Magnesium in PDB 7mnz: Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 4 in Complex with Ran-Gppnhp

The structure of Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 4 in Complex with Ran-Gppnhp, PDB code: 7mnz 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)	29.36 / 2.35
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	142.69, 142.69, 96.65, 90, 90, 120
R / Rfree (%)	18.3 / 22.5

The binding sites of Magnesium atom in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 4 in Complex with Ran-Gppnhp (pdb code 7mnz). 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 NUP358/RANBP2 Ran-Binding Domain 4 in Complex with Ran-Gppnhp, PDB code: 7mnz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 4 in Complex with Ran-Gppnhp


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 NUP358/RANBP2 Ran-Binding Domain 4 in Complex with Ran-Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:33.9 occ:1.00 O2G A:GNP301 1.9 32.1 1.0 OG1 A:THR24 2.0 33.4 1.0 OG1 A:THR42 2.0 34.1 1.0 O A:HOH409 2.1 31.6 1.0 O A:HOH418 2.2 35.5 1.0 O2B A:GNP301 2.2 34.8 1.0 HB A:THR24 3.0 44.3 1.0 CB A:THR24 3.1 36.9 1.0 H A:THR42 3.1 43.6 1.0 HB A:THR42 3.1 43.5 1.0 CB A:THR42 3.1 36.2 1.0 PG A:GNP301 3.2 34.8 1.0 H A:THR24 3.3 41.9 1.0 PB A:GNP301 3.4 35.7 1.0 N3B A:GNP301 3.4 38.6 1.0 N A:THR42 3.7 36.3 1.0 N A:THR24 3.9 34.8 1.0 HG21 A:THR24 3.9 44.7 1.0 O A:HOH405 4.0 40.2 1.0 OD2 A:ASP65 4.0 40.3 1.0 O3G A:GNP301 4.0 35.9 1.0 CA A:THR42 4.0 35.4 1.0 HB2 A:LYS23 4.0 40.3 1.0 CA A:THR24 4.0 36.9 1.0 CG2 A:THR24 4.1 37.2 1.0 HG21 A:THR42 4.2 42.3 1.0 HNB3 A:GNP301 4.2 46.4 1.0 O2A A:GNP301 4.2 38.2 1.0 HE2 A:LYS23 4.2 41.0 1.0 O1G A:GNP301 4.2 42.0 1.0 OD1 A:ASP65 4.2 39.4 1.0 CG2 A:THR42 4.3 35.1 1.0 O3A A:GNP301 4.4 35.6 1.0 HA A:THR24 4.4 44.4 1.0 HA A:THR42 4.4 41.9 1.0 HA A:ALA41 4.4 45.1 1.0 O1B A:GNP301 4.4 37.4 1.0 CG A:ASP65 4.5 34.9 1.0 O A:THR66 4.5 35.8 1.0 O A:VAL40 4.6 37.5 1.0 PA A:GNP301 4.6 36.0 1.0 HA A:ALA67 4.6 42.7 1.0 HG23 A:THR24 4.6 44.7 1.0 HE1 A:TYR39 4.7 47.7 1.0 O1A A:GNP301 4.7 34.8 1.0 HG23 A:THR42 4.7 42.3 1.0 C A:ALA41 4.7 39.2 1.0 HZ2 A:LYS23 4.8 46.6 1.0 HG22 A:THR24 4.8 44.7 1.0 O A:HOH422 4.9 37.7 1.0 HZ1 A:LYS23 4.9 46.6 1.0 CB A:LYS23 5.0 33.5 1.0 HG22 A:THR42 5.0 42.3 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 4 in Complex with Ran-Gppnhp


