Magnesium in PDB 7mnp: Crystal Structure of the ZNF2 of Nucleoporin NUP358/RANBP2 in Complex with Ran-Gdp

The structure of Crystal Structure of the ZNF2 of Nucleoporin NUP358/RANBP2 in Complex with Ran-Gdp, PDB code: 7mnp was solved by C.J.Bley, S.Nie, G.W.Mobbs, S.Petrovic, A.T.Gres, X.Liu, S.Mukherjee, S.Harvey, F.M.Huber, D.H.Lin, B.Brown, A.W.Tang, E.J.Rundlet, A.R.Correia, S.Chen, S.G.Regmi, T.A.Stevens, C.A.Jette, M.Dasso, A.Patke, A.F.Palazzo, A.A.Kossiakoff, A.Hoelz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.02 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.23, 79.84, 108.75, 90, 90, 90
R / Rfree (%)	19.4 / 23.1

The structure of Crystal Structure of the ZNF2 of Nucleoporin NUP358/RANBP2 in Complex with Ran-Gdp also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of the ZNF2 of Nucleoporin NUP358/RANBP2 in Complex with Ran-Gdp (pdb code 7mnp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the ZNF2 of Nucleoporin NUP358/RANBP2 in Complex with Ran-Gdp, PDB code: 7mnp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the ZNF2 of Nucleoporin NUP358/RANBP2 in Complex with Ran-Gdp


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 the ZNF2 of Nucleoporin NUP358/RANBP2 in Complex with Ran-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:29.3 occ:1.00 O3B A:GDP301 2.1 27.0 1.0 OG1 A:THR24 2.1 23.3 1.0 O A:HOH505 2.1 24.4 1.0 O A:HOH540 2.2 24.1 1.0 O A:HOH526 2.2 21.6 1.0 O A:HOH501 2.2 24.7 1.0 HB A:THR24 3.1 33.2 1.0 CB A:THR24 3.2 27.6 1.0 H A:THR24 3.2 28.5 1.0 PB A:GDP301 3.3 27.7 1.0 O2B A:GDP301 3.4 25.8 1.0 N A:THR24 3.8 23.8 1.0 HB2 A:LYS23 3.9 31.2 1.0 O2A A:GDP301 4.0 26.3 1.0 CA A:THR24 4.1 23.7 1.0 HG21 A:THR24 4.1 30.8 1.0 OD1 A:ASP65 4.2 23.6 1.0 O1B A:GDP301 4.2 28.2 1.0 O A:THR66 4.2 24.1 1.0 OD2 A:ASP65 4.2 23.9 1.0 HE2 A:LYS23 4.2 30.6 1.0 CG2 A:THR24 4.3 25.7 1.0 OG1 A:THR66 4.3 28.1 1.0 O3A A:GDP301 4.4 25.4 1.0 HA A:THR24 4.4 28.4 1.0 OE2 A:GLU70 4.4 28.9 1.0 H A:GLY68 4.6 31.4 1.0 PA A:GDP301 4.6 29.7 1.0 O A:HOH591 4.6 40.0 1.0 HG1 A:THR66 4.6 33.7 1.0 CG A:ASP65 4.6 28.8 1.0 HA2 A:GLY68 4.6 31.3 1.0 O1A A:GDP301 4.6 29.7 1.0 HZ1 A:LYS23 4.6 32.4 1.0 HZ3 A:LYS23 4.6 32.4 1.0 HG23 A:THR24 4.8 30.8 1.0 O A:HOH521 4.8 34.2 1.0 CB A:LYS23 4.9 26.0 1.0 N A:GLY68 4.9 26.2 1.0 O A:HOH588 4.9 48.6 1.0 C A:LYS23 4.9 26.2 1.0 H A:LYS23 4.9 30.1 1.0 NZ A:LYS23 4.9 27.0 1.0 HG22 A:THR24 5.0 30.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the ZNF2 of Nucleoporin NUP358/RANBP2 in Complex with Ran-Gdp


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 the ZNF2 of Nucleoporin NUP358/RANBP2 in Complex with Ran-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:30.7 occ:1.00 O C:HOH445 2.1 28.5 1.0 O1B C:GDP301 2.1 27.2 1.0 OG1 C:THR24 2.1 31.6 1.0 O C:HOH409 2.2 25.8 1.0 O C:HOH434 2.2 27.9 1.0 O C:HOH402 2.2 28.5 1.0 CB C:THR24 3.2 31.3 1.0 HB C:THR24 3.2 37.6 1.0 H C:THR24 3.3 35.4 1.0 PB C:GDP301 3.3 28.7 1.0 O2B C:GDP301 3.5 30.0 1.0 N C:THR24 3.9 29.5 1.0 HB2 C:LYS23 4.0 35.9 1.0 O1A C:GDP301 4.1 28.0 1.0 HG21 C:THR24 4.1 38.1 1.0 OD2 C:ASP65 4.2 30.1 1.0 CA C:THR24 4.2 29.7 1.0 HE2 C:LYS23 4.2 36.5 1.0 OD1 C:ASP65 4.2 26.6 1.0 O C:THR66 4.2 29.5 1.0 O3B C:GDP301 4.2 28.8 1.0 OG1 C:THR66 4.3 29.8 1.0 CG2 C:THR24 4.3 31.7 1.0 O C:HOH502 4.3 44.9 1.0 HA C:THR24 4.4 35.7 1.0 OE2 C:GLU70 4.4 34.0 1.0 O3A C:GDP301 4.5 28.1 1.0 HZ1 C:LYS23 4.5 38.2 1.0 H C:GLY68 4.5 38.7 1.0 HG1 C:THR66 4.5 35.7 1.0 HA2 C:GLY68 4.6 39.7 1.0 CG C:ASP65 4.6 30.1 1.0 PA C:GDP301 4.6 32.4 1.0 HZ3 C:LYS23 4.7 38.2 1.0 O2A C:GDP301 4.7 34.5 1.0 HG23 C:THR24 4.8 38.1 1.0 N C:GLY68 4.9 32.3 1.0 NZ C:LYS23 4.9 31.8 1.0 O C:HOH439 4.9 34.7 1.0 C C:THR66 5.0 30.0 1.0 CB C:LYS23 5.0 29.9 1.0 CE C:LYS23 5.0 30.4 1.0

C.J.Bley, S.Nie, G.W.Mobbs, S.Petrovic, A.T.Gres, X.Liu, S.Mukherjee, S.Harvey, F.M.Huber, D.H.Lin, B.Brown, A.W.Tang, E.J.Rundlet, A.R.Correia, S.Chen, S.G.Regmi, T.A.Stevens, C.A.Jette, M.Dasso, A.Patke, A.F.Palazzo, A.A.Kossiakoff, A.Hoelz. Architecture of the Cytoplasmic Face of the Nuclear Pore. Science V. 376 M9129 2022.
ISSN: ESSN 1095-9203
PubMed: 35679405
DOI: 10.1126/SCIENCE.ABM9129