Zinc 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:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the ZNF2 of Nucleoporin NUP358/RANBP2 in Complex with Ran-Gdp, PDB code: 7mnp:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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 B:Zn1501 b:35.9 occ:1.00 SG B:CYS1424 2.3 31.9 1.0 SG B:CYS1421 2.4 32.9 1.0 SG B:CYS1438 2.4 36.3 1.0 SG B:CYS1435 2.4 40.3 1.0 HB3 B:CYS1435 3.1 44.5 1.0 H B:CYS1438 3.1 42.0 1.0 HB3 B:CYS1421 3.1 44.0 1.0 CB B:CYS1435 3.2 37.1 1.0 CB B:CYS1421 3.2 36.6 1.0 HB3 B:CYS1438 3.2 37.2 1.0 HB2 B:CYS1435 3.2 44.5 1.0 HB3 B:CYS1424 3.3 31.5 1.0 HB2 B:CYS1421 3.3 44.0 1.0 H B:CYS1424 3.3 40.1 1.0 CB B:CYS1438 3.4 31.0 1.0 CB B:CYS1424 3.4 26.3 1.0 HB B:ILE1423 3.7 46.5 1.0 HB3 B:ALA1437 3.8 49.6 1.0 HB B:VAL1426 3.9 37.7 1.0 N B:CYS1438 3.9 35.0 1.0 N B:CYS1424 3.9 33.4 1.0 H B:VAL1426 4.1 43.9 1.0 HB2 B:CYS1424 4.2 31.5 1.0 HB2 B:CYS1438 4.2 37.2 1.0 CA B:CYS1424 4.2 30.6 1.0 CA B:CYS1438 4.2 36.8 1.0 HB2 B:ASN1440 4.4 46.7 1.0 HD21 B:ASN1428 4.4 53.0 1.0 H B:ASN1440 4.4 48.1 1.0 H B:ILE1423 4.5 45.4 1.0 H B:LEU1425 4.5 40.7 1.0 H B:ALA1437 4.5 50.9 1.0 HD22 B:ASN1440 4.5 41.8 1.0 H B:GLN1439 4.6 47.3 1.0 CB B:ILE1423 4.6 38.8 1.0 CA B:CYS1435 4.7 43.6 1.0 CA B:CYS1421 4.7 37.5 1.0 C B:CYS1424 4.7 30.5 1.0 CB B:ALA1437 4.8 41.3 1.0 CB B:VAL1426 4.8 31.4 1.0 N B:LEU1425 4.8 33.9 1.0 C B:CYS1438 4.9 39.5 1.0 N B:VAL1426 4.9 36.6 1.0 C B:ILE1423 4.9 31.3 1.0 N B:GLN1439 5.0 39.4 1.0 HG22 B:ILE1423 5.0 41.8 1.0 C B:ALA1437 5.0 40.7 1.0

Zinc 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 Zinc with other atoms in the Zn 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 D:Zn1501 b:40.0 occ:1.00 SG D:CYS1438 2.3 56.9 1.0 SG D:CYS1435 2.3 60.0 1.0 SG D:CYS1424 2.3 39.8 1.0 SG D:CYS1421 2.4 45.9 1.0 HB3 D:CYS1421 3.0 55.5 1.0 HB3 D:CYS1424 3.1 45.4 1.0 CB D:CYS1421 3.1 46.3 1.0 H D:CYS1438 3.2 64.5 1.0 H D:CYS1424 3.2 47.7 1.0 HB3 D:CYS1435 3.2 76.8 1.0 CB D:CYS1435 3.2 64.0 1.0 HB2 D:CYS1421 3.2 55.5 1.0 HB2 D:CYS1435 3.3 76.8 1.0 HB3 D:CYS1438 3.3 63.5 1.0 CB D:CYS1424 3.3 37.9 1.0 CB D:CYS1438 3.4 52.9 1.0 HB D:ILE1423 3.7 54.6 1.0 N D:CYS1424 3.8 39.8 1.0 HB D:VAL1426 3.8 49.5 1.0 N D:CYS1438 3.9 53.8 1.0 HB3 D:ALA1437 3.9 61.0 1.0 H D:VAL1426 4.0 51.0 1.0 CA D:CYS1424 4.1 37.7 1.0 HB2 D:CYS1424 4.1 45.4 1.0 HB2 D:CYS1438 4.2 63.5 1.0 CA D:CYS1438 4.2 53.6 1.0 HB2 D:ASN1440 4.4 77.7 1.0 HD21 D:ASN1428 4.4 79.1 1.0 H D:ASN1440 4.4 77.0 1.0 H D:LEU1425 4.4 47.1 1.0 H D:ALA1437 4.5 69.6 1.0 H D:ILE1423 4.5 52.5 1.0 HD22 D:ASN1440 4.6 70.5 1.0 CA D:CYS1421 4.6 47.3 1.0 C D:CYS1424 4.6 37.5 1.0 H D:GLN1439 4.6 71.2 1.0 CB D:ILE1423 4.6 45.5 1.0 CA D:CYS1435 4.7 66.5 1.0 N D:LEU1425 4.8 39.2 1.0 CB D:VAL1426 4.8 41.2 1.0 C D:ILE1423 4.9 39.5 1.0 N D:VAL1426 4.9 42.5 1.0 CB D:ALA1437 4.9 50.9 1.0 HG22 D:ILE1423 4.9 52.2 1.0 C D:CYS1438 4.9 56.5 1.0 HA D:CYS1424 4.9 45.2 1.0 HH2 C:TRP64 4.9 40.9 1.0 HA D:CYS1435 5.0 79.8 1.0 HG23 D:VAL1426 5.0 47.4 1.0 N D:GLN1439 5.0 59.4 1.0 HA D:CYS1421 5.0 56.8 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