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

Protein crystallography data

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

Other elements in 7mnp:

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

Magnesium Binding Sites:

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 7mnp

Go back to Magnesium Binding Sites List in 7mnp
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 7mnp

Go back to Magnesium Binding Sites List in 7mnp
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

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: Wed Apr 5 13:20:57 2023

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