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Magnesium in PDB 7mnw: Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 1 in Complex with Ran-Gppnhp

Protein crystallography data

The structure of Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 1 in Complex with Ran-Gppnhp, PDB code: 7mnw 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) 28.96 / 2.40
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 137.37, 137.834, 172.934, 90, 90, 90
R / Rfree (%) 20 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 1 in Complex with Ran-Gppnhp (pdb code 7mnw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 1 in Complex with Ran-Gppnhp, PDB code: 7mnw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7mnw

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Magnesium binding site 1 out of 4 in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 1 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 1 in Complex with Ran-Gppnhp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:32.1
occ:1.00
OG1 A:THR24 2.0 31.8 1.0
OG1 A:THR42 2.1 31.0 1.0
O2G A:GNP301 2.1 33.3 1.0
O2B A:GNP301 2.1 33.8 1.0
O A:HOH407 2.1 29.6 1.0
O A:HOH428 2.1 32.8 1.0
H A:THR42 3.0 40.0 1.0
HB A:THR42 3.1 43.8 1.0
CB A:THR42 3.1 36.5 1.0
CB A:THR24 3.2 33.3 1.0
HB A:THR24 3.2 40.0 1.0
PG A:GNP301 3.3 29.3 1.0
PB A:GNP301 3.3 30.0 1.0
H A:THR24 3.3 39.5 1.0
N3B A:GNP301 3.5 32.2 1.0
N A:THR42 3.6 33.4 1.0
N A:THR24 3.9 32.9 1.0
OD2 A:ASP65 4.0 28.8 1.0
CA A:THR42 4.0 33.4 1.0
O3G A:GNP301 4.0 30.1 1.0
HB2 A:LYS23 4.0 38.3 1.0
HG21 A:THR24 4.0 42.2 1.0
CA A:THR24 4.1 33.1 1.0
OD1 A:ASP65 4.1 30.5 1.0
HE2 A:LYS23 4.2 37.8 1.0
CG2 A:THR24 4.2 35.2 1.0
HG21 A:THR42 4.2 43.0 1.0
HA A:ALA41 4.2 41.6 1.0
HNB3 A:GNP301 4.2 38.6 1.0
O1A A:GNP301 4.2 31.0 1.0
CG2 A:THR42 4.3 35.9 1.0
O3A A:GNP301 4.3 27.2 1.0
HA A:THR42 4.4 40.1 1.0
O1B A:GNP301 4.4 31.8 1.0
O1G A:GNP301 4.4 38.0 1.0
CG A:ASP65 4.4 30.9 1.0
HA A:THR24 4.4 39.6 1.0
O A:HOH408 4.4 29.5 1.0
HA A:ALA67 4.5 46.5 1.0
O2A A:GNP301 4.5 36.7 1.0
PA A:GNP301 4.6 31.6 1.0
O A:VAL40 4.6 33.1 1.0
HG23 A:THR24 4.6 42.2 1.0
C A:ALA41 4.6 36.0 1.0
O A:THR66 4.7 29.6 1.0
HG23 A:THR42 4.7 43.0 1.0
O A:HOH419 4.7 37.8 1.0
HZ1 A:LYS23 4.9 38.4 1.0
CB A:LYS23 4.9 31.9 1.0
CA A:ALA41 4.9 34.7 1.0
HZ3 A:LYS23 4.9 38.4 1.0
HG22 A:THR24 5.0 42.2 1.0

