Magnesium in PDB 5nm5: Tubulin Darpin Room-Temperature Structure in Complex with Colchicine Determined By Serial Millisecond Crystallography

The structure of Tubulin Darpin Room-Temperature Structure in Complex with Colchicine Determined By Serial Millisecond Crystallography, PDB code: 5nm5 was solved by T.Weinert, N.Olieric, D.James, D.Gashi, P.Nogly, K.Jaeger, M.O.Steinmetz, J.Standfuss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.00 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.920, 85.020, 84.340, 90.00, 97.32, 90.00
R / Rfree (%)	19.3 / 23.9

The binding sites of Magnesium atom in the Tubulin Darpin Room-Temperature Structure in Complex with Colchicine Determined By Serial Millisecond Crystallography (pdb code 5nm5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Tubulin Darpin Room-Temperature Structure in Complex with Colchicine Determined By Serial Millisecond Crystallography, PDB code: 5nm5:

Magnesium binding site 1 out of 1 in the Tubulin Darpin Room-Temperature Structure in Complex with Colchicine Determined By Serial Millisecond Crystallography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin Darpin Room-Temperature Structure in Complex with Colchicine Determined By Serial Millisecond Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:48.1 occ:1.00 O A:HOH604 2.0 52.0 1.0 O A:HOH609 2.0 56.9 1.0 O A:HOH608 2.1 59.0 1.0 O3G A:GTP501 2.1 52.5 1.0 O A:HOH602 2.1 54.6 1.0 O2B A:GTP501 2.3 60.2 1.0 HZ1 B:LYS254 2.7 73.9 1.0 HB2 A:GLN11 3.3 60.2 1.0 PG A:GTP501 3.3 57.5 1.0 PB A:GTP501 3.4 62.9 1.0 NZ B:LYS254 3.6 72.6 1.0 O3B A:GTP501 3.7 65.2 1.0 H A:GLN11 3.7 60.4 1.0 O3A A:GTP501 3.8 52.4 1.0 HZ3 B:LYS254 3.8 72.4 1.0 OE1 A:GLU71 3.9 73.4 1.0 HZ2 B:LYS254 3.9 73.1 1.0 HG3 A:GLU71 3.9 66.5 1.0 O2G A:GTP501 4.0 51.2 1.0 HD22 B:ASN249 4.0 85.4 1.0 HB2 A:ASP98 4.2 60.0 1.0 ND2 B:ASN249 4.2 86.1 1.0 HG2 A:GLU71 4.2 65.7 1.0 CB A:GLN11 4.2 59.3 1.0 OD2 A:ASP98 4.2 61.6 1.0 HD21 B:ASN249 4.3 86.5 1.0 O2A A:GTP501 4.3 58.2 1.0 HB3 A:GLN11 4.3 59.0 1.0 OD2 A:ASP69 4.4 64.0 1.0 HG1 A:THR145 4.4 65.4 1.0 OD1 A:ASP69 4.4 59.4 1.0 CG A:GLU71 4.5 66.3 1.0 N A:GLN11 4.5 60.5 1.0 O1G A:GTP501 4.5 48.8 1.0 HB3 B:ASN249 4.6 90.2 1.0 OE1 A:GLN11 4.6 78.4 1.0 HB3 A:ASP98 4.6 60.6 1.0 PA A:GTP501 4.6 57.3 1.0 CD A:GLU71 4.7 77.9 1.0 CE B:LYS254 4.7 61.2 1.0 O1B A:GTP501 4.8 67.5 1.0 HG23 A:VAL74 4.8 73.9 1.0 HE3 B:LYS254 4.8 61.4 1.0 HG21 A:VAL74 4.8 72.9 1.0 CB A:ASP98 4.8 60.4 1.0 HE2 B:LYS254 4.8 61.1 1.0 CG A:ASP98 4.8 68.4 1.0 CG A:ASP69 4.9 63.1 1.0 CG B:ASN249 4.9 1.0 1.0 CA A:GLN11 4.9 58.5 1.0

T.Weinert, N.Olieric, R.Cheng, S.Brunle, D.James, D.Ozerov, D.Gashi, L.Vera, M.Marsh, K.Jaeger, F.Dworkowski, E.Panepucci, S.Basu, P.Skopintsev, A.S.Dore, T.Geng, R.M.Cooke, M.Liang, A.E.Prota, V.Panneels, P.Nogly, U.Ermler, G.Schertler, M.Hennig, M.O.Steinmetz, M.Wang, J.Standfuss. Serial Millisecond Crystallography For Routine Room-Temperature Structure Determination at Synchrotrons. Nat Commun V. 8 542 2017.
ISSN: ESSN 2041-1723
PubMed: 28912485
DOI: 10.1038/S41467-017-00630-4