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 NUP358/RANBP2 Ran-Binding Domain 4 in Complex with Ran-Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:36.1 occ:1.00 OG1 C:THR24 2.0 32.5 1.0 O C:HOH418 2.0 38.8 1.0 O2B C:GNP301 2.1 30.3 1.0 OG1 C:THR42 2.1 36.5 1.0 O2G C:GNP301 2.1 35.4 1.0 O C:HOH409 2.2 33.0 1.0 HB C:THR42 3.0 50.9 1.0 HB C:THR24 3.1 43.8 1.0 CB C:THR24 3.1 36.4 1.0 CB C:THR42 3.1 42.3 1.0 H C:THR42 3.1 49.2 1.0 H C:THR24 3.3 44.6 1.0 PG C:GNP301 3.3 33.8 1.0 PB C:GNP301 3.3 34.5 1.0 N3B C:GNP301 3.5 37.9 1.0 N C:THR42 3.7 40.9 1.0 N C:THR24 3.9 37.1 1.0 HG21 C:THR24 3.9 43.9 1.0 OD2 C:ASP65 4.0 40.7 1.0 CA C:THR42 4.0 35.9 1.0 O3G C:GNP301 4.0 38.3 1.0 HB2 C:LYS23 4.0 40.4 1.0 CA C:THR24 4.0 38.1 1.0 CG2 C:THR24 4.1 36.5 1.0 HG21 C:THR42 4.2 44.5 1.0 HNB3 C:GNP301 4.2 45.6 1.0 CG2 C:THR42 4.3 37.0 1.0 HE2 C:LYS23 4.3 43.5 1.0 O2A C:GNP301 4.3 31.9 1.0 O C:HOH428 4.3 39.6 1.0 OD1 C:ASP65 4.3 41.1 1.0 O3A C:GNP301 4.3 41.8 1.0 HA C:ALA41 4.4 50.7 1.0 HA C:THR24 4.4 45.9 1.0 HA C:THR42 4.4 42.7 1.0 O1G C:GNP301 4.4 45.4 1.0 O1B C:GNP301 4.4 31.1 1.0 CG C:ASP65 4.5 40.0 1.0 O C:VAL40 4.5 40.9 1.0 HG23 C:THR24 4.6 43.9 1.0 PA C:GNP301 4.6 36.0 1.0 O1A C:GNP301 4.6 32.6 1.0 O C:THR66 4.7 35.0 1.0 HA C:ALA67 4.7 45.3 1.0 HZ3 C:LYS23 4.7 43.7 1.0 C C:ALA41 4.7 42.8 1.0 HE1 C:TYR39 4.7 50.4 1.0 HZ2 C:LYS23 4.8 43.7 1.0 HG23 C:THR42 4.8 44.5 1.0 HG22 C:THR24 4.8 43.9 1.0 HG22 C:THR42 4.9 44.5 1.0 CB C:LYS23 5.0 33.6 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 4 in Complex with Ran-Gppnhp


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 NUP358/RANBP2 Ran-Binding Domain 4 in Complex with Ran-Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg302 b:49.8 occ:1.00 OG1 E:THR24 2.0 46.3 1.0 OG1 E:THR42 2.0 49.5 1.0 O E:HOH402 2.1 53.9 1.0 O E:HOH405 2.1 52.6 1.0 O2G E:GNP301 2.1 44.5 1.0 O2B E:GNP301 2.2 44.4 1.0 HB E:THR42 3.0 72.8 1.0 H E:THR42 3.0 67.7 1.0 CB E:THR42 3.1 60.6 1.0 CB E:THR24 3.1 52.5 1.0 HB E:THR24 3.1 63.0 1.0 H E:THR24 3.3 58.8 1.0 PG E:GNP301 3.3 47.3 1.0 PB E:GNP301 3.4 46.7 1.0 N3B E:GNP301 3.5 54.3 1.0 N E:THR42 3.6 56.3 1.0 OD2 E:ASP65 3.8 51.0 1.0 N E:THR24 3.9 48.9 1.0 CA E:THR42 3.9 58.1 1.0 HG21 E:THR24 4.0 56.4 1.0 HB2 E:LYS23 4.0 53.4 1.0 CA E:THR24 4.1 48.3 1.0 CG2 E:THR24 4.1 46.9 1.0 HG21 E:THR42 4.1 68.4 1.0 O3G E:GNP301 4.2 48.3 1.0 OD1 E:ASP65 4.2 55.7 1.0 HNB3 E:GNP301 4.2 65.3 1.0 HE2 E:LYS23 4.2 60.8 1.0 CG2 E:THR42 4.2 56.9 1.0 HA E:THR42 4.3 69.9 1.0 CG E:ASP65 4.4 56.8 1.0 O3A E:GNP301 4.4 46.2 1.0 HA E:THR24 4.4 58.0 1.0 HA E:ALA41 4.4 69.0 1.0 O1G E:GNP301 4.4 54.5 1.0 O2A E:GNP301 4.4 41.0 1.0 O1B E:GNP301 4.5 41.0 1.0 O E:VAL40 4.5 57.2 1.0 O1A E:GNP301 4.5 50.3 1.0 HG23 E:THR24 4.6 56.4 1.0 PA E:GNP301 4.6 45.4 1.0 O E:THR66 4.7 56.1 1.0 C E:ALA41 4.7 57.4 1.0 HG23 E:THR42 4.7 68.4 1.0 HE1 E:TYR39 4.7 60.7 1.0 HA E:ALA67 4.7 68.8 1.0 HG22 E:THR24 4.9 56.4 1.0 CB E:LYS23 4.9 44.4 1.0 HG22 E:THR42 4.9 68.4 1.0 HZ2 E:LYS23 5.0 64.6 1.0 HZ3 E:LYS23 5.0 64.6 1.0 O E:HOH410 5.0 49.1 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 4 in Complex with Ran-Gppnhp


