Magnesium in PDB 7jfr: Auristatin Bound to Tubulin

The structure of Auristatin Bound to Tubulin, PDB code: 7jfr was solved by P.N.Moquist, A.Waight, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.74 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.491, 155.148, 181.885, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 25.6

The structure of Auristatin Bound to Tubulin also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Auristatin Bound to Tubulin (pdb code 7jfr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Auristatin Bound to Tubulin, PDB code: 7jfr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Auristatin Bound to Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Auristatin Bound to Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:56.1 occ:1.00 O A:HOH609 2.1 55.8 1.0 O1G A:GTP501 2.1 64.3 1.0 O A:HOH603 2.1 60.1 1.0 O1B A:GTP501 2.4 54.0 1.0 OE1 A:GLU71 2.9 86.0 1.0 HZ3 B:LYS254 3.1 86.7 1.0 HB2 A:GLN11 3.2 78.7 1.0 PG A:GTP501 3.3 47.6 1.0 PB A:GTP501 3.5 53.5 1.0 O2G A:GTP501 3.7 50.4 1.0 O3B A:GTP501 3.8 79.5 1.0 HB3 A:GLU71 3.8 95.6 1.0 OE1 A:GLN11 3.8 82.7 1.0 NZ B:LYS254 3.9 72.2 1.0 HZ1 B:LYS254 3.9 86.7 1.0 O3A A:GTP501 3.9 71.9 1.0 H A:GLN11 4.0 64.0 1.0 HB3 A:GLN11 4.0 78.7 1.0 CB A:GLN11 4.0 65.6 1.0 CD A:GLU71 4.1 99.1 1.0 HB2 A:GLU71 4.1 95.6 1.0 HB2 A:ASP98 4.1 65.7 1.0 HZ2 B:LYS254 4.2 86.7 1.0 OD1 A:ASP69 4.2 58.3 1.0 CB A:GLU71 4.4 79.7 1.0 OD2 A:ASP98 4.5 63.4 1.0 OD2 A:ASP69 4.5 74.5 1.0 O3G A:GTP501 4.5 57.0 1.0 O1A A:GTP501 4.7 58.3 1.0 N A:GLN11 4.7 53.4 1.0 HB3 A:ASP98 4.7 65.7 1.0 CB A:ASP98 4.8 54.8 1.0 CD A:GLN11 4.8 71.8 1.0 HG1 A:THR145 4.8 67.2 1.0 O2B A:GTP501 4.8 59.1 1.0 CG A:ASP69 4.8 64.7 1.0 CG A:GLU71 4.9 77.7 1.0 PA A:GTP501 4.9 58.4 1.0 CG A:ASP98 4.9 66.4 1.0 HG21 A:VAL74 4.9 81.2 1.0 CA A:GLN11 4.9 61.9 1.0 OE2 A:GLU71 4.9 0.1 1.0

Magnesium binding site 2 out of 5 in the Auristatin Bound to Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Auristatin Bound to Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:76.7 occ:1.00 O B:HOH626 2.1 51.1 1.0 O B:HOH647 2.5 62.1 1.0 OE1 B:GLN11 3.0 62.2 1.0 OE1 C:GLU254 3.5 98.6 1.0 CD B:GLN11 4.2 62.1 1.0 CD C:GLU254 4.4 80.1 1.0 OE2 B:GLU71 4.5 95.8 1.0 O1A B:GDP501 4.6 51.8 1.0 HE22 B:GLN11 4.6 77.3 1.0 OE2 C:GLU254 4.6 55.8 1.0 HD21 B:ASN101 4.6 71.1 1.0 HB2 B:GLN11 4.8 65.8 1.0 NE2 B:GLN11 4.9 64.4 1.0

Magnesium binding site 3 out of 5 in the Auristatin Bound to Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Auristatin Bound to Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:72.2 occ:1.00 OE1 B:GLU113 2.7 92.2 1.0 OE2 B:GLU113 3.1 87.4 1.0 CD B:GLU113 3.3 90.6 1.0 OE1 B:GLU110 4.2 50.6 1.0 CG B:GLU113 4.8 61.9 1.0 HB3 B:SER97 4.8 83.3 1.0 OE2 B:GLU110 4.9 86.3 1.0 CD B:GLU110 4.9 54.0 1.0

