Zinc in PDB 5m3m: Free Monomeric Rna Polymerase I at 4.0A Resolution

All present enzymatic activity of Free Monomeric Rna Polymerase I at 4.0A Resolution:
2.7.7.6;

The binding sites of Zinc atom in the Free Monomeric Rna Polymerase I at 4.0A Resolution (pdb code 5m3m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Free Monomeric Rna Polymerase I at 4.0A Resolution, PDB code: 5m3m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Free Monomeric Rna Polymerase I at 4.0A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Free Monomeric Rna Polymerase I at 4.0A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3001 b:75.2 occ:1.00 SG A:CYS65 2.3 55.2 1.0 CD A:PRO73 2.4 51.5 1.0 CA A:CYS72 2.4 53.1 1.0 CD1 A:LEU67 2.6 56.6 1.0 CB A:CYS72 2.9 53.8 1.0 SG A:CYS72 2.9 61.7 1.0 N A:PRO73 3.0 53.4 1.0 C A:CYS72 3.1 55.6 1.0 CB A:CYS65 3.4 61.9 1.0 CG A:LEU67 3.4 64.5 1.0 N A:CYS72 3.5 64.0 1.0 CB A:LEU67 3.6 64.8 1.0 CG A:PRO73 3.6 50.5 1.0 O A:PHE71 3.7 73.7 1.0 NE2 A:HIS75 3.8 58.8 1.0 C A:PHE71 4.0 70.6 1.0 CE1 A:HIS75 4.3 61.6 1.0 N A:GLY74 4.3 56.6 1.0 O A:CYS72 4.3 51.9 1.0 CA A:PRO73 4.3 49.6 1.0 CB A:PRO73 4.7 49.4 1.0 CD2 A:HIS75 4.8 57.5 1.0 CA A:CYS65 4.8 70.8 1.0 CA A:LEU67 4.8 66.7 1.0 C A:PRO73 4.9 55.0 1.0 CD2 A:LEU67 4.9 61.9 1.0 N A:LEU67 5.0 67.0 1.0

Zinc binding site 2 out of 7 in the Free Monomeric Rna Polymerase I at 4.0A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Free Monomeric Rna Polymerase I at 4.0A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3002 b:77.5 occ:1.00 O A:CYS102 2.0 68.4 1.0 N A:CYS105 2.0 81.3 1.0 N A:HIS106 2.1 78.2 1.0 N A:PHE104 2.2 73.4 1.0 C A:PHE104 2.3 80.0 1.0 C A:CYS102 2.6 68.7 1.0 CA A:PHE104 2.7 74.7 1.0 CA A:CYS105 2.9 73.5 1.0 C A:CYS105 2.9 75.7 1.0 C A:LEU103 2.9 79.2 1.0 O A:PHE104 3.2 76.4 1.0 CA A:HIS106 3.2 78.0 1.0 SG A:CYS105 3.3 72.6 1.0 N A:LEU103 3.3 69.5 1.0 CB A:CYS102 3.4 77.8 1.0 SG A:CYS102 3.5 75.2 1.0 CB A:PHE104 3.5 76.7 1.0 CA A:CYS102 3.6 73.9 1.0 CA A:LEU103 3.6 79.6 1.0 CB A:CYS105 3.6 74.3 1.0 O A:LEU103 3.6 83.6 1.0 N A:HIS107 4.0 77.9 1.0 O A:CYS105 4.1 74.4 1.0 C A:HIS106 4.1 75.3 1.0 CB A:HIS106 4.3 84.2 1.0 CG A:HIS106 4.4 94.7 1.0 N A:CYS102 4.4 66.2 1.0 CG A:PHE104 4.5 82.8 1.0 O A:HIS107 4.5 65.5 1.0 ND1 A:HIS106 4.6 0.9 1.0 CD2 A:PHE104 4.7 84.8 1.0 CD2 A:HIS106 4.8 98.0 1.0 CB A:LEU103 5.0 70.2 1.0 SG A:CYS236 5.0 79.3 1.0

