Magnesium in PDB 5j2u: Tubulin-Mmaf Complex

The structure of Tubulin-Mmaf Complex, PDB code: 5j2u was solved by A.B.Waight, K.Bargsten, S.Doronina, M.O.Steinmetz, D.Sussman, A.E.Prota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.65 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.567, 155.390, 182.524, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25

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

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Tubulin-Mmaf Complex (pdb code 5j2u). 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-Mmaf Complex, PDB code: 5j2u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Mmaf Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:55.6 occ:1.00 O1B A:GTP501 2.2 57.0 1.0 O2G A:GTP501 2.3 58.4 1.0 OE1 A:GLU71 2.5 80.2 1.0 O1G A:GTP501 3.1 52.7 1.0 PG A:GTP501 3.1 52.7 1.0 HB2 A:GLN11 3.2 80.2 1.0 PB A:GTP501 3.4 56.6 1.0 HZ3 B:LYS254 3.5 68.8 1.0 HB3 A:GLU71 3.6 90.6 1.0 O3B A:GTP501 3.6 67.4 1.0 CD A:GLU71 3.7 87.5 1.0 OD1 A:ASP69 3.8 60.8 1.0 H A:GLN11 3.8 70.7 1.0 HB3 A:GLN11 3.9 80.2 1.0 OE1 A:GLN11 4.0 87.3 1.0 CB A:GLN11 4.0 66.8 1.0 O3A A:GTP501 4.0 65.9 1.0 HB2 A:ASP98 4.0 65.4 1.0 OD2 A:ASP69 4.1 70.1 1.0 HZ1 B:LYS254 4.3 68.8 1.0 NZ B:LYS254 4.3 57.3 1.0 CB A:GLU71 4.3 75.5 1.0 OD2 A:ASP98 4.3 53.3 1.0 HB2 A:GLU71 4.4 90.6 1.0 HG1 A:THR145 4.4 72.4 1.0 OE2 A:GLU71 4.4 0.9 1.0 CG A:ASP69 4.4 63.4 1.0 N A:GLN11 4.5 59.0 1.0 O3G A:GTP501 4.5 55.3 1.0 HZ2 B:LYS254 4.6 68.8 1.0 CG A:GLU71 4.6 72.1 1.0 O2B A:GTP501 4.6 70.0 1.0 CB A:ASP98 4.8 54.5 1.0 CA A:GLN11 4.8 66.6 1.0 CG A:ASP98 4.8 55.6 1.0 OG1 A:THR145 4.9 60.4 1.0 HB3 A:ASP98 4.9 65.4 1.0 CD A:GLN11 4.9 71.4 1.0 O1A A:GTP501 4.9 62.5 1.0 HG21 A:VAL74 4.9 83.4 1.0 HB A:THR145 4.9 67.4 1.0 HG23 A:VAL74 4.9 83.4 1.0 HA A:GLN11 4.9 79.9 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Mmaf Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:74.2 occ:1.00 O B:HOH618 2.6 47.0 1.0 O B:HOH632 2.7 42.0 1.0 O B:HOH641 2.7 57.8 1.0 OE1 B:GLN11 3.2 70.2 1.0 O B:HOH651 3.2 53.2 1.0 OE1 C:GLU254 3.6 77.6 1.0 OE2 B:GLU71 4.1 75.5 1.0 O C:HOH619 4.2 51.1 1.0 CD B:GLN11 4.3 57.0 1.0 O B:HOH644 4.4 50.6 1.0 CD C:GLU254 4.5 65.7 1.0 O C:HOH641 4.6 52.0 1.0 HB2 B:GLN11 4.8 59.3 1.0 OE2 C:GLU254 4.8 44.9 1.0 HE22 B:GLN11 4.9 56.1 1.0 HD21 B:ASN101 4.9 53.6 1.0 O1A B:GDP501 4.9 57.7 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Mmaf Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:52.7 occ:1.00 O B:HOH621 2.4 60.0 1.0 OE1 B:GLU113 2.7 72.0 1.0 OE2 B:GLU113 3.0 65.5 1.0 CD B:GLU113 3.2 65.5 1.0 OE1 B:GLU110 4.2 57.5 1.0 CG B:GLU113 4.7 52.1 1.0 OE2 B:GLU110 4.8 78.9 1.0 CD B:GLU110 4.9 56.3 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Mmaf Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:39.3 