Zinc in PDB 5w5y: Rna Polymerase I Initial Transcribing Complex

All present enzymatic activity of Rna Polymerase I Initial Transcribing Complex:
2.7.7.6;

The binding sites of Zinc atom in the Rna Polymerase I Initial Transcribing Complex (pdb code 5w5y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Rna Polymerase I Initial Transcribing Complex, PDB code: 5w5y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Rna Polymerase I Initial Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase I Initial Transcribing Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1701 b:0.0 occ:1.00 SG A:CYS105 1.9 0.0 1.0 SG A:CYS102 2.0 0.0 1.0 SG A:CYS233 2.2 0.0 1.0 SG A:CYS236 2.3 0.0 1.0 CB A:CYS102 2.3 0.0 1.0 CB A:CYS233 3.3 0.0 1.0 CB A:CYS236 3.4 0.0 1.0 CB A:CYS105 3.5 0.0 1.0 CA A:CYS102 3.8 0.0 1.0 N A:CYS236 3.9 0.0 1.0 O A:HIS107 4.0 0.0 1.0 CA A:CYS236 4.2 0.0 1.0 N A:HIS107 4.4 0.0 1.0 N A:CYS105 4.4 0.0 1.0 CA A:CYS105 4.5 0.0 1.0 CB A:HIS107 4.5 0.0 1.0 C A:HIS107 4.6 0.0 1.0 C A:CYS102 4.6 0.0 1.0 N A:HIS106 4.6 0.0 1.0 CA A:CYS233 4.7 0.0 1.0 N A:CYS102 4.7 0.0 1.0 CA A:HIS107 4.7 0.0 1.0 CB A:ASN235 4.7 0.0 1.0 C A:ASN235 4.8 0.0 1.0 CG A:ARG109 4.9 0.0 1.0 C A:CYS105 4.9 0.0 1.0 C A:CYS236 4.9 0.0 1.0 ND2 A:ASN235 4.9 0.0 1.0 O A:CYS102 5.0 0.0 1.0 N A:ASN235 5.0 0.0 1.0

Zinc binding site 2 out of 6 in the Rna Polymerase I Initial Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase I Initial Transcribing Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:0.0 occ:1.00 NE2 A:HIS75 2.0 0.0 1.0 SG A:CYS62 2.1 0.0 1.0 SG A:CYS65 2.1 0.0 1.0 SG A:CYS72 2.1 0.0 1.0 CD2 A:HIS75 2.5 0.0 1.0 CB A:CYS62 2.7 0.0 1.0 CE1 A:HIS75 3.1 0.0 1.0 CB A:CYS65 3.4 0.0 1.0 N A:CYS65 3.4 0.0 1.0 CB A:CYS72 3.7 0.0 1.0 CG A:HIS75 3.8 0.0 1.0 CA A:CYS65 4.0 0.0 1.0 ND1 A:HIS75 4.0 0.0 1.0 CA A:CYS62 4.2 0.0 1.0 CA A:GLY55 4.2 0.0 1.0 C A:THR64 4.2 0.0 1.0 N A:GLY74 4.3 0.0 1.0 CB A:THR64 4.4 0.0 1.0 CA A:GLY74 4.4 0.0 1.0 CA A:CYS72 4.5 0.0 1.0 N A:THR64 4.6 0.0 1.0 C A:CYS62 4.6 0.0 1.0 CA A:THR64 4.6 0.0 1.0 O A:CYS62 4.7 0.0 1.0 C A:GLY74 4.7 0.0 1.0 C A:CYS65 4.7 0.0 1.0 N A:GLY66 4.8 0.0 1.0 C A:GLY55 4.8 0.0 1.0 N A:GLY55 4.8 0.0 1.0 CG2 A:THR64 4.9 0.0 1.0 CD A:PRO73 4.9 0.0 1.0 N A:HIS75 4.9 0.0 1.0 CB A:LEU67 5.0 0.0 1.0 N A:ALA56 5.0 0.0 1.0

Zinc binding site 3 out of 6 in the Rna Polymerase I Initial Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase I Initial Transcribing Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:0.0 occ:1.00 SG B:CYS1131 2.1 0.0 1.0 SG B:CYS1107 2.1 0.0 1.0 SG B:CYS1128 2.2 0.0 1.0 SG B:CYS1104 2.3 0.0 1.0 CB B:CYS1107 2.7 0.0 1.0 CB B:CYS1104 3.0 0.0 1.0 CB B:CYS1131 3.6 0.0 1.0 N B:CYS1131 3.6 0.0 1.0 CB B:CYS1128 3.6 0.0 1.0 CB B:ARG1130 3.7 0.0 1.0 CA B:CYS1107 3.9 0.0 1.0 N B:CYS1107 3.9 0.0 1.0 NE B:ARG1130 3.9 0.0 1.0 C B:ARG1130 4.1 0.0 1.0 CA B:CYS1131 4.1 0.0 1.0 OG1 B:THR1112 4.3 0.0 1.0 CA B:ARG1130 4.3 0.0 1.0 NH2 B:ARG1130 4.4 0.0 1.0 N B:ARG1130 4.4 0.0 1.0 CA B:CYS1104 4.4 0.0 1.0 CG B:ARG1130 4.5 0.0 1.0 C B:GLU1106 4.6 0.0 1.0 CZ B:ARG1130 4.7 0.0 1.0 C B:CYS1107 4.7 0.0 1.0 CD B:ARG1130 4.8 0.0 1.0 CA B:CYS1128 4.9 0.0 1.0 O B:CYS1104 4.9 0.0 1.0 C B:CYS1104 4.9 0.0 1.0 O B:ARG1130 5.0 0.0 1.0