Zinc binding site 3 out of 7 in the Free Monomeric Rna Polymerase I at 4.0A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Free Monomeric Rna Polymerase I at 4.0A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1302 b:53.6 occ:1.00 O B:GLU1172 1.9 61.9 1.0 N B:GLU1106 2.0 58.5 1.0 CB B:GLU1106 2.4 71.6 1.0 SG B:CYS1104 2.4 49.9 1.0 CA B:GLU1106 2.6 61.1 1.0 C B:GLU1172 2.9 58.2 1.0 CB B:GLU1172 3.0 67.1 1.0 C B:ARG1105 3.1 52.9 1.0 N B:ARG1105 3.1 56.4 1.0 CA B:GLU1172 3.3 60.5 1.0 C B:CYS1104 3.4 55.9 1.0 CA B:ARG1105 3.5 52.2 1.0 N B:GLU1172 3.6 64.1 1.0 CB B:CYS1104 3.6 50.2 1.0 C B:GLU1106 3.7 52.4 1.0 N B:CYS1107 3.7 44.8 1.0 CA B:CYS1104 3.7 48.7 1.0 CG B:GLU1106 3.8 78.6 1.0 CB B:ARG1105 3.8 61.7 1.0 OE1 B:GLU1106 3.9 84.3 1.0 O B:CYS1104 4.0 64.2 1.0 N B:THR1173 4.1 47.6 1.0 O B:ARG1105 4.2 56.5 1.0 CG B:GLU1172 4.3 80.9 1.0 CD B:GLU1106 4.4 82.2 1.0 CG2 B:THR1173 4.5 47.3 1.0 SG B:CYS1131 4.6 75.4 1.0 CG B:ARG1105 4.7 78.0 1.0 CA B:THR1173 4.8 44.7 1.0 O B:GLU1106 4.8 54.4 1.0 C B:ASN1171 4.9 65.9 1.0

Zinc binding site 4 out of 7 in the Free Monomeric Rna Polymerase I at 4.0A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Free Monomeric Rna Polymerase I at 4.0A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn3001 b:74.0 occ:1.00 N I:ASP12 2.1 85.6 1.0 N I:CYS13 2.2 91.4 1.0 O I:CYS10 2.3 92.5 1.0 C I:CYS10 2.3 79.3 1.0 SG I:CYS10 2.4 78.7 1.0 CB I:CYS10 2.5 74.2 1.0 C I:ASP12 2.6 88.5 1.0 O I:CYS13 2.6 0.2 1.0 CA I:ASP12 2.7 86.9 1.0 C I:LEU11 2.9 85.2 1.0 N I:LEU11 2.9 71.9 1.0 CA I:CYS10 2.9 76.6 1.0 CA I:CYS13 3.1 85.0 1.0 C I:CYS13 3.1 95.5 1.0 CB I:ASP12 3.3 89.0 1.0 CA I:LEU11 3.4 75.2 1.0 SG I:CYS13 3.4 73.5 1.0 O I:ASP12 3.5 89.0 1.0 O I:LEU11 3.8 95.5 1.0 CB I:CYS13 3.8 85.7 1.0 N I:CYS10 3.9 73.3 1.0 SG I:CYS33 4.2 71.0 1.0 OH I:TYR37 4.2 86.5 1.0 CG I:ASP12 4.3 99.1 1.0 N I:GLY14 4.3 54.8 1.0 CB I:LEU11 4.7 65.7 1.0 OD1 I:ASP12 4.7 97.8 1.0 C I:PHE9 4.9 72.3 1.0 N I:ASP15 5.0 72.6 1.0

Zinc binding site 5 out of 7 in the Free Monomeric Rna Polymerase I at 4.0A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Free Monomeric Rna Polymerase I at 4.0A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn3002 b:77.9 occ:0.75 CB I:TYR119 2.3 75.0 1.0 SG I:CYS86 2.3 77.8 1.0 CB I:CYS114 2.4 85.7 1.0 CD2 I:TYR119 2.4 92.5 1.0 CG I:TYR119 2.7 89.1 1.0 O I:TYR119 2.8 84.2 1.0 CA I:TYR119 3.0 92.6 1.0 C I:TYR119 3.1 85.9 1.0 SG I:CYS114 3.3 74.3 1.0 N I:TYR119 3.4 93.8 1.0 CA I:CYS114 3.4 80.4 1.0 CE I:MET94 3.6 70.0 1.0 CB I:CYS86 3.6 95.0 1.0 SG I:CYS117 3.7 87.3 1.0 CE2 I:TYR119 3.7 93.6 1.0 N I:CYS114 3.7 69.9 1.0 SD I:MET94 4.1 70.0 1.0 CD1 I:TYR119 4.1 88.6 1.0 N I:LYS120 4.1 82.3 1.0 CA I:CYS86 4.4 92.9 1.0 C I:GLY118 4.4 89.6 1.0 CB I:GLN88 4.5 89.3 1.0 CG I:MET94 4.7 69.7 1.0 C I:CYS114 4.8 86.0 1.0 CZ I:TYR119 4.8 97.2 1.0 C I:THR113 4.8 72.4 1.0 N I:GLN88 4.9 93.5 1.0 CD I:PRO87 4.9 91.5 1.0 SG I:CYS89 4.9 90.7 1.0 OE1 I:GLN88 4.9 0.2 1.0 CA I:LYS120 4.9 76.3 1.0 CE1 I:TYR119 4.9 90.0 1.0 C I:CYS86 5.0 95.6 1.0

