Magnesium in PDB 8clf: Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex

The structure of Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex, PDB code: 8clf was solved by M.Wranik, Q.Bertrand, M.Kepa, T.Weinert, M.Steinmetz, J.Standfuss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.35 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.65, 160.33, 180.95, 90, 90, 90
R / Rfree (%)	16.8 / 21.7

The structure of Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex also contains other interesting chemical elements:

Bromine	(Br)	1 atom
Calcium	(Ca)	2 atoms

The binding sites of Magnesium atom in the Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex (pdb code 8clf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex, PDB code: 8clf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:71.8 occ:1.00 O A:HOH602 1.9 59.3 1.0 O1B A:GTP501 2.2 57.3 1.0 O1G A:GTP501 2.9 62.1 1.0 HG2 A:GLU71 3.1 101.1 1.0 OD1 A:ASP69 3.3 72.7 1.0 O2G A:GTP501 3.3 64.7 1.0 HB2 A:ASP98 3.4 68.2 1.0 HG3 A:GLU71 3.4 101.1 1.0 PG A:GTP501 3.5 70.8 1.0 PB A:GTP501 3.5 54.0 1.0 OD2 A:ASP69 3.6 76.0 1.0 CG A:GLU71 3.7 101.1 1.0 HB3 A:ASP98 3.7 68.2 1.0 HB2 A:GLN11 3.8 66.7 1.0 O3B A:GTP501 3.8 79.9 1.0 CG A:ASP69 3.9 72.7 1.0 H A:GLN11 3.9 64.0 1.0 CB A:ASP98 4.0 68.2 1.0 OD2 A:ASP98 4.1 71.2 1.0 HZ1 B:LYS254 4.1 80.0 1.0 HB A:THR145 4.3 60.7 1.0 HG1 A:THR145 4.3 63.0 1.0 OE2 A:GLU71 4.4 100.1 1.0 CG A:ASP98 4.4 66.7 1.0 HA2 A:GLY10 4.4 63.1 1.0 O3A A:GTP501 4.5 62.8 1.0 N A:GLN11 4.5 64.0 1.0 OG1 A:THR145 4.6 63.0 1.0 CD A:GLU71 4.6 99.3 1.0 O2B A:GTP501 4.6 54.7 1.0 CB A:GLN11 4.6 66.7 1.0 HB3 A:GLN11 4.6 66.7 1.0 HB3 A:GLU71 4.7 86.3 1.0 H A:LEU70 4.8 80.8 1.0 CB A:GLU71 4.8 86.3 1.0 H A:GLU71 4.9 80.8 1.0 NZ B:LYS254 4.9 80.0 1.0 CB A:THR145 4.9 60.7 1.0 O3G A:GTP501 5.0 46.1 1.0 H A:ALA99 5.0 62.8 1.0 HZ2 B:LYS254 5.0 80.0 1.0

Magnesium binding site 2 out of 4 in the Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:65.2 occ:1.00 HE21 B:GLN11 2.2 67.4 1.0 O1A B:GDP501 2.5 73.0 1.0 HE22 B:GLN11 2.5 67.4 1.0 NE2 B:GLN11 2.7 67.4 1.0 O B:HOH606 2.7 60.3 1.0 OD1 B:ASP179 3.2 77.7 1.0 H5'' B:GDP501 3.7 46.7 1.0 OD1 B:ASN101 3.7 65.1 1.0 PA B:GDP501 3.7 42.7 1.0 O3A B:GDP501 3.9 60.0 1.0 CD B:GLN11 4.0 84.1 1.0 HD21 B:ASN101 4.1 62.6 1.0 HB3 B:GLN11 4.1 53.1 1.0 CG B:ASP179 4.2 75.1 1.0 H8 B:GDP501 4.3 57.6 1.0 HB3 B:ASP179 4.3 71.5 1.0 OE1 C:GLU254 4.4 85.0 1.0 C5' B:GDP501 4.4 46.7 1.0 H5' B:GDP501 4.4 46.7 1.0 O5' B:GDP501 4.6 51.5 1.0 CG B:ASN101 4.6 66.6 1.0 ND2 B:ASN101 4.7 62.6 1.0 HB2 B:GLN11 4.7 53.1 1.0 CB B:GLN11 4.7 53.1 1.0 CB B:ASP179 4.7 71.5 1.0 CG B:GLN11 4.7 73.3 1.0 HG2 B:GLN11 4.8 73.3 1.0 HB2 B:ASP179 4.8 71.5 1.0 OE1 B:GLN11 4.9 82.8 1.0 O1B B:GDP501 4.9 51.3 1.0 O2A B:GDP501 4.9 76.2 1.0

