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Magnesium in PDB 7mnt: Crystal Structure of the ZNF5 or ZNF6 of Nucleoporin NUP358/RANBP2 in Complex with Ran-Gdp

Protein crystallography data

The structure of Crystal Structure of the ZNF5 or ZNF6 of Nucleoporin NUP358/RANBP2 in Complex with Ran-Gdp, PDB code: 7mnt 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) 29.52 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.02, 94.27, 108.16, 90, 90, 90
R / Rfree (%) 21.2 / 25.7

Other elements in 7mnt:

The structure of Crystal Structure of the ZNF5 or ZNF6 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 ZNF5 or ZNF6 of Nucleoporin NUP358/RANBP2 in Complex with Ran-Gdp (pdb code 7mnt). 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 ZNF5 or ZNF6 of Nucleoporin NUP358/RANBP2 in Complex with Ran-Gdp, PDB code: 7mnt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7mnt

Go back to Magnesium Binding Sites List in 7mnt
Magnesium binding site 1 out of 2 in the Crystal Structure of the ZNF5 or ZNF6 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 ZNF5 or ZNF6 of Nucleoporin NUP358/RANBP2 in Complex with Ran-Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:75.7
occ:1.00
O3B A:GDP301 2.0 69.6 1.0
O A:HOH403 2.1 79.3 1.0
O A:HOH402 2.1 84.1 1.0
OG1 A:THR24 2.1 65.3 1.0
O A:HOH409 2.1 59.5 1.0
O A:HOH405 2.2 62.8 1.0
PB A:GDP301 3.2 57.9 1.0
CB A:THR24 3.3 65.9 1.0
HB A:THR24 3.3 79.9 1.0
H A:THR24 3.3 67.4 1.0
O2B A:GDP301 3.4 74.5 1.0
O2A A:GDP301 3.9 57.0 1.0
N A:THR24 4.0 55.5 1.0
O1B A:GDP301 4.1 62.2 1.0
O A:THR66 4.1 79.4 1.0
HB2 A:LYS23 4.1 64.3 1.0
HG21 A:THR24 4.2 61.6 1.0
CA A:THR24 4.2 55.1 1.0
OD2 A:ASP65 4.2 68.8 1.0
HZ2 A:LYS23 4.3 72.8 1.0
OD1 A:ASP65 4.3 66.2 1.0
CG2 A:THR24 4.3 50.7 1.0
O3A A:GDP301 4.4 63.6 1.0
PA A:GDP301 4.5 76.5 1.0
HA A:THR24 4.5 67.0 1.0
HZ3 A:LYS23 4.6 72.8 1.0
O1A A:GDP301 4.6 53.7 1.0
HE22 A:GLN69 4.6 164.7 1.0
CG A:ASP65 4.7 66.2 1.0
OG1 A:THR66 4.7 91.7 1.0
HE2 A:LYS23 4.7 82.1 1.0
HG23 A:THR24 4.8 61.6 1.0
NZ A:LYS23 4.8 60.0 1.0
HE21 A:GLN69 4.9 164.7 1.0
NE2 A:GLN69 4.9 136.6 1.0
HA A:ALA67 5.0 117.1 1.0

Magnesium binding site 2 out of 2 in 7mnt

Go back to Magnesium Binding Sites List in 7mnt
Magnesium binding site 2 out of 2 in the Crystal Structure of the ZNF5 or ZNF6 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 ZNF5 or ZNF6 of Nucleoporin NUP358/RANBP2 in Complex with Ran-Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:102.2
occ:1.00
O1B C:GDP301 2.0 101.8 1.0
O C:HOH401 2.1 96.5 1.0
O C:HOH402 2.1 125.7 1.0
OG1 C:THR24 2.1 110.0 1.0
O C:HOH405 2.2 114.5 1.0
O C:HOH404 2.2 91.3 1.0
HB C:THR24 3.2 117.7 1.0
PB C:GDP301 3.2 90.0 1.0
CB C:THR24 3.2 97.4 1.0
O2B C:GDP301 3.4 113.4 1.0
H C:THR24 3.5 116.5 1.0
O1A C:GDP301 3.9 80.2 1.0
O C:THR66 3.9 103.4 1.0
HG21 C:THR24 3.9 114.2 1.0
O3B C:GDP301 4.1 64.0 1.0
N C:THR24 4.1 96.5 1.0
CG2 C:THR24 4.2 94.5 1.0
CA C:THR24 4.3 109.0 1.0
HB2 C:LYS23 4.3 110.5 1.0
OD2 C:ASP65 4.4 87.8 1.0
O3A C:GDP301 4.4 79.3 1.0
HZ1 C:LYS23 4.4 113.9 1.0
HE2 C:LYS23 4.5 131.5 1.0
OD1 C:ASP65 4.5 92.6 1.0
HA C:THR24 4.6 131.5 1.0
PA C:GDP301 4.6 97.2 1.0
HZ3 C:LYS23 4.6 113.9 1.0
HG23 C:THR24 4.7 114.2 1.0
HA C:ALA67 4.8 142.0 1.0
O2A C:GDP301 4.8 103.5 1.0
HG22 C:THR24 4.9 114.2 1.0
CG C:ASP65 4.9 98.5 1.0
OG1 C:THR66 4.9 106.6 1.0
NZ C:LYS23 4.9 94.2 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 01:02:18 2024

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