Magnesium binding site 2 out of 4 in 7mnw

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Magnesium binding site 2 out of 4 in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 1 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 1 in Complex with Ran-Gppnhp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:34.6
occ:1.00
OG1 C:THR24 2.0 35.0 1.0
OG1 C:THR42 2.1 37.4 1.0
O2G C:GNP301 2.1 35.8 1.0
O C:HOH402 2.1 30.7 1.0
O C:HOH410 2.2 34.6 1.0
O2B C:GNP301 2.3 34.9 1.0
HB C:THR42 3.0 45.9 1.0
CB C:THR42 3.1 38.3 1.0
CB C:THR24 3.1 34.7 1.0
HB C:THR24 3.1 41.6 1.0
H C:THR42 3.2 51.1 1.0
PG C:GNP301 3.3 33.1 1.0
H C:THR24 3.3 41.8 1.0
PB C:GNP301 3.4 33.7 1.0
N3B C:GNP301 3.5 38.9 1.0
N C:THR42 3.7 42.6 1.0
OD2 C:ASP65 3.8 36.2 1.0
N C:THR24 3.9 34.8 1.0
HB2 C:LYS23 3.9 38.6 1.0
CA C:THR42 4.0 41.8 1.0
HG21 C:THR24 4.0 42.2 1.0
O3G C:GNP301 4.0 35.4 1.0
OD1 C:ASP65 4.1 36.0 1.0
CA C:THR24 4.1 34.0 1.0
HNB3 C:GNP301 4.1 46.6 1.0
HG21 C:THR42 4.1 50.4 1.0
HE2 C:LYS23 4.2 42.5 1.0
CG2 C:THR24 4.2 35.2 1.0
CG2 C:THR42 4.2 42.0 1.0
CG C:ASP65 4.3 36.2 1.0
O1A C:GNP301 4.3 34.2 1.0
HA C:THR42 4.3 50.1 1.0
O C:HOH421 4.3 36.2 1.0
HA C:THR24 4.4 40.7 1.0
O1G C:GNP301 4.4 43.4 1.0
O3A C:GNP301 4.4 32.7 1.0
HA C:ALA41 4.4 52.7 1.0
O2A C:GNP301 4.5 38.1 1.0
HA C:ALA67 4.5 54.8 1.0
O C:VAL40 4.5 41.8 1.0
O1B C:GNP301 4.6 34.1 1.0
PA C:GNP301 4.6 38.2 1.0
HG23 C:THR24 4.6 42.2 1.0
C C:ALA41 4.7 42.9 1.0
HZ1 C:LYS23 4.7 43.5 1.0
HG23 C:THR42 4.7 50.4 1.0
HZ3 C:LYS23 4.7 43.5 1.0
O C:THR66 4.7 38.8 1.0
CB C:LYS23 4.9 32.2 1.0
HG22 C:THR24 4.9 42.2 1.0
HG22 C:THR42 4.9 50.4 1.0
C C:LYS23 4.9 33.3 1.0

Magnesium binding site 3 out of 4 in 7mnw

Go back to Magnesium Binding Sites List in 7mnw
Magnesium binding site 3 out of 4 in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 1 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 1 in Complex with Ran-Gppnhp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:54.4
occ:1.00
OG1 E:THR24 2.0 53.5 1.0
O2B E:GNP301 2.0 49.6 1.0
OG1 E:THR42 2.0 58.3 1.0
O E:HOH408 2.1 60.8 1.0
O2G E:GNP301 2.1 64.1 1.0
O E:HOH404 2.2 50.4 1.0
H E:THR42 3.1 77.8 1.0
CB E:THR24 3.2 52.9 1.0
CB E:THR42 3.2 60.5 1.0
HB E:THR42 3.2 72.5 1.0
HB E:THR24 3.2 63.5 1.0
PB E:GNP301 3.3 56.1 1.0
PG E:GNP301 3.3 60.2 1.0
H E:THR24 3.3 59.6 1.0
N3B E:GNP301 3.5 64.6 1.0
N E:THR42 3.7 64.9 1.0
N E:THR24 3.9 49.7 1.0
HB2 E:LYS23 4.0 59.0 1.0
CA E:THR42 4.0 65.0 1.0
HG21 E:THR24 4.0 62.6 1.0
O3G E:GNP301 4.0 60.5 1.0
OD2 E:ASP65 4.1 48.3 1.0
CA E:THR24 4.1 51.8 1.0
CG2 E:THR24 4.2 52.2 1.0
HE2 E:LYS23 4.2 65.4 1.0
HA E:ALA41 4.2 89.7 1.0
HG21 E:THR42 4.2 71.3 1.0
HNB3 E:GNP301 4.2 77.5 1.0
OD1 E:ASP65 4.2 52.0 1.0
CG2 E:THR42 4.3 59.5 1.0
O3A E:GNP301 4.3 54.5 1.0
HA E:THR42 4.3 78.0 1.0
O1B E:GNP301 4.4 56.0 1.0
HA E:ALA67 4.4 79.4 1.0
O1A E:GNP301 4.4 59.5 1.0
O2A E:GNP301 4.4 62.1 1.0
HA E:THR24 4.5 62.1 1.0
O1G E:GNP301 4.5 74.7 1.0
CG E:ASP65 4.5 50.5 1.0
HG23 E:THR24 4.6 62.6 1.0
PA E:GNP301 4.6 56.9 1.0
C E:ALA41 4.6 71.2 1.0
O E:VAL40 4.7 66.8 1.0
HG23 E:THR42 4.7 71.3 1.0
O E:THR66 4.7 55.1 1.0
CB E:LYS23 4.9 49.2 1.0
HZ3 E:LYS23 4.9 72.5 1.0
HZ1 E:LYS23 4.9 72.5 1.0
CA E:ALA41 4.9 74.8 1.0
HG22 E:THR24 4.9 62.6 1.0
C E:LYS23 5.0 49.6 1.0