Magnesium binding site 3 out of 4 in the Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:61.9 occ:1.00 O C:HOH608 2.3 42.2 1.0 O C:HOH601 2.4 41.5 1.0 HB2 C:GLN11 2.5 50.3 1.0 O C:HOH602 2.6 51.9 1.0 OD2 C:ASP69 2.8 53.9 1.0 O1B C:GTP501 3.1 52.1 1.0 HG21 C:VAL74 3.2 66.6 1.0 OE2 C:GLU71 3.3 64.7 1.0 H C:GLN11 3.4 50.7 1.0 HG3 C:GLU71 3.4 56.0 1.0 CB C:GLN11 3.5 50.3 1.0 HG23 C:VAL74 3.5 66.6 1.0 CG C:ASP69 3.6 56.0 1.0 HG2 C:GLU71 3.6 56.0 1.0 OD1 C:ASP69 3.6 57.1 1.0 N C:GLN11 3.8 50.7 1.0 CG2 C:VAL74 3.8 66.6 1.0 CG C:GLU71 3.9 56.0 1.0 HB3 C:GLN11 3.9 50.3 1.0 HA C:GLN11 3.9 54.8 1.0 OE1 C:GLN11 4.0 77.1 1.0 CA C:GLN11 4.0 54.8 1.0 CD C:GLU71 4.0 66.7 1.0 O1G C:GTP501 4.1 52.5 1.0 HG3 C:GLN11 4.3 45.1 1.0 CG C:GLN11 4.4 45.1 1.0 HG22 C:VAL74 4.4 66.6 1.0 HA2 C:GLY10 4.5 49.1 1.0 PB C:GTP501 4.5 47.3 1.0 HB C:VAL74 4.5 70.3 1.0 CD C:GLN11 4.6 69.5 1.0 C C:GLY10 4.7 55.5 1.0 CB C:VAL74 4.8 70.3 1.0 HZ1 D:LYS254 4.9 66.9 1.0 HB3 C:ASP98 4.9 54.5 1.0 HB2 C:ASP98 4.9 54.5 1.0 O3A C:GTP501 4.9 60.2 1.0

Magnesium binding site 4 out of 4 in the Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:98.2 occ:1.00 O1A D:GDP501 2.4 121.8 1.0 OD2 D:ASP179 2.8 144.7 1.0 OE1 D:GLN11 3.0 106.7 1.0 HD21 D:ASN101 3.3 134.8 1.0 PA D:GDP501 3.6 88.8 1.0 O3A D:GDP501 3.7 104.1 1.0 CD D:GLN11 3.7 115.8 1.0 H5'' D:GDP501 3.7 95.7 1.0 CG D:ASP179 3.8 145.9 1.0 OD1 D:ASP179 4.0 144.2 1.0 HE22 D:GLN11 4.0 111.5 1.0 HB3 D:GLN11 4.0 107.9 1.0 OD1 D:ASN101 4.1 135.1 1.0 ND2 D:ASN101 4.1 134.8 1.0 NE2 D:GLN11 4.2 111.5 1.0 HB2 D:GLN11 4.2 107.9 1.0 H8 D:GDP501 4.3 85.6 1.0 CG D:ASN101 4.5 130.8 1.0 CB D:GLN11 4.5 107.9 1.0 C5' D:GDP501 4.5 95.7 1.0 O5' D:GDP501 4.6 88.8 1.0 O2A D:GDP501 4.7 93.7 1.0 HD22 D:ASN101 4.7 134.8 1.0 CG D:GLN11 4.8 110.0 1.0 H5' D:GDP501 4.8 95.7 1.0 HE21 D:GLN11 4.9 111.5 1.0 O1B D:GDP501 5.0 71.5 1.0

M.Wranik, M.W.Kepa, E.V.Beale, D.James, Q.Bertrand, T.Weinert, A.Furrer, H.Glover, D.Gashi, M.Carrillo, Y.Kondo, R.T.Stipp, G.Khusainov, K.Nass, D.Ozerov, C.Cirelli, P.J.M.Johnson, F.Dworkowski, J.H.Beale, S.Stubbs, T.Zamofing, M.Schneider, K.Krauskopf, L.Gao, O.Thorn-Seshold, C.Bostedt, C.Bacellar, M.O.Steinmetz, C.Milne, J.Standfuss. A Multi-Reservoir Extruder For Time-Resolved Serial Protein Crystallography and Compound Screening at X-Ray Free-Electron Lasers. Nat Commun V. 14 7956 2023.
ISSN: ESSN 2041-1723
PubMed: 38042952
DOI: 10.1038/S41467-023-43523-5