 A:ASP98 4.8 71.6 1.0 PA A:GTP501 4.8 58.2 1.0 CD A:GLN11 4.9 64.8 1.0 CG A:ASP98 4.9 64.8 1.0 CG A:GLN11 4.9 56.4 1.0 CD A:GLU71 4.9 72.2 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z1251207602-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z1251207602-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:52.4 occ:1.00 O B:HOH601 1.9 67.4 1.0 O1A B:GDP501 2.2 53.3 1.0 O B:HOH611 2.3 64.2 1.0 OE1 B:GLN11 2.3 61.1 1.0 O B:HOH617 2.3 61.0 1.0 O C:HOH641 2.4 58.1 1.0 PA B:GDP501 3.5 51.6 1.0 CD B:GLN11 3.5 60.6 1.0 O3A B:GDP501 3.8 55.1 1.0 OD1 B:ASN101 4.0 58.9 1.0 CB B:GLN11 4.1 53.1 1.0 O C:HOH611 4.1 65.8 1.0 OD2 B:ASP179 4.1 60.3 1.0 O1B B:GDP501 4.2 52.5 1.0 O5' B:GDP501 4.3 52.3 1.0 C5' B:GDP501 4.3 55.7 1.0 CG B:GLN11 4.3 56.3 1.0 NE2 B:GLN11 4.5 63.6 1.0 OE1 C:GLU254 4.5 74.6 1.0 O2A B:GDP501 4.6 50.0 1.0 PB B:GDP501 4.6 54.7 1.0 CG B:ASN101 4.8 55.0 1.0 ND2 B:ASN101 4.9 61.6 1.0 O B:HOH607 5.0 55.8 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z1251207602-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z1251207602-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:61.7 occ:1.00 O1G C:GTP501 1.8 48.7 1.0 O C:HOH609 1.9 55.4 1.0 O1B C:GTP501 2.0 52.0 1.0 O C:HOH651 2.1 54.4 1.0 O C:HOH672 2.1 56.5 1.0 O C:HOH625 2.2 59.4 1.0 PG C:GTP501 3.0 56.9 1.0 PB C:GTP501 3.1 52.1 1.0 O3B C:GTP501 3.4 59.5 1.0 O2G C:GTP501 3.6 54.5 1.0 O3A C:GTP501 3.7 57.3 1.0 NZ D:LYS254 3.7 63.4 1.0 OD2 C:ASP98 4.0 60.2 1.0 OD1 C:ASP69 4.1 60.3 1.0 OE2 C:GLU71 4.2 67.2 1.0 O3G C:GTP501 4.2 50.0 1.0 CG C:GLU71 4.3 64.3 1.0 CB C:GLN11 4.4 53.3 1.0 OD2 C:ASP69 4.4 55.4 1.0 O2B C:GTP501 4.4 59.0 1.0 CB C:ASP98 4.5 58.9 1.0 N C:GLN11 4.5 53.3 1.0 O1A C:GTP501 4.6 55.4 1.0 CG C:ASP98 4.7 59.9 1.0 O C:HOH622 4.7 70.6 1.0 CG C:ASP69 4.7 62.1 1.0 PA C:GTP501 4.7 51.2 1.0 CE D:LYS254 4.7 60.4 1.0 OE1 C:GLN11 4.8 69.5 1.0 CD C:GLU71 4.8 65.9 1.0 OG1 C:THR145 5.0 55.2 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z1251207602-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z1251207602-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:82.9 occ:1.00 O D:HOH602 2.0 70.8 1.0 OE1 D:GLN11 2.1 87.2 1.0 O1A D:GDP501 2.4 99.2 1.0 CD D:GLN11 3.1 86.8 1.0 CB D:GLN11 3.5 82.2 1.0 PA D:GDP501 3.6 81.5 1.0 O2A D:GDP501 3.8 75.8 1.0 O1B D:GDP501 3.8 79.8 1.0 CG D:GLN11 3.9 87.6 1.0 NE2 D:GLN11 4.1 91.1 1.0 O3B D:GDP501 4.1 96.0 1.0 PB D:GDP501 4.4 81.7 1.0 OD1 D:ASN101 4.4 85.9 1.0 O3A D:GDP501 4.5 84.0 1.0 OE2 D:GLU71 4.8 125.7 1.0 O5' D:GDP501 4.9 84.2 1.0 CA D:GLN11 4.9 87.8 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z1251207602-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z1251207602-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:106.9 occ:1.00 O1B F:ACP401 2.2 126.5 1.0 OE2 F:GLU331 2.6 111.2 1.0 O3G F:ACP401 2.8 113.7 1.0 OE1 F:GLU331 2.9 114.8 1.0 CD F:GLU331 3.1 109.9 1.0 OD1 F:ASN333 3.3 109.4 1.0 NZ F:LYS74 3.5 119.1 1.0 PB F:ACP401 3.5 130.3 1.0 O2B F:ACP401 3.9 134.6 1.0 PG F:ACP401 4.3 132.0 1.0 CG F:ASN333 4.4 101.4 1.0 CG F:GLU331 4.6 98.3 1.0 C3B F:ACP401 4.6 129.3 1.0 O3A F:ACP401 4.6 128.8 1.0 CE F:LYS74 4.7 118.7 1.0 O1A F:ACP401 4.7 118.7 1.0 ND2 F:ASN333 4.9 99.5 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