Magnesium binding site 4 out of 4 in 7mnw

Go back to Magnesium Binding Sites List in 7mnw
Magnesium binding site 4 out of 4 in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 1 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 1 in Complex with Ran-Gppnhp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg302

b:45.9
occ:1.00
OG1 G:THR24 2.0 42.9 1.0
OG1 G:THR42 2.0 47.4 1.0
O G:HOH812 2.1 48.1 1.0
O2B G:GNP301 2.1 38.2 1.0
O1G G:GNP301 2.1 45.4 1.0
O G:HOH807 2.2 35.2 1.0
H G:THR42 3.1 60.5 1.0
HB G:THR42 3.1 62.4 1.0
CB G:THR42 3.1 52.0 1.0
CB G:THR24 3.2 43.1 1.0
HB G:THR24 3.2 51.7 1.0
PG G:GNP301 3.3 45.3 1.0
PB G:GNP301 3.3 39.0 1.0
H G:THR24 3.4 49.4 1.0
N3B G:GNP301 3.5 44.4 1.0
N G:THR42 3.6 50.5 1.0
N G:THR24 3.9 41.2 1.0
CA G:THR42 4.0 51.1 1.0
HB2 G:LYS23 4.0 47.7 1.0
HG21 G:THR24 4.0 53.0 1.0
O2G G:GNP301 4.0 42.3 1.0
OD2 G:ASP65 4.0 41.9 1.0
CA G:THR24 4.1 46.3 1.0
CG2 G:THR24 4.2 44.1 1.0
HG21 G:THR42 4.2 59.0 1.0
HNB3 G:GNP301 4.2 53.3 1.0
OD1 G:ASP65 4.2 38.5 1.0
HE2 G:LYS23 4.2 53.3 1.0
HA G:ALA41 4.3 64.8 1.0
CG2 G:THR42 4.3 49.2 1.0
HA G:THR42 4.3 61.3 1.0
O3A G:GNP301 4.4 44.8 1.0
O1B G:GNP301 4.4 40.0 1.0
O2A G:GNP301 4.4 43.0 1.0
HA G:ALA67 4.4 54.0 1.0
HA G:THR24 4.5 55.5 1.0
O3G G:GNP301 4.5 52.0 1.0
CG G:ASP65 4.5 40.5 1.0
O G:VAL40 4.5 56.0 1.0
O1A G:GNP301 4.5 50.3 1.0
HG23 G:THR24 4.6 53.0 1.0
C G:ALA41 4.6 53.1 1.0
PA G:GNP301 4.6 45.6 1.0
O G:THR66 4.7 40.2 1.0
HG23 G:THR42 4.7 59.0 1.0
HZ2 G:LYS23 4.8 52.1 1.0
HZ1 G:LYS23 4.8 52.1 1.0
CB G:LYS23 4.9 39.8 1.0
HG22 G:THR24 4.9 53.0 1.0
CA G:ALA41 4.9 54.0 1.0
C G:LYS23 5.0 41.9 1.0
HG22 G:THR42 5.0 59.0 1.0

Reference:

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
Page generated: Thu Oct 3 01:03:12 2024

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