Magnesium in PDB 6gf3: Tubulin-Jerantinine B Acetate Complex

The structure of Tubulin-Jerantinine B Acetate Complex, PDB code: 6gf3 was solved by C.J.Smedley, P.A.Stanley, M.E.Qazzaz, A.E.Prota, N.Olieric, H.Collins, H.Eastman, A.S.Barrow, K.-H.Lim, T.-S.Kam, B.J.Smith, H.M.Duivenvoorden, B.S.Parker, T.D.Bradshaw, M.O.Steinmetz, J.E.Moses, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.96 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.720, 158.150, 180.950, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.1

The structure of Tubulin-Jerantinine B Acetate Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Tubulin-Jerantinine B Acetate Complex (pdb code 6gf3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Tubulin-Jerantinine B Acetate Complex, PDB code: 6gf3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Tubulin-Jerantinine B Acetate Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Jerantinine B Acetate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:57.3 occ:1.00 O3G A:GTP501 2.1 54.1 1.0 O A:HOH602 2.1 65.0 1.0 O1B A:GTP501 2.1 50.7 1.0 O A:HOH601 2.3 61.1 1.0 O A:HOH615 2.3 74.0 1.0 O A:HOH624 2.3 59.6 1.0 OE1 A:GLU71 3.2 0.0 1.0 PB A:GTP501 3.2 57.6 1.0 PG A:GTP501 3.2 62.2 1.0 O3A A:GTP501 3.6 67.6 1.0 O3B A:GTP501 3.6 71.8 1.0 O1G A:GTP501 3.7 59.0 1.0 O A:HOH625 3.9 87.1 1.0 CB A:GLN11 4.0 57.8 1.0 OD2 A:ASP98 4.0 65.0 1.0 OE1 A:GLN11 4.3 69.3 1.0 CD A:GLU71 4.3 0.9 1.0 OD1 A:ASP69 4.4 69.3 1.0 N A:GLN11 4.5 62.2 1.0 O2G A:GTP501 4.5 53.0 1.0 O2B A:GTP501 4.6 66.5 1.0 O1A A:GTP501 4.6 69.3 1.0 PA A:GTP501 4.7 59.6 1.0 OD2 A:ASP69 4.7 71.0 1.0 CB A:ASP98 4.7 63.3 1.0 CG A:ASP98 4.8 67.2 1.0 CA A:GLN11 4.8 60.1 1.0 CB A:GLU71 4.9 0.7 1.0 CD A:GLN11 4.9 62.6 1.0

Magnesium binding site 2 out of 4 in the Tubulin-Jerantinine B Acetate Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Jerantinine B Acetate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:52.9 occ:1.00 NE2 B:GLN11 2.0 77.0 1.0 O B:HOH617 2.0 55.9 1.0 O B:HOH607 2.2 73.2 1.0 O C:HOH605 2.2 62.9 1.0 O B:HOH626 2.2 56.6 1.0 O1A B:GDP501 2.3 58.5 1.0 CD B:GLN11 3.3 61.9 1.0 PA B:GDP501 3.7 49.5 1.0 OD2 B:ASP179 3.8 62.6 1.0 OE1 B:GLN11 4.0 75.2 1.0 CB B:GLN11 4.1 46.0 1.0 O3A B:GDP501 4.2 52.6 1.0 ND2 B:ASN101 4.2 62.8 1.0 CG B:GLN11 4.3 53.8 1.0 O1B B:GDP501 4.4 56.9 1.0 OE1 C:GLU254 4.5 75.0 1.0 C5' B:GDP501 4.5 51.3 1.0 O2A B:GDP501 4.6 49.1 1.0 O5' B:GDP501 4.6 44.7 1.0 CG B:ASP179 4.9 58.9 1.0 PB B:GDP501 4.9 55.3 1.0 C8 B:GDP501 4.9 55.2 1.0 OE2 C:GLU254 5.0 73.3 1.0

Magnesium binding site 3 out of 4 in the Tubulin-Jerantinine B Acetate Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Jerantinine B Acetate Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:52.0 occ:1.00 O C:HOH621 2.2 45.8 1.0 O1G C:GTP501 2.3 46.5 1.0 O C:HOH607 2.3 40.3 1.0 O1B C:GTP501 2.4 58.7 1.0 O C:HOH604 2.4 36.5 1.0 O3A C:GTP501 3.2 61.4 1.0 PB C:GTP501 3.3 72.6 1.0 PG C:GTP501 3.5 62.5 1.0 NZ D:LYS254 3.6 68.4 1.0 NE2 C:GLN11 3.7 70.8 1.0 CB C:GLN11 3.7 42.9 1.0 O3B C:GTP501 3.8 70.3 1.0 O1A C:GTP501 3.9 62.2 1.0 OE1 C:GLU71 4.0 77.5 1.0 O C:HOH639 4.1 75.5 1.0 PA C:GTP501 4.2 48.2 1.0 O3G C:GTP501 4.3 47.3 1.0 CD C:GLN11 4.5 58.9 1.0 N C:GLN11 4.5 51.0 1.0 OD2 C:ASP98 4.5 67.5 1.0 O2B C:GTP501 4.6 63.0 1.0 CG C:GLN11 4.7 48.2 1.0 O2G C:GTP501 4.7 49.1 1.0 CA C:GLN11 4.7 49.9 1.0 OD2 C:ASP69 4.8 56.7 1.0 O2A C:GTP501 4.9 52.0 1.0 CD C:GLU71 4.9 75.7 1.0 CE D:LYS254 5.0 62.8 1.0

Magnesium binding site 4 out of 4 in the Tubulin-Jerantinine B Acetate Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Jerantinine B Acetate Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:0.3 occ:1.00 OE1 D:GLN11 2.1 1.0 1.0 O1A D:GDP501 2.2 0.1 1.0 OD2 D:ASP179 2.6 0.8 1.0 CD D:GLN11 2.9 0.8 1.0 O D:HOH602 3.3 79.3 1.0 NE2 D:GLN11 3.4 0.5 1.0 PA D:GDP501 3.7 90.1 1.0 CG D:ASP179 3.8 0.4 1.0 ND2 D:ASN101 3.8 0.6 1.0 O1B D:GDP501 3.9 0.8 1.0 OD1 D:ASN101 4.0 0.8 1.0 CG D:GLN11 4.0 0.1 1.0 O2A D:GDP501 4.2 80.1 1.0 CG D:ASN101 4.4 0.4 1.0 C5' D:GDP501 4.4 89.9 1.0 CB D:GLN11 4.5 98.4 1.0 O5' D:GDP501 4.6 87.1 1.0 CB D:ASP179 4.6 0.3 1.0 OD1 D:ASP179 4.7 0.0 1.0 O3A D:GDP501 4.7 90.5 1.0 PB D:GDP501 4.9 96.6 1.0

C.J.Smedley, P.A.Stanley, M.E.Qazzaz, A.E.Prota, N.Olieric, H.Collins, H.Eastman, A.S.Barrow, K.H.Lim, T.S.Kam, B.J.Smith, H.M.Duivenvoorden, B.S.Parker, T.D.Bradshaw, M.O.Steinmetz, J.E.Moses. Sustainable Syntheses of (-)-Jerantinines A & E and Structural Characterisation of the Jerantinine-Tubulin Complex at the Colchicine Binding Site. Sci Rep V. 8 10617 2018.
ISSN: ESSN 2045-2322
PubMed: 30006510
DOI: 10.1038/S41598-018-28880-2