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Zinc 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:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7mnt

Go back to Zinc Binding Sites List in 7mnt
Zinc 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 Zinc with other atoms in the Zn 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
B:Zn1701

b:61.5
occ:1.00
SG B:CYS1612 2.3 57.2 1.0
SG B:CYS1629 2.4 62.8 1.0
SG B:CYS1615 2.4 91.8 1.0
SG B:CYS1626 2.4 64.9 1.0
HB3 B:CYS1626 3.0 73.2 1.0
CB B:CYS1626 3.1 64.3 1.0
HB3 B:CYS1612 3.2 64.7 1.0
CB B:CYS1612 3.2 53.9 1.0
H B:CYS1615 3.2 61.5 1.0
HB2 B:CYS1626 3.2 73.2 1.0
HB2 B:CYS1612 3.2 64.7 1.0
H B:CYS1629 3.3 73.0 1.0
HB3 B:CYS1615 3.3 66.8 1.0
CB B:CYS1615 3.4 55.0 1.0
HB3 B:ASN1631 3.6 79.0 1.0
HB3 B:CYS1629 3.6 71.0 1.0
CB B:CYS1629 3.6 62.5 1.0
HB B:VAL1614 3.7 94.2 1.0
HB3 B:ALA1628 3.8 72.1 1.0
N B:CYS1615 3.8 54.6 1.0
HB B:VAL1617 4.0 62.1 1.0
N B:CYS1629 4.0 63.2 1.0
H B:ASN1631 4.0 84.3 1.0
H B:VAL1617 4.1 78.0 1.0
CA B:CYS1615 4.2 69.4 1.0
HB2 B:CYS1615 4.2 66.8 1.0
HD21 B:ASN1619 4.3 81.5 1.0
CA B:CYS1629 4.3 66.2 1.0
HB2 B:CYS1629 4.4 71.0 1.0
H B:LEU1616 4.4 69.5 1.0
H B:VAL1614 4.4 72.0 1.0
HD22 B:ASN1631 4.4 93.2 1.0
H B:ALA1628 4.5 72.9 1.0
CB B:ASN1631 4.5 65.2 1.0
HG12 B:VAL1614 4.5 71.8 1.0
CB B:VAL1614 4.6 77.8 1.0
CA B:CYS1626 4.6 64.8 1.0
H B:GLN1630 4.6 82.8 1.0
CA B:CYS1612 4.6 54.3 1.0
HB2 B:ASN1631 4.7 79.0 1.0
C B:CYS1615 4.7 62.5 1.0
CB B:ALA1628 4.7 63.4 1.0
N B:LEU1616 4.8 57.3 1.0
N B:ASN1631 4.8 69.5 1.0
C B:VAL1614 4.9 67.5 1.0
C B:CYS1629 4.9 63.0 1.0
CB B:VAL1617 4.9 51.2 1.0
HG23 B:VAL1617 4.9 70.1 1.0
N B:GLN1630 4.9 68.3 1.0
N B:VAL1617 4.9 64.4 1.0
HA B:CYS1612 5.0 64.1 1.0

Zinc binding site 2 out of 2 in 7mnt

Go back to Zinc Binding Sites List in 7mnt
Zinc 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 Zinc with other atoms in the Zn 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
D:Zn1701

b:88.8
occ:1.00
SG D:CYS1626 2.3 77.4 1.0
SG D:CYS1615 2.3 67.1 1.0
SG D:CYS1629 2.3 81.0 1.0
SG D:CYS1612 2.4 73.3 1.0
HB3 D:CYS1626 3.0 107.1 1.0
CB D:CYS1626 3.1 88.6 1.0
H D:CYS1629 3.1 113.5 1.0
HB3 D:CYS1612 3.1 85.4 1.0
HB2 D:CYS1626 3.1 107.1 1.0
CB D:CYS1612 3.2 70.5 1.0
HB2 D:CYS1612 3.2 85.4 1.0
H D:CYS1615 3.2 95.8 1.0
HB3 D:CYS1615 3.3 94.6 1.0
HB3 D:CYS1629 3.4 121.4 1.0
CB D:CYS1615 3.4 78.2 1.0
CB D:CYS1629 3.5 100.5 1.0
HB D:VAL1614 3.6 114.2 1.0
HB3 D:ALA1628 3.7 107.9 1.0
N D:CYS1629 3.8 93.9 1.0
N D:CYS1615 3.9 79.2 1.0
HB D:VAL1617 4.0 94.2 1.0
HB2 D:ASN1631 4.0 116.1 1.0
H D:ASN1631 4.2 116.6 1.0
CA D:CYS1615 4.2 72.9 1.0
H D:VAL1617 4.2 89.7 1.0
CA D:CYS1629 4.2 94.1 1.0
HB2 D:CYS1615 4.2 94.6 1.0
HB2 D:CYS1629 4.3 121.4 1.0
HD21 D:ASN1619 4.3 92.9 1.0
H D:ALA1628 4.3 107.4 1.0
H D:VAL1614 4.4 99.5 1.0
H D:LEU1616 4.5 88.0 1.0
CA D:CYS1626 4.5 90.9 1.0
CB D:VAL1614 4.5 94.5 1.0
H D:GLN1630 4.6 122.9 1.0
HD22 D:ASN1631 4.6 119.9 1.0
CB D:ALA1628 4.7 89.3 1.0
CA D:CYS1612 4.7 74.3 1.0
HG12 D:VAL1614 4.7 98.1 1.0
C D:CYS1629 4.8 99.3 1.0
C D:CYS1615 4.8 74.8 1.0
N D:LEU1616 4.9 72.7 1.0
C D:VAL1614 4.9 77.4 1.0
N D:GLN1630 4.9 101.8 1.0
HG23 D:VAL1617 4.9 89.8 1.0
HA D:CYS1626 4.9 109.9 1.0
C D:ALA1628 4.9 84.8 1.0
CB D:VAL1617 4.9 77.8 1.0
CB D:ASN1631 5.0 96.1 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: Sat Apr 8 00:52:33 2023

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