Magnesium binding site 4 out of 5 in the Auristatin Bound to Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Auristatin Bound to Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:48.7 occ:1.00 O1G C:GTP501 2.1 41.5 1.0 O1B C:GTP501 2.3 47.3 1.0 O C:HOH618 2.3 51.1 1.0 HZ1 D:LYS254 2.8 65.6 1.0 PG C:GTP501 3.4 47.7 1.0 PB C:GTP501 3.5 43.3 1.0 HB2 C:GLN11 3.5 58.2 1.0 NZ D:LYS254 3.5 54.7 1.0 OE1 C:GLU71 3.5 69.9 1.0 HZ2 D:LYS254 3.6 65.6 1.0 HZ3 D:LYS254 3.7 65.6 1.0 O3B C:GTP501 3.8 63.1 1.0 O3A C:GTP501 3.9 53.0 1.0 HB2 C:ASP98 3.9 54.5 1.0 O2G C:GTP501 4.0 40.9 1.0 H C:GLN11 4.1 53.3 1.0 HB3 C:ASP98 4.2 54.5 1.0 OD2 C:ASP98 4.2 54.2 1.0 HB3 C:GLN11 4.3 58.2 1.0 CB C:GLN11 4.3 48.5 1.0 OE1 C:GLN11 4.4 58.1 1.0 CB C:ASP98 4.4 45.5 1.0 O3G C:GTP501 4.5 47.3 1.0 HB3 C:GLU71 4.5 70.4 1.0 OD1 C:ASP69 4.6 38.5 1.0 CD C:GLU71 4.6 69.9 1.0 O1A C:GTP501 4.6 41.3 1.0 OD2 C:ASP69 4.6 46.2 1.0 CG C:ASP98 4.7 44.9 1.0 O2B C:GTP501 4.8 44.9 1.0 CE D:LYS254 4.8 42.6 1.0 N C:GLN11 4.8 44.4 1.0 HG21 C:VAL74 4.8 55.5 1.0 PA C:GTP501 4.9 40.7 1.0 HE3 D:LYS254 4.9 51.1 1.0 HE2 D:LYS254 4.9 51.1 1.0

Magnesium binding site 5 out of 5 in the Auristatin Bound to Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Auristatin Bound to Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:82.9 occ:1.00 OG1 C:THR41 2.0 84.8 1.0 OE2 C:GLU55 2.0 67.2 1.0 OD2 C:ASP39 2.4 67.5 1.0 OD1 C:ASP39 2.4 86.5 1.0 HA3 C:GLY45 2.6 95.9 1.0 CG C:ASP39 2.7 68.2 1.0 HZ C:PHE49 3.0 66.5 1.0 O C:GLY44 3.0 77.0 1.0 CD C:GLU55 3.1 70.4 1.0 OD2 C:ASP47 3.3 82.5 1.0 HD21 C:ASN50 3.3 63.8 1.0 CB C:THR41 3.4 89.4 1.0 O C:THR41 3.4 87.3 1.0 CA C:GLY45 3.5 79.9 1.0 OE1 C:GLU55 3.6 80.7 1.0 HA2 C:GLY45 3.6 95.9 1.0 CZ C:PHE49 3.6 55.4 1.0 HE1 C:PHE49 3.7 68.2 1.0 OD1 C:ASN50 3.7 61.9 1.0 HB C:THR41 3.8 0.3 1.0 C C:GLY44 3.9 79.8 1.0 HG21 C:THR41 3.9 86.9 1.0 ND2 C:ASN50 4.0 53.1 1.0 CG2 C:THR41 4.0 72.5 1.0 CE1 C:PHE49 4.0 56.8 1.0 HG23 C:THR41 4.1 86.9 1.0 N C:GLY45 4.1 87.3 1.0 H C:THR41 4.1 90.3 1.0 CB C:ASP39 4.2 71.6 1.0 C C:THR41 4.3 88.4 1.0 CA C:THR41 4.3 86.2 1.0 CG C:ASN50 4.3 68.6 1.0 HG3 C:GLU55 4.4 73.2 1.0 CG C:GLU55 4.4 61.0 1.0 HB2 C:ASP47 4.4 76.4 1.0 HB2 C:ASP39 4.4 85.9 1.0 CG C:ASP47 4.4 76.4 1.0 H C:ASP47 4.5 88.4 1.0 C C:GLY45 4.5 76.8 1.0 HB3 C:ASP39 4.6 85.9 1.0 N C:THR41 4.6 75.3 1.0 H C:ASP46 4.7 94.4 1.0 CE2 C:PHE49 4.7 59.1 1.0 HD22 C:ASN50 4.7 63.8 1.0 HG2 C:GLU55 4.8 73.2 1.0 NE2 C:HIS61 4.8 63.2 1.0 HE2 C:PHE49 4.9 71.0 1.0 HA C:ASP39 4.9 86.0 1.0 H C:GLY45 4.9 0.7 1.0 N C:ASP46 4.9 78.6 1.0 CB C:ASP47 5.0 63.6 1.0 HG22 C:THR41 5.0 86.9 1.0

P.N.Moquist, A.Waight. Auristatin Bound to Tubulin To Be Published.