Zinc in PDB 8hk1: The Cryo-Em Structure of Human Pre-17S U2 Snrnp

All present enzymatic activity of The Cryo-Em Structure of Human Pre-17S U2 Snrnp:
3.6.4.13;

The binding sites of Zinc atom in the The Cryo-Em Structure of Human Pre-17S U2 Snrnp (pdb code 8hk1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Cryo-Em Structure of Human Pre-17S U2 Snrnp, PDB code: 8hk1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Cryo-Em Structure of Human Pre-17S U2 Snrnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Cryo-Em Structure of Human Pre-17S U2 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ 6:Zn201 b:55.0 occ:1.00 SG 6:CYS61 2.4 32.3 1.0 SG 6:CYS23 2.4 30.0 1.0 SG 6:CYS26 2.5 30.5 1.0 SG 6:CYS58 2.6 30.1 1.0 CB 6:CYS61 3.2 32.3 1.0 CB 6:CYS58 3.4 30.1 1.0 CB 6:CYS26 3.5 30.5 1.0 CB 6:CYS23 3.6 30.0 1.0 CE 6:LYS25 3.9 33.6 1.0 N 6:CYS61 3.9 32.3 1.0 CA 6:CYS61 4.2 32.3 1.0 NZ 6:LYS25 4.3 33.6 1.0 N 6:CYS26 4.3 30.5 1.0 N 6:CYS23 4.4 30.0 1.0 CA 6:CYS26 4.5 30.5 1.0 CA 6:CYS23 4.5 30.0 1.0 N 6:GLY62 4.7 32.2 1.0 CB 6:ILE60 4.7 27.4 1.0 C 6:CYS61 4.9 32.3 1.0 CG2 6:ILE60 4.9 27.4 1.0 CA 6:CYS58 4.9 30.1 1.0 CB 6:LYS25 4.9 33.6 1.0 N 6:GLY63 4.9 31.2 1.0 C 6:ILE60 4.9 27.4 1.0

Zinc binding site 2 out of 4 in the The Cryo-Em Structure of Human Pre-17S U2 Snrnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Cryo-Em Structure of Human Pre-17S U2 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ 6:Zn202 b:44.0 occ:1.00 SG 6:CYS11 2.4 25.7 1.0 SG 6:CYS46 2.4 22.6 1.0 SG 6:CYS85 2.4 22.1 1.0 SG 6:CYS49 2.6 35.4 1.0 CB 6:CYS85 2.7 22.1 1.0 CB 6:CYS11 3.0 25.7 1.0 CB 6:CYS46 3.6 22.6 1.0 CB 6:CYS49 3.8 35.4 1.0 OE1 6:GLU48 3.9 34.7 1.0 N 6:CYS46 4.1 22.6 1.0 CA 6:CYS85 4.2 22.1 1.0 CB 6:LYS13 4.4 22.7 1.0 CA 6:CYS46 4.5 22.6 1.0 CA 6:CYS11 4.5 25.7 1.0 CB 6:LYS87 4.5 28.4 1.0 C 6:CYS85 4.6 22.1 1.0 O 6:CYS85 4.7 22.1 1.0 N 6:CYS49 4.7 35.4 1.0 CG 6:GLU48 4.8 34.7 1.0 CD 6:GLU48 4.8 34.7 1.0 N 6:LYS13 4.8 22.7 1.0 CD 6:LYS13 4.8 22.7 1.0 CA 6:CYS49 4.9 35.4 1.0 C 6:CYS11 4.9 25.7 1.0 CG 6:LYS13 4.9 22.7 1.0 N 6:CYS85 4.9 22.1 1.0 N 6:ARG12 5.0 22.3 1.0

Zinc binding site 3 out of 4 in the The Cryo-Em Structure of Human Pre-17S U2 Snrnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Cryo-Em Structure of Human Pre-17S U2 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ 6:Zn203 b:40.8 occ:1.00 SG 6:CYS33 2.4 21.2 1.0 SG 6:CYS30 2.4 19.7 1.0 SG 6:CYS72 2.4 15.2 1.0 SG 6:CYS75 2.5 15.2 1.0 CB 6:CYS75 3.2 15.2 1.0 CB 6:CYS33 3.4 21.2 1.0 CB 6:CYS72 3.6 15.2 1.0 CB 6:CYS30 3.6 19.7 1.0 N 6:CYS33 3.8 21.2 1.0 N 6:CYS72 3.9 15.2 1.0 N 6:CYS75 4.2 15.2 1.0 CA 6:CYS33 4.2 21.2 1.0 CA 6:CYS75 4.3 15.2 1.0 CA 6:CYS72 4.3 15.2 1.0 CB 6:ILE32 4.6 19.9 1.0 C 6:ILE32 4.8 19.9 1.0 O 6:CYS72 4.9 15.2 1.0 N 6:ILE32 4.9 19.9 1.0 C 6:CYS72 4.9 15.2 1.0 C 6:CYS33 5.0 21.2 1.0

Zinc binding site 4 out of 4 in the The Cryo-Em Structure of Human Pre-17S U2 Snrnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Cryo-Em Structure of Human Pre-17S U2 Snrnp within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1000 b:104.8 occ:1.00 NE2 C:HIS425 2.3 91.5 1.0 ND1 C:HIS431 2.3 99.3 1.0 SG C:CYS408 2.5 93.5 1.0 CE1 C:HIS431 2.6 99.3 1.0 CB C:CYS408 2.9 93.5 1.0 CD2 C:HIS425 2.9 91.5 1.0 CE1 C:HIS425 3.3 91.5 1.0 CB C:CYS411 3.3 98.8 1.0 SG C:CYS411 3.4 98.8 1.0 CG C:HIS431 3.6 99.3 1.0 NE2 C:HIS431 3.9 99.3 1.0 N C:CYS411 4.0 98.8 1.0 CG C:HIS425 4.1 91.5 1.0 CE2 C:TYR416 4.2 93.9 1.0 ND1 C:HIS425 4.3 91.5 1.0 CB C:HIS431 4.3 99.3 1.0 CA C:CYS411 4.3 98.8 1.0 CD2 C:HIS431 4.3 99.3 1.0 OH C:TYR416 4.4 93.9 1.0 CA C:CYS408 4.4 93.5 1.0 CE1 C:PHE426 4.5 88.5 1.0 CZ C:TYR416 4.7 93.9 1.0 CD1 C:PHE426 4.7 88.5 1.0 CB C:ILE410 4.7 94.2 1.0 C C:ILE410 4.7 94.2 1.0 C C:CYS408 4.9 93.5 1.0 O C:CYS408 4.9 93.5 1.0 CA C:HIS431 4.9 99.3 1.0

F.Yang, T.Bian, X.Zhan, Z.Chen, Z.Xing, N.A.Larsen, X.Zhang, Y.Shi. Mechanisms of the Rna Helicases DDX42 and DDX46 in Human U2 Snrnp Assembly. Nat Commun V. 14 897 2023.
ISSN: ESSN 2041-1723
PubMed: 36797247
DOI: 10.1038/S41467-023-36489-X