occ:1.00 O D:HOH601 2.0 44.2 1.0 O C:HOH622 2.1 40.9 1.0 O C:HOH608 2.1 38.6 1.0 O1G C:GTP501 2.1 43.0 1.0 O C:HOH628 2.1 46.2 1.0 O1B C:GTP501 2.2 46.0 1.0 HZ2 D:LYS254 3.1 64.2 1.0 PG C:GTP501 3.3 39.2 1.0 HB2 C:GLN11 3.4 58.3 1.0 PB C:GTP501 3.4 46.7 1.0 O2G C:GTP501 3.6 37.1 1.0 OE1 C:GLU71 3.7 58.7 1.0 HZ3 D:LYS254 3.8 64.2 1.0 O3B C:GTP501 3.8 64.4 1.0 HB2 C:ASP98 3.8 49.5 1.0 NZ D:LYS254 3.8 53.5 1.0 H C:GLN11 3.8 47.9 1.0 O3A C:GTP501 3.8 54.0 1.0 HZ1 D:LYS254 4.0 64.2 1.0 HB3 C:ASP98 4.1 49.5 1.0 OD1 C:ASP69 4.2 38.9 1.0 CB C:GLN11 4.2 48.6 1.0 HB3 C:GLN11 4.2 58.3 1.0 OD2 C:ASP69 4.3 47.0 1.0 CB C:ASP98 4.3 41.3 1.0 HB3 C:GLU71 4.4 60.0 1.0 OD2 C:ASP98 4.5 46.6 1.0 O3G C:GTP501 4.5 43.3 1.0 N C:GLN11 4.5 40.0 1.0 OE1 C:GLN11 4.6 62.2 1.0 O2B C:GTP501 4.7 56.0 1.0 CG C:ASP69 4.7 39.5 1.0 HG21 C:VAL74 4.7 67.2 1.0 CG C:ASP98 4.8 41.6 1.0 O1A C:GTP501 4.8 46.2 1.0 CD C:GLU71 4.8 64.4 1.0 HG1 C:THR145 4.9 54.3 1.0 PA C:GTP501 4.9 44.5 1.0 HB C:THR145 4.9 60.5 1.0 HG23 C:VAL74 4.9 67.2 1.0 CA C:GLN11 5.0 42.6 1.0 HA2 C:GLY10 5.0 46.5 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Mmaf Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:87.8 occ:1.00 OE2 C:GLU55 1.9 68.3 1.0 OG1 C:THR41 2.0 84.8 1.0 OD2 C:ASP39 2.3 67.8 1.0 OD1 C:ASP39 2.4 81.0 1.0 HA3 C:GLY45 2.5 0.9 1.0 CG C:ASP39 2.7 68.6 1.0 O C:GLY44 2.8 80.8 1.0 HZ C:PHE49 3.0 71.2 1.0 CD C:GLU55 3.0 72.5 1.0 O C:THR41 3.2 82.1 1.0 HD21 C:ASN50 3.3 62.8 1.0 OD2 C:ASP47 3.4 83.8 1.0 CA C:GLY45 3.4 84.9 1.0 CB C:THR41 3.4 79.8 1.0 HA2 C:GLY45 3.6 0.9 1.0 OE1 C:GLU55 3.6 85.0 1.0 HE1 C:PHE49 3.7 65.0 1.0 C C:GLY44 3.7 83.0 1.0 CZ C:PHE49 3.7 59.3 1.0 OD1 C:ASN50 3.8 70.5 1.0 HB C:THR41 3.8 95.7 1.0 N C:GLY45 4.0 93.1 1.0 ND2 C:ASN50 4.0 52.3 1.0 CE1 C:PHE49 4.0 54.2 1.0 HG3 C:GLU55 4.1 79.2 1.0 C C:THR41 4.2 81.2 1.0 HG23 C:THR41 4.2 0.1 1.0 CB C:ASP39 4.2 72.8 1.0 HG21 C:THR41 4.2 0.1 1.0 CG2 C:THR41 4.2 84.3 1.0 CG C:GLU55 4.2 66.0 1.0 H C:THR41 4.2 97.4 1.0 CA C:THR41 4.3 82.5 1.0 CG C:ASN50 4.3 61.5 1.0 HB2 C:ASP39 4.5 87.4 1.0 C C:GLY45 4.5 75.5 1.0 HB2 C:ASP47 4.5 77.7 1.0 H C:ASP47 4.5 83.4 1.0 CG C:ASP47 4.6 76.3 1.0 HB3 C:ASP39 4.6 87.4 1.0 N C:THR41 4.6 81.2 1.0 HG2 C:GLU55 4.7 79.2 1.0 H C:ASP46 4.7 97.4 1.0 HD22 C:ASN50 4.8 62.8 1.0 CE2 C:PHE49 4.8 57.2 1.0 NE2 C:HIS61 4.8 66.6 1.0 H C:GLY45 4.8 0.8 1.0 HA C:ASP39 4.8 86.5 1.0 H C:GLY44 4.9 0.8 1.0 N C:ASP46 4.9 81.1 1.0 HE2 C:PHE49 5.0 68.6 1.0

A.B.Waight, K.Bargsten, S.Doronina, M.O.Steinmetz, D.Sussman, A.E.Prota. Structural Basis of Microtubule Destabilization By Potent Auristatin Anti-Mitotics. Plos One V. 11 60890 2016.
ISSN: ESSN 1932-6203
PubMed: 27518442
DOI: 10.1371/JOURNAL.PONE.0160890