Magnesium in PDB 5kx5: Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex, PDB code: 5kx5 was solved by K.Parris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.47 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.790, 153.900, 185.200, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 25.1

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex (pdb code 5kx5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex, PDB code: 5kx5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:50.2 occ:1.00 O1G A:GTP501 2.3 53.1 1.0 O1B A:GTP501 2.4 40.5 1.0 OE1 A:GLU71 3.2 0.1 1.0 OD1 A:ASP69 3.4 61.4 1.0 OD2 A:ASP69 3.4 73.4 1.0 PG A:GTP501 3.6 49.8 1.0 PB A:GTP501 3.6 43.7 1.0 CG A:GLU71 3.7 81.7 1.0 CG A:ASP69 3.8 63.4 1.0 CD A:GLU71 3.9 0.1 1.0 O3B A:GTP501 3.9 48.6 1.0 O2G A:GTP501 4.0 51.9 1.0 CB A:GLN11 4.0 47.5 1.0 NZ B:LYS254 4.2 58.8 1.0 O3A A:GTP501 4.2 49.1 1.0 N A:GLN11 4.3 47.6 1.0 OD2 A:ASP98 4.6 55.7 1.0 CB A:ASP98 4.7 48.4 1.0 CA A:GLN11 4.7 46.1 1.0 OE1 A:GLN11 4.7 55.5 1.0 O2B A:GTP501 4.8 45.6 1.0 CG A:ASP98 4.9 49.9 1.0 O3G A:GTP501 4.9 46.4 1.0 O1A A:GTP501 4.9 49.2 1.0 CG2 A:VAL74 4.9 64.7 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:57.4 occ:1.00 OE2 B:GLU71 3.4 90.2 1.0 O1B B:GDP501 3.5 38.9 1.0 O1A B:GDP501 3.8 40.5 1.0 CB B:GLN11 3.9 40.3 1.0 O B:HOH612 3.9 37.9 1.0 O3A B:GDP501 4.0 38.0 1.0 CD B:GLU71 4.1 88.5 1.0 O B:HOH621 4.1 40.4 1.0 OE1 B:GLU71 4.2 66.1 1.0 NE2 B:GLN11 4.2 55.7 1.0 PB B:GDP501 4.3 40.2 1.0 O3B B:GDP501 4.5 43.2 1.0 CD B:GLN11 4.5 66.9 1.0 PA B:GDP501 4.6 38.9 1.0 OD1 B:ASN101 4.7 45.5 1.0 CG B:GLN11 4.7 45.0 1.0 N B:GLN11 5.0 39.2 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg505 b:78.8 occ:1.00 O B:HOH619 2.7 69.9 1.0 OG B:SER298 3.0 57.5 0.6 N B:SER298 3.0 52.9 1.0 CB B:SER298 3.5 52.8 1.0 OD1 B:ASP297 3.5 70.5 1.0 CA B:ASP297 3.8 52.3 1.0 CA B:SER298 3.8 51.8 1.0 C B:ASP297 3.9 56.6 1.0 CD B:ARG308 4.1 99.3 1.0 O B:PHE296 4.3 54.7 1.0 NH1 B:ARG308 4.4 0.2 1.0 CG B:ARG308 4.4 76.1 1.0 CG B:ASP297 4.5 68.7 1.0 CB B:ASP297 4.6 53.9 1.0 OD1 B:ASP306 4.8 68.1 1.0 N B:ASP297 4.9 52.2 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:47.4 occ:1.00 O1G C:GTP501 2.3 48.2 1.0 O1B C:GTP501 2.6 45.9 1.0 OE1 C:GLU71 3.3 81.1 1.0 OD2 C:ASP69 3.5 52.0 1.0 PG C:GTP501 3.6 45.1 1.0 OD1 C:ASP69 3.7 43.7 1.0 CG C:GLU71 3.8 55.4 1.0 PB C:GTP501 3.8 45.3 1.0 CD C:GLU71 4.0 77.9 1.0 CG C:ASP69 4.0 45.6 1.0 O3B C:GTP501 4.1 48.8 1.0 OD2 C:ASP98 4.1 44.3 1.0 CB C:GLN11 4.1 36.4 1.0 O2G C:GTP501 4.1 44.2 1.0 NZ D:LYS254 4.4 54.1 1.0 N C:GLN11 4.4 35.9 1.0 O3A C:GTP501 4.5 46.2 1.0 CB C:ASP98 4.6 45.6 1.0 O1A C:GTP501 4.6 47.5 1.0 OE1 C:GLN11 4.7 58.5 1.0 CG C:ASP98 4.7 47.0 1.0 CG2 C:VAL74 4.8 53.3 1.0 CA C:GLN11 4.9 34.6 1.0 O3G C:GTP501 4.9 38.5 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:65.0 occ:1.00 OG1 D:THR180 3.1 92.5 1.0 OG D:SER178 3.2 97.7 1.0 OE2 D:GLU183 3.3 0.1 1.0 C5' D:GDP501 3.3 64.6 1.0 MG D:MG503 3.4 61.9 1.0 C3' D:GDP501 3.7 66.4 1.0 OD1 D:ASN101 4.0 83.0 1.0 C4' D:GDP501 4.1 64.5 1.0 CB D:THR180 4.1 92.2 1.0 CB D:SER178 4.2 91.3 1.0 C2' D:GDP501 4.2 65.8 1.0 CG D:ASN101 4.4 98.4 1.0 ND2 D:ASN101 4.4 95.3 1.0 O5' D:GDP501 4.5 65.7 1.0 O1A D:GDP501 4.5 67.2 1.0 CD D:GLU183 4.5 0.6 1.0 CG2 D:THR180 4.6 87.8 1.0 O3' D:GDP501 4.8 66.5 1.0 O4' D:GDP501 5.0 62.8 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Tubulin-Stathmin-Ttl-Compound 11 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:61.9 occ:1.00 O1A D:GDP501 2.5 67.2 1.0 O D:HOH601 2.6 59.4 1.0 OE1 D:GLN11 2.8 81.5 1.0 OD1 D:ASN101 3.1 83.0 1.0 MG D:MG502 3.4 65.0 1.0 PA D:GDP501 3.4 66.3 1.0 O3A D:GDP501 3.5 66.9 1.0 C5' D:GDP501 4.0 64.6 1.0 CD D:GLN11 4.0 90.9 1.0 O5' D:GDP501 4.1 65.7 1.0 CG D:ASN101 4.1 98.4 1.0 ND2 D:ASN101 4.5 95.3 1.0 CB D:GLN11 4.7 61.6 1.0 O2A D:GDP501 4.8 67.6 1.0 O1B D:GDP501 4.8 65.7 1.0 PB D:GDP501 4.8 67.9 1.0 NE2 D:GLN11 4.8 86.7 1.0

C.A.Leverett, S.C.Sukuru, B.C.Vetelino, S.Musto, K.Parris, J.Pandit, F.Loganzo, A.H.Varghese, G.Bai, B.Liu, D.Liu, S.Hudson, V.R.Doppalapudi, J.Stock, C.J.O'donnell, C.Subramanyam. Design, Synthesis, and Cytotoxic Evaluation of Novel Tubulysin Analogues As Adc Payloads. Acs Med Chem Lett V. 7 999 2016.
ISSN: ISSN 1948-5875
PubMed: 27882198
DOI: 10.1021/ACSMEDCHEMLETT.6B00274