Magnesium in PDB 6agk: The Structure of Ch-II-77-Tubulin Complex

The structure of The Structure of Ch-II-77-Tubulin Complex, PDB code: 6agk was solved by H.Chen, K.Arnst, Y.Wang, D.Miller, W.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.084, 157.062, 182.897, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 26.4

The structure of The Structure of Ch-II-77-Tubulin Complex also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the The Structure of Ch-II-77-Tubulin Complex (pdb code 6agk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the The Structure of Ch-II-77-Tubulin Complex, PDB code: 6agk:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the The Structure of Ch-II-77-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Ch-II-77-Tubulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:20.9 occ:1.00 O A:HOH603 2.0 38.6 1.0 O A:HOH605 2.0 17.3 1.0 O2G A:GTP501 2.1 29.6 1.0 O A:HOH602 2.3 29.3 1.0 O1B A:GTP501 2.4 27.3 1.0 O A:HOH604 2.5 33.0 1.0 PG A:GTP501 3.2 30.6 1.0 PB A:GTP501 3.4 28.8 1.0 O1G A:GTP501 3.5 29.2 1.0 O3B A:GTP501 3.6 31.3 1.0 O3A A:GTP501 3.9 29.1 1.0 OE2 A:GLU71 4.2 50.6 1.0 OD1 A:ASP69 4.3 38.4 1.0 CG A:GLU71 4.3 48.5 1.0 CB A:ASP98 4.3 41.1 1.0 NZ B:LYS252 4.3 50.5 1.0 CB A:GLN11 4.4 36.0 1.0 O3G A:GTP501 4.5 30.0 1.0 OE1 A:GLN11 4.5 35.9 1.0 O1A A:GTP501 4.6 30.2 1.0 OD2 A:ASP69 4.7 43.7 1.0 N A:GLN11 4.7 33.9 1.0 CG A:ASP98 4.7 41.9 1.0 CD A:GLU71 4.8 49.4 1.0 OD2 A:ASP98 4.8 44.2 1.0 O2B A:GTP501 4.8 28.6 1.0 PA A:GTP501 4.9 29.4 1.0 CG A:ASP69 5.0 42.0 1.0

Magnesium binding site 2 out of 3 in the The Structure of Ch-II-77-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Ch-II-77-Tubulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:30.0 occ:1.00 OE1 B:GLN11 2.3 33.6 1.0 O1A B:GDP501 2.5 19.8 1.0 O B:HOH603 2.7 19.8 1.0 OD2 B:ASP177 3.1 41.1 1.0 CD B:GLN11 3.5 33.5 1.0 PA B:GDP501 3.8 18.3 1.0 OD1 B:ASN99 4.0 22.7 1.0 CG B:ASP177 4.2 39.3 1.0 O3A B:GDP501 4.2 19.0 1.0 C5' B:GDP501 4.2 20.9 1.0 NE2 B:GLN11 4.3 34.3 1.0 OE1 C:GLU254 4.4 47.9 1.0 O5' B:GDP501 4.4 18.8 1.0 CB B:GLN11 4.5 32.0 1.0 CG B:GLN11 4.5 32.9 1.0 CB B:ASP177 4.8 37.0 1.0 OE2 C:GLU254 4.9 45.1 1.0 ND2 B:ASN99 4.9 21.6 1.0 CG B:ASN99 4.9 21.7 1.0 CD C:GLU254 4.9 42.7 1.0 C8 B:GDP501 5.0 26.9 1.0

Magnesium binding site 3 out of 3 in the The Structure of Ch-II-77-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of Ch-II-77-Tubulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:24.9 occ:1.00 O1G C:GTP501 1.9 19.5 1.0 O1B C:GTP501 2.0 22.0 1.0 O C:HOH606 2.0 25.8 1.0 O C:HOH604 2.1 14.7 1.0 O C:HOH608 2.1 20.0 1.0 O C:HOH601 2.2 13.6 1.0 PB C:GTP501 3.0 22.8 1.0 PG C:GTP501 3.0 19.8 1.0 O3B C:GTP501 3.3 21.2 1.0 O3A C:GTP501 3.6 23.3 1.0 O2G C:GTP501 3.6 19.0 1.0 OD1 C:ASP69 4.1 25.1 1.0 NZ D:LYS252 4.1 65.2 1.0 OE2 C:GLU71 4.2 32.2 1.0 O1A C:GTP501 4.3 24.1 1.0 CB C:GLN11 4.3 25.2 1.0 O3G C:GTP501 4.4 20.4 1.0 O2B C:GTP501 4.4 23.2 1.0 OD2 C:ASP69 4.5 24.9 1.0 CG C:GLU71 4.5 31.8 1.0 OD2 C:ASP98 4.5 34.6 1.0 N C:GLN11 4.5 23.3 1.0 CB C:ASP98 4.5 34.0 1.0 PA C:GTP501 4.6 23.6 1.0 ND2 D:ASN247 4.7 77.7 1.0 OE1 C:GLN11 4.7 27.5 1.0 CG C:ASP69 4.8 25.4 1.0 CG C:ASP98 4.8 35.1 1.0 OG1 C:THR145 4.9 24.0 1.0 CD C:GLU71 4.9 31.6 1.0

H.Chen, K.Arnst, Y.Wang, D.Miller, W.Li. The Structure of Ch-II-77-Tubulin Complex To Be Published.