Sodium in PDB 7ep0: Crystal Structure of ZYG11B Bound to Gste Degron

The structure of Crystal Structure of ZYG11B Bound to Gste Degron, PDB code: 7ep0 was solved by X.Yan, Y.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.75 / 2.16
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	131.495, 131.495, 87.03, 90, 90, 90
R / Rfree (%)	19 / 22.2

The binding sites of Sodium atom in the Crystal Structure of ZYG11B Bound to Gste Degron (pdb code 7ep0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of ZYG11B Bound to Gste Degron, PDB code: 7ep0:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of ZYG11B Bound to Gste Degron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of ZYG11B Bound to Gste Degron within 5.0Å range: probe atom residue distance (Å) B Occ A:Na801 b:75.9 occ:1.00 NAA A:CGO801 0.0 75.9 1.0 OAA A:CGO801 1.9 60.4 1.0 OAC A:CGO801 2.5 68.8 0.3 SAD A:CGO801 2.6 75.1 0.4 OAE A:CGO801 3.5 70.8 0.4 NZ B:LYS504 3.8 67.8 1.0 CAI A:CGO801 4.1 64.2 1.0 CAJ A:CGO801 4.3 58.5 1.0 CE B:LYS504 4.8 60.1 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of ZYG11B Bound to Gste Degron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of ZYG11B Bound to Gste Degron within 5.0Å range: probe atom residue distance (Å) B Occ A:Na801 b:66.6 occ:1.00 NAU A:CGO801 0.0 66.6 1.0 OAU A:CGO801 1.9 32.5 1.0 OBE A:CGO801 2.6 46.2 1.0 SBC A:CGO801 2.8 46.9 1.0 NE2 A:GLN486 3.1 64.0 1.0 CBT A:CGO801 3.4 43.2 1.0 CD A:GLN486 3.5 60.8 1.0 ND2 B:ASN523 3.5 34.9 1.0 OBF A:CGO801 3.7 42.6 1.0 CB B:ASN523 3.7 32.4 1.0 CBR A:CGO801 3.7 40.9 1.0 CG A:GLN486 3.8 53.4 1.0 CBS A:CGO801 3.9 38.5 1.0 CBP A:CGO802 3.9 37.5 1.0 CG B:ASN523 3.9 39.8 1.0 OE1 A:GLN486 4.1 60.0 1.0 CAB A:CGO802 4.3 43.0 1.0 CAB A:CGO801 4.4 40.3 1.0 CBO A:CGO802 4.4 35.4 1.0 CBQ A:CGO801 4.8 38.2 1.0 OD1 B:ASN523 4.9 39.7 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of ZYG11B Bound to Gste Degron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of ZYG11B Bound to Gste Degron within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:72.9 occ:1.00 NAA A:CGO802 0.0 72.9 1.0 OAA A:CGO802 1.9 65.5 0.5 SAD A:CGO802 2.6 79.5 0.7 CAI A:CGO802 2.8 64.8 1.0 OAE A:CGO802 3.1 65.1 0.5 CAH A:CGO802 3.4 61.7 1.0 CAG A:CGO802 3.5 63.5 1.0 CAJ A:CGO802 3.8 59.9 1.0 OAC A:CGO802 3.8 61.6 1.0 CB A:GLN503 3.9 43.8 1.0 CAM A:CGO802 4.3 61.7 0.8 CAF A:CGO802 4.4 60.1 1.0 CE A:LYS504 4.4 56.0 1.0 CG A:GLN503 4.4 53.1 1.0 NE2 A:GLN503 4.5 59.0 1.0 CD A:LYS504 4.5 52.9 1.0 CG A:LYS504 4.8 44.9 1.0 CAO A:CGO802 4.8 58.5 0.4 NZ A:LYS504 4.8 66.9 1.0 N A:LYS504 4.9 43.2 1.0 C A:GLN503 4.9 44.1 1.0 CAN A:CGO802 5.0 58.1 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of ZYG11B Bound to Gste Degron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of ZYG11B Bound to Gste Degron within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:72.5 occ:1.00 NAU A:CGO802 0.0 72.5 1.0 OAU A:CGO802 1.9 40.8 1.0 OBE A:CGO802 2.5 51.3 1.0 SBC A:CGO802 2.8 47.8 1.0 O B:HOH817 3.5 48.8 1.0 OBF A:CGO802 3.5 49.2 1.0 ND2 A:ASN523 3.6 32.1 1.0 CBT A:CGO802 3.7 34.4 1.0 CB A:ASN523 3.8 35.2 1.0 CG A:ASN523 3.9 38.2 1.0 CBR A:CGO802 4.0 40.2 1.0 CBP A:CGO801 4.3 36.2 1.0 CBS A:CGO802 4.3 37.2 1.0 CG B:GLN486 4.3 49.8 1.0 OD1 A:ASN523 4.7 34.7 1.0 CAB A:CGO802 4.7 43.0 1.0 CAB A:CGO801 4.9 40.3 1.0

X.Yan, Y.Li, G.Wang, Z.Zhou, G.Song, Q.Feng, Y.Zhao, W.Mi, Z.Ma, C.Dong. Molecular Basis For Recognition of Gly/N-Degrons By CRL2 ZYG11B and CRL2 ZER1. Mol.Cell 2021.
ISSN: ISSN 1097-2765
PubMed: 34214466
DOI: 10.1016/J.MOLCEL.2021.06.010