Zinc in PDB 6v4x: Cryo-Em Structure of An Active Human Histone Pre-Mrna 3'-End Processing Machinery at 3.2 Angstrom Resolution

The binding sites of Zinc atom in the Cryo-Em Structure of An Active Human Histone Pre-Mrna 3'-End Processing Machinery at 3.2 Angstrom Resolution (pdb code 6v4x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of An Active Human Histone Pre-Mrna 3'-End Processing Machinery at 3.2 Angstrom Resolution, PDB code: 6v4x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of An Active Human Histone Pre-Mrna 3'-End Processing Machinery at 3.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of An Active Human Histone Pre-Mrna 3'-End Processing Machinery at 3.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn701 b:46.1 occ:1.00 OD2 H:ASP179 2.3 32.9 1.0 NE2 H:HIS71 2.5 24.2 1.0 NE2 H:HIS158 2.5 30.2 1.0 ND1 H:HIS73 2.5 28.6 1.0 OP1 Y:C27 2.5 43.0 1.0 CE1 H:HIS71 3.2 24.2 1.0 CG H:ASP179 3.2 32.9 1.0 CE1 H:HIS158 3.2 30.2 1.0 CE1 H:HIS73 3.3 28.6 1.0 CB H:ASP179 3.3 32.9 1.0 ZN H:ZN702 3.4 46.4 1.0 P Y:C27 3.4 43.0 1.0 CD2 H:HIS71 3.5 24.2 1.0 OP2 Y:C27 3.5 43.0 1.0 CD2 H:HIS158 3.6 30.2 1.0 CG H:HIS73 3.6 28.6 1.0 CD2 H:HIS76 3.8 29.1 1.0 NE2 H:HIS76 3.9 29.1 1.0 CB H:HIS73 4.0 28.6 1.0 C5' Y:C27 4.2 43.0 1.0 ND1 H:HIS71 4.3 24.2 1.0 O5' Y:C27 4.3 43.0 1.0 OD1 H:ASP179 4.4 32.9 1.0 ND1 H:HIS158 4.4 30.2 1.0 NE2 H:HIS73 4.5 28.6 1.0 CG H:HIS71 4.5 24.2 1.0 CG H:HIS158 4.6 30.2 1.0 NE2 H:HIS396 4.6 42.8 1.0 CE1 H:HIS396 4.7 42.8 1.0 CD2 H:HIS73 4.7 28.6 1.0 OD2 H:ASP75 4.7 32.3 1.0 O3' Y:A26 4.8 56.4 1.0 CA H:ASP179 4.8 32.9 1.0 CG H:HIS76 4.9 29.1 1.0 NE2 H:HIS418 5.0 34.7 1.0 CE1 H:HIS76 5.0 29.1 1.0 OD1 H:ASP75 5.0 32.3 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of An Active Human Histone Pre-Mrna 3'-End Processing Machinery at 3.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of An Active Human Histone Pre-Mrna 3'-End Processing Machinery at 3.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn702 b:46.4 occ:1.00 NE2 H:HIS418 1.7 34.7 1.0 NE2 H:HIS76 2.0 29.1 1.0 OD2 H:ASP179 2.0 32.9 1.0 OD2 H:ASP75 2.3 32.3 1.0 OP2 Y:C27 2.6 43.0 1.0 CD2 H:HIS418 2.6 34.7 1.0 CE1 H:HIS418 2.7 34.7 1.0 CD2 H:HIS76 2.8 29.1 1.0 CG H:ASP179 3.0 32.9 1.0 CE1 H:HIS76 3.1 29.1 1.0 OD1 H:ASP179 3.3 32.9 1.0 CG H:ASP75 3.4 32.3 1.0 ZN H:ZN701 3.4 46.1 1.0 CG H:HIS418 3.7 34.7 1.0 ND1 H:HIS418 3.7 34.7 1.0 P Y:C27 3.8 43.0 1.0 OD1 H:ASP75 4.0 32.3 1.0 CG H:HIS76 4.0 29.1 1.0 ND1 H:HIS76 4.1 29.1 1.0 OP1 Y:C27 4.2 43.0 1.0 CB H:ASP179 4.4 32.9 1.0 CB H:ASP75 4.6 32.3 1.0 NE2 H:HIS71 4.6 24.2 1.0 CE1 H:HIS71 4.7 24.2 1.0 O5' Y:C27 4.8 43.0 1.0 O3' Y:A26 4.8 56.4 1.0 C5' Y:C27 4.9 43.0 1.0

Y.Sun, Y.Zhang, W.S.Aik, X.C.Yang, W.F.Marzluff, T.Walz, Z.Dominski, L.Tong. Structure of An Active Human Histone Pre-Mrna 3'-End Processing Machinery. Science V. 367 700 2020.
ISSN: ESSN 1095-9203
PubMed: 32029631
DOI: 10.1126/SCIENCE.AAZ7758