Zinc binding site 6 out of 7 in the Free Monomeric Rna Polymerase I at 4.0A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Free Monomeric Rna Polymerase I at 4.0A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn3001 b:0.2 occ:1.01 N J:CYS46 2.1 84.7 1.0 C J:CYS45 2.2 81.9 1.0 SG J:CYS7 2.3 59.1 1.0 SG J:CYS10 2.4 55.2 1.0 SG J:CYS46 2.5 61.8 1.0 CB J:CYS45 2.6 53.5 1.0 SG J:CYS45 2.7 99.9 1.0 CA J:CYS46 2.7 79.5 1.0 O J:CYS45 2.8 75.8 1.0 CA J:CYS45 3.0 81.3 1.0 CB J:CYS46 3.1 75.7 1.0 CB J:CYS10 3.3 56.0 1.0 CB J:CYS7 3.6 60.2 1.0 N J:CYS45 3.8 73.2 1.0 N J:CYS10 4.1 70.0 1.0 C J:CYS46 4.2 75.5 1.0 CA J:CYS10 4.3 63.8 1.0 CB J:ARG43 4.3 60.1 1.0 O J:ARG43 4.4 61.5 1.0 C J:TYR44 4.6 60.0 1.0 O J:TYR44 4.8 56.4 1.0 N J:ARG47 4.8 70.8 1.0 CD J:ARG43 4.8 62.1 1.0 CA J:CYS7 4.9 59.1 1.0 C J:ARG43 4.9 57.4 1.0 O J:CYS46 5.0 75.8 1.0

Zinc binding site 7 out of 7 in the Free Monomeric Rna Polymerase I at 4.0A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Free Monomeric Rna Polymerase I at 4.0A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn3001 b:87.2 occ:1.00 SG L:CYS48 2.2 79.1 1.0 SG L:CYS51 2.3 0.1 1.0 SG L:CYS31 2.3 82.4 1.0 SG L:CYS34 2.4 85.1 1.0 CB L:CYS51 2.7 87.7 1.0 CB L:CYS48 3.0 0.7 1.0 CB L:CYS34 3.3 73.9 1.0 CB L:CYS31 3.5 74.2 1.0 N L:CYS51 3.5 90.7 1.0 N L:CYS34 3.6 82.0 1.0 CA L:CYS51 3.7 88.9 1.0 CD2 L:HIS53 3.8 0.7 1.0 CA L:CYS34 4.0 79.3 1.0 NE2 L:HIS53 4.4 0.3 1.0 OG L:SER36 4.5 0.3 1.0 CA L:CYS48 4.5 0.3 1.0 N L:GLY52 4.7 99.2 1.0 CB L:GLU33 4.7 84.5 1.0 C L:CYS51 4.7 94.1 1.0 C L:GLU33 4.7 79.3 1.0 CB L:ASP50 4.7 0.3 1.0 C L:ASP50 4.7 0.1 1.0 CA L:CYS31 4.8 76.8 1.0 N L:GLU33 4.9 82.8 1.0 C L:CYS34 4.9 85.2 1.0 CG L:HIS53 4.9 0.1 1.0 CA L:GLU33 5.0 82.4 1.0

S.Neyer, M.Kunz, C.Geiss, M.Hantsche, V.V.Hodirnau, A.Seybert, C.Engel, M.P.Scheffer, P.Cramer, A.S.Frangakis. Structure of Rna Polymerase I Transcribing Ribosomal Dna Genes. Nature V. 540 607 2016.
ISSN: ISSN 0028-0836
PubMed: 27842382
DOI: 10.1038/NATURE20561