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 NUP358/RANBP2 Ran-Binding Domain 4 in Complex with Ran-Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg302 b:33.6 occ:1.00 OG1 G:THR24 2.0 31.1 1.0 OG1 G:THR42 2.1 33.8 1.0 O2B G:GNP301 2.1 30.9 1.0 O G:HOH418 2.1 31.4 1.0 O2G G:GNP301 2.1 36.0 1.0 O G:HOH414 2.2 38.3 1.0 HB G:THR24 3.1 39.9 1.0 CB G:THR24 3.1 33.1 1.0 HB G:THR42 3.1 49.6 1.0 H G:THR42 3.1 48.2 1.0 CB G:THR42 3.1 41.3 1.0 PG G:GNP301 3.3 33.9 1.0 H G:THR24 3.3 38.5 1.0 PB G:GNP301 3.3 33.9 1.0 N3B G:GNP301 3.5 38.2 1.0 N G:THR42 3.7 40.1 1.0 HG21 G:THR24 3.9 43.4 1.0 N G:THR24 3.9 32.0 1.0 OD2 G:ASP65 3.9 34.3 1.0 O3G G:GNP301 4.0 36.2 1.0 CA G:THR42 4.0 34.9 1.0 HB2 G:LYS23 4.1 38.3 1.0 CA G:THR24 4.1 34.0 1.0 CG2 G:THR24 4.1 36.1 1.0 HG21 G:THR42 4.2 49.0 1.0 O G:HOH411 4.2 41.5 1.0 HNB3 G:GNP301 4.2 46.0 1.0 O2A G:GNP301 4.3 30.6 1.0 CG2 G:THR42 4.3 40.7 1.0 OD1 G:ASP65 4.3 38.7 1.0 HE2 G:LYS23 4.3 43.3 1.0 O3A G:GNP301 4.3 37.2 1.0 HA G:THR42 4.4 42.0 1.0 HA G:THR24 4.4 41.0 1.0 O1B G:GNP301 4.4 32.4 1.0 HA G:ALA41 4.4 47.5 1.0 O1G G:GNP301 4.4 42.1 1.0 CG G:ASP65 4.5 36.1 1.0 O G:VAL40 4.5 41.0 1.0 O1A G:GNP301 4.5 32.0 1.0 PA G:GNP301 4.6 32.1 1.0 HG23 G:THR24 4.6 43.4 1.0 HA G:ALA67 4.6 42.6 1.0 O G:THR66 4.7 33.9 1.0 HE1 G:TYR39 4.7 44.3 1.0 C G:ALA41 4.7 38.0 1.0 HG23 G:THR42 4.7 49.0 1.0 HG22 G:THR24 4.8 43.4 1.0 HZ1 G:LYS23 4.8 43.4 1.0 HZ3 G:LYS23 4.9 43.4 1.0 HG22 G:THR42 5.0 49.0 1.0 CB G:LYS23 5.0 31.8 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 4 in Complex with Ran-Gppnhp