Zinc binding site 4 out of 6 in the Rna Polymerase I Initial Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase I Initial Transcribing Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:0.0 occ:1.00 SG I:CYS10 2.0 0.0 1.0 CB I:CYS10 2.2 0.0 1.0 SG I:CYS30 2.2 0.0 1.0 SG I:CYS13 2.3 0.0 1.0 SG I:CYS33 2.4 0.0 1.0 CB I:CYS30 2.7 0.0 1.0 CB I:CYS13 3.7 0.0 1.0 CA I:CYS10 3.7 0.0 1.0 CB I:ASP15 3.8 0.0 1.0 CB I:CYS33 4.0 0.0 1.0 CA I:CYS30 4.1 0.0 1.0 N I:CYS13 4.2 0.0 1.0 N I:CYS33 4.2 0.0 1.0 N I:ASP15 4.2 0.0 1.0 CA I:CYS13 4.4 0.0 1.0 N I:CYS10 4.5 0.0 1.0 O I:ASP15 4.5 0.0 1.0 C I:CYS10 4.5 0.0 1.0 CA I:ASP15 4.5 0.0 1.0 N I:GLY14 4.7 0.0 1.0 CB I:GLN32 4.7 0.0 1.0 CA I:CYS33 4.7 0.0 1.0 C I:CYS13 4.7 0.0 1.0 CG I:ASP15 4.9 0.0 1.0 C I:ASP15 4.9 0.0 1.0 O I:CYS10 4.9 0.0 1.0 C I:CYS30 5.0 0.0 1.0 N I:CYS30 5.0 0.0 1.0

Zinc binding site 5 out of 6 in the Rna Polymerase I Initial Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase I Initial Transcribing Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:0.0 occ:1.00 SG J:CYS7 2.2 0.0 1.0 SG J:CYS45 2.2 0.0 1.0 SG J:CYS46 2.2 0.0 1.0 SG J:CYS10 2.3 0.0 1.0 N J:CYS46 2.6 0.0 1.0 CB J:CYS7 2.8 0.0 1.0 CA J:CYS46 2.8 0.0 1.0 C J:CYS45 2.9 0.0 1.0 CB J:CYS46 3.0 0.0 1.0 CB J:CYS10 3.3 0.0 1.0 CB J:CYS45 3.3 0.0 1.0 O J:CYS45 3.3 0.0 1.0 CA J:CYS45 3.7 0.0 1.0 N J:CYS10 4.0 0.0 1.0 CA J:CYS7 4.2 0.0 1.0 CA J:CYS10 4.3 0.0 1.0 C J:CYS46 4.3 0.0 1.0 N J:CYS45 4.4 0.0 1.0 C J:CYS7 4.8 0.0 1.0 O J:CYS7 4.8 0.0 1.0 N J:GLY11 4.8 0.0 1.0 O J:ARG43 4.8 0.0 1.0 NE J:ARG43 4.9 0.0 1.0 O J:CYS46 5.0 0.0 1.0

Zinc binding site 6 out of 6 in the Rna Polymerase I Initial Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase I Initial Transcribing Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:0.0 occ:1.00 SG L:CYS51 2.0 0.0 1.0 SG L:CYS34 2.1 0.0 1.0 SG L:CYS31 2.1 0.0 1.0 CB L:CYS34 2.3 0.0 1.0 SG L:CYS48 2.4 0.0 1.0 CB L:CYS51 2.6 0.0 1.0 CB L:CYS31 3.0 0.0 1.0 N L:CYS34 3.2 0.0 1.0 CA L:CYS34 3.3 0.0 1.0 CB L:CYS48 3.3 0.0 1.0 N L:CYS51 3.7 0.0 1.0 CA L:CYS51 3.8 0.0 1.0 C L:GLU33 4.1 0.0 1.0 C L:CYS34 4.3 0.0 1.0 CA L:CYS31 4.4 0.0 1.0 CB L:HIS53 4.5 0.0 1.0 C L:ASP50 4.6 0.0 1.0 N L:GLY52 4.6 0.0 1.0 OG L:SER36 4.6 0.0 1.0 N L:GLU33 4.6 0.0 1.0 N L:SER35 4.7 0.0 1.0 C L:CYS51 4.7 0.0 1.0 CA L:GLU33 4.8 0.0 1.0 CA L:CYS48 4.8 0.0 1.0 C L:CYS31 4.8 0.0 1.0 O L:GLU33 4.8 0.0 1.0 N L:HIS53 4.9 0.0 1.0 CB L:GLU33 4.9 0.0 1.0 CB L:ASP50 4.9 0.0 1.0 O L:CYS31 5.0 0.0 1.0

Y.Han, C.Yan, T.H.D.Nguyen, A.J.Jackobel, I.Ivanov, B.A.Knutson, Y.He. Structural Mechanism of Atp-Independent Transcription Initiation By Rna Polymerase I. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28623663
DOI: 10.7554/ELIFE.27414