Magnesium in PDB 6i5c: Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex

The structure of Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex, PDB code: 6i5c was solved by S.Basu, V.Olieric, N.Matsugaki, Y.Kawano, T.Takashi, C.Y.Huang, F.Leonarski, Y.Yamada, L.Vera, N.Olieric, J.Basquin, J.A.Wojdyla, K.Diederichs, M.Yamamoto, O.Bunk, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.46 / 2.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.240, 156.830, 179.540, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.8

The structure of Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex also contains other interesting chemical elements:

Calcium	(Ca)	5 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex (pdb code 6i5c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex, PDB code: 6i5c:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:58.5 occ:1.00 O A:HOH655 2.0 53.6 1.0 O1B A:GTP501 2.1 45.8 1.0 O A:HOH625 2.1 49.3 1.0 O2G A:GTP501 2.1 46.1 1.0 O A:HOH644 2.1 52.6 1.0 O A:HOH642 2.1 46.0 1.0 PG A:GTP501 3.2 50.8 1.0 PB A:GTP501 3.3 54.8 1.0 O1G A:GTP501 3.5 56.8 1.0 O3B A:GTP501 3.6 61.4 1.0 O3A A:GTP501 3.9 69.3 1.0 NZ B:LYS254 3.9 70.3 1.0 OD1 A:ASP69 4.0 62.5 1.0 OE1 A:GLU71 4.0 70.6 1.0 CG A:GLU71 4.2 69.2 1.0 CB A:GLN11 4.2 58.3 1.0 OD2 A:ASP98 4.3 71.0 1.0 N A:GLN11 4.4 61.9 1.0 CB A:ASP98 4.4 64.3 1.0 OD2 A:ASP69 4.4 67.1 1.0 O3G A:GTP501 4.4 41.2 1.0 O2B A:GTP501 4.5 54.0 1.0 CD A:GLU71 4.6 78.8 1.0 CG A:ASP69 4.6 62.9 1.0 O1A A:GTP501 4.7 59.5 1.0 CG A:ASP98 4.8 71.5 1.0 PA A:GTP501 4.8 52.2 1.0 CA A:GLN11 4.9 59.4 1.0 OE1 A:GLN11 4.9 72.9 1.0 CE B:LYS254 5.0 59.6 1.0

Magnesium binding site 2 out of 3 in the Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:47.2 occ:1.00 O C:HOH716 2.1 51.8 1.0 O C:HOH708 2.1 41.5 1.0 O C:HOH721 2.3 43.6 1.0 O1B C:GTP501 2.4 43.2 1.0 O1G C:GTP501 3.3 40.7 1.0 OE1 C:GLU71 3.3 74.2 1.0 OD2 C:ASP69 3.3 48.6 1.0 CB C:GLN11 3.6 59.4 1.0 OD1 C:ASP69 3.7 58.5 1.0 CG C:GLU71 3.8 51.9 1.0 PB C:GTP501 3.9 52.7 1.0 N C:GLN11 3.9 45.9 1.0 CG C:ASP69 3.9 53.4 1.0 CD C:GLU71 4.0 65.2 1.0 CA C:GLN11 4.2 50.5 1.0 OE1 C:GLN11 4.2 60.7 1.0 PG C:GTP501 4.4 59.3 1.0 CG2 C:VAL74 4.5 55.4 1.0 O3A C:GTP501 4.5 61.2 1.0 O3B C:GTP501 4.6 52.9 1.0 CG C:GLN11 4.6 54.0 1.0 NZ D:LYS254 4.7 53.0 1.0 CD C:GLN11 4.8 56.4 1.0 O2B C:GTP501 4.8 48.2 1.0 O2G C:GTP501 4.9 45.6 1.0 O1A C:GTP501 4.9 42.6 1.0 C C:GLY10 4.9 48.7 1.0

Magnesium binding site 3 out of 3 in the Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:95.9 occ:1.00 O F:HOH501 2.1 0.8 1.0 C3B F:ACP402 2.6 0.6 1.0 OE2 F:GLU331 3.1 0.3 1.0 NH1 F:ARG222 3.2 1.0 1.0 OD2 F:ASP318 3.2 99.6 1.0 O3G F:ACP402 3.4 0.5 1.0 NH2 F:ARG202 3.5 70.9 1.0 PG F:ACP402 3.6 0.6 1.0 OD1 F:ASN333 3.6 1.0 1.0 PB F:ACP402 3.9 0.8 1.0 O3A F:ACP402 4.0 0.9 1.0 ND2 F:ASN333 4.1 0.1 1.0 CG F:ASN333 4.2 0.9 1.0 O1G F:ACP402 4.3 0.3 1.0 CZ F:ARG222 4.3 96.1 1.0 CD F:GLU331 4.3 0.3 1.0 CG F:ASP318 4.3 90.0 1.0 ND2 F:ASN242 4.4 0.6 1.0 O2B F:ACP402 4.5 0.2 1.0 NH2 F:ARG222 4.5 86.3 1.0 O F:HOH533 4.7 73.3 1.0 OD1 F:ASP318 4.7 88.3 1.0 CZ F:ARG202 4.8 78.2 1.0 O2G F:ACP402 4.9 0.6 1.0

S.Basu, V.Olieric, F.Leonarski, N.Matsugaki, Y.Kawano, T.Takashi, C.Y.Huang, Y.Yamada, L.Vera, N.Olieric, J.Basquin, J.A.Wojdyla, O.Bunk, K.Diederichs, M.Yamamoto, M.Wang. Long-Wavelength Native-Sad Phasing: Opportunities and Challenges. Iucrj V. 6 373 2019.
ISSN: ESSN 2052-2525
PubMed: 31098019
DOI: 10.1107/S2052252519002756