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 NUP358/RANBP2 Ran-Binding Domain 4 in Complex with Ran-Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg302 b:41.5 occ:1.00 OG1 I:THR24 2.0 42.0 1.0 O3G I:GNP301 2.0 43.2 1.0 OG1 I:THR42 2.0 44.8 1.0 O2B I:GNP301 2.1 37.6 1.0 O I:HOH409 2.2 46.8 1.0 O I:HOH405 2.2 46.5 1.0 H I:THR42 3.0 58.1 1.0 HB I:THR24 3.1 55.8 1.0 HB I:THR42 3.1 62.2 1.0 CB I:THR24 3.1 46.4 1.0 CB I:THR42 3.1 51.7 1.0 PG I:GNP301 3.3 42.0 1.0 H I:THR24 3.3 54.6 1.0 PB I:GNP301 3.3 45.3 1.0 N3B I:GNP301 3.5 50.2 1.0 N I:THR42 3.7 48.4 1.0 OD2 I:ASP65 3.9 45.5 1.0 N I:THR24 3.9 45.4 1.0 HG21 I:THR24 3.9 47.5 1.0 CA I:THR42 4.0 51.2 1.0 HB2 I:LYS23 4.0 53.8 1.0 O1G I:GNP301 4.0 50.4 1.0 CA I:THR24 4.1 46.6 1.0 O2A I:GNP301 4.1 40.2 1.0 CG2 I:THR24 4.1 40.1 1.0 HG21 I:THR42 4.1 61.6 1.0 OD1 I:ASP65 4.2 49.0 1.0 CG2 I:THR42 4.2 51.2 1.0 HNB3 I:GNP301 4.3 60.4 1.0 O3A I:GNP301 4.3 49.6 1.0 HE2 I:LYS23 4.3 61.4 1.0 HA I:THR42 4.3 61.5 1.0 HA I:THR24 4.4 56.0 1.0 O1B I:GNP301 4.4 44.6 1.0 CG I:ASP65 4.4 49.9 1.0 HA I:ALA41 4.4 62.3 1.0 O2G I:GNP301 4.4 52.2 1.0 PA I:GNP301 4.5 46.6 1.0 O1A I:GNP301 4.6 43.2 1.0 O I:VAL40 4.6 46.9 1.0 HG23 I:THR24 4.6 47.5 1.0 HA I:ALA67 4.7 67.7 1.0 HG23 I:THR42 4.7 61.6 1.0 O I:THR66 4.8 52.2 1.0 C I:ALA41 4.8 54.5 1.0 HE1 I:TYR39 4.8 57.8 1.0 O I:HOH403 4.8 44.6 1.0 HG22 I:THR24 4.8 47.5 1.0 CB I:LYS23 4.9 44.8 1.0 HG22 I:THR42 5.0 61.6 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 4 in Complex with Ran-Gppnhp


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 NUP358/RANBP2 Ran-Binding Domain 4 in Complex with Ran-Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg302 b:44.6 occ:1.00 OG1 K:THR24 2.0 39.4 1.0 OG1 K:THR42 2.1 36.6 1.0 O2G K:GNP301 2.1 39.5 1.0 O K:HOH408 2.2 38.1 1.0 O K:HOH406 2.2 39.4 1.0 O2B K:GNP301 2.2 35.3 1.0 HB K:THR24 3.1 50.5 1.0 CB K:THR24 3.1 42.0 1.0 H K:THR42 3.1 48.6 1.0 HB K:THR42 3.1 49.8 1.0 CB K:THR42 3.1 41.4 1.0 PG K:GNP301 3.3 36.6 1.0 H K:THR24 3.3 48.3 1.0 PB K:GNP301 3.4 36.6 1.0 N3B K:GNP301 3.5 43.7 1.0 N K:THR42 3.7 40.4 1.0 N K:THR24 3.9 40.2 1.0 HG21 K:THR24 3.9 51.6 1.0 CA K:THR42 4.0 40.9 1.0 OD2 K:ASP65 4.0 50.6 1.0 O3G K:GNP301 4.1 34.1 1.0 HB2 K:LYS23 4.1 46.7 1.0 CA K:THR24 4.1 43.0 1.0 O K:HOH404 4.1 42.0 1.0 CG2 K:THR24 4.1 42.9 1.0 HG21 K:THR42 4.2 49.5 1.0 HNB3 K:GNP301 4.2 52.5 1.0 OD1 K:ASP65 4.3 44.0 1.0 CG2 K:THR42 4.3 41.1 1.0 HE2 K:LYS23 4.3 50.2 1.0 O1G K:GNP301 4.4 43.0 1.0 HA K:THR42 4.4 49.1 1.0 HA K:ALA41 4.4 55.3 1.0 O3A K:GNP301 4.4 46.6 1.0 HA K:THR24 4.4 51.8 1.0 O2A K:GNP301 4.5 39.5 1.0 CG K:ASP65 4.5 48.6 1.0 O1B K:GNP301 4.5 41.9 1.0 O K:VAL40 4.5 41.6 1.0 HG23 K:THR24 4.6 51.6 1.0 O1A K:GNP301 4.6 42.2 1.0 HA K:ALA67 4.6 52.6 1.0 PA K:GNP301 4.7 39.9 1.0 C K:ALA41 4.7 41.5 1.0 O K:THR66 4.7 39.8 1.0 HG23 K:THR42 4.7 49.5 1.0 HE1 K:TYR39 4.7 52.5 1.0 HZ3 K:LYS23 4.8 51.6 1.0 HZ1 K:LYS23 4.8 51.6 1.0 HG22 K:THR24 4.8 51.6 1.0 HG22 K:THR42 5.0 49.5 1.0 CB K:LYS23 5.0 38.8 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