Zinc in PDB 8ffz: Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene

The binding sites of Zinc atom in the Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene (pdb code 8ffz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene, PDB code: 8ffz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:64.7 occ:1.00 NE2 A:HIS74 1.9 23.7 1.0 NE2 A:HIS69 1.9 26.2 1.0 SG A:CYS56 2.0 20.4 1.0 SG A:CYS51 2.1 27.9 1.0 CD2 A:HIS74 2.9 23.7 1.0 CE1 A:HIS69 2.9 26.2 1.0 CE1 A:HIS74 2.9 23.7 1.0 CD2 A:HIS69 3.1 26.2 1.0 CB A:CYS56 3.1 20.4 1.0 CB A:CYS51 3.2 27.9 1.0 CG A:HIS74 4.0 23.7 1.0 ND1 A:HIS74 4.0 23.7 1.0 ND1 A:HIS69 4.1 26.2 1.0 CG A:HIS69 4.2 26.2 1.0 CA A:CYS56 4.5 20.4 1.0 CA A:CYS51 4.6 27.9 1.0 CG A:GLN70 4.8 28.6 1.0 CB A:TYR53 4.9 25.4 1.0 CD1 A:TYR53 5.0 25.4 1.0

Zinc binding site 2 out of 9 in the Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:113.5 occ:1.00 SG A:CYS85 1.9 55.3 1.0 SG A:CYS82 1.9 49.4 1.0 NE2 A:HIS98 1.9 41.2 1.0 NE2 A:HIS102 2.0 54.8 1.0 CD2 A:HIS98 2.9 41.2 1.0 CE1 A:HIS102 3.0 54.8 1.0 CB A:CYS82 3.0 49.4 1.0 CE1 A:HIS98 3.1 41.2 1.0 CD2 A:HIS102 3.1 54.8 1.0 CB A:CYS85 3.4 55.3 1.0 N A:CYS85 3.5 55.3 1.0 CA A:CYS85 3.9 55.3 1.0 CG A:HIS98 4.0 41.2 1.0 ND1 A:HIS102 4.1 54.8 1.0 ND1 A:HIS98 4.1 41.2 1.0 C A:LYS84 4.2 61.5 1.0 CG A:HIS102 4.2 54.8 1.0 CA A:CYS82 4.4 49.4 1.0 C A:CYS85 4.5 55.3 1.0 N A:LYS84 4.6 61.5 1.0 CB A:LYS84 4.6 61.5 1.0 CA A:LYS84 4.7 61.5 1.0 O A:CYS85 4.7 55.3 1.0 C A:CYS82 5.0 49.4 1.0 O A:LYS84 5.0 61.5 1.0

Zinc binding site 3 out of 9 in the Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:129.3 occ:1.00 NE2 A:HIS126 1.9 54.0 1.0 SG A:CYS110 1.9 62.5 1.0 SG A:CYS113 1.9 64.5 1.0 CB A:CYS110 2.3 62.5 1.0 CD2 A:HIS126 2.8 54.0 1.0 CE1 A:HIS126 2.9 54.0 1.0 NE2 A:HIS130 3.4 46.8 1.0 CB A:CYS113 3.5 64.5 1.0 N A:CYS113 3.7 64.5 1.0 CA A:CYS110 3.8 62.5 1.0 N A:LYS115 3.8 66.8 1.0 CB A:LYS115 3.9 66.8 1.0 CD2 A:HIS130 3.9 46.8 1.0 N A:GLY114 3.9 64.4 1.0 CG A:HIS126 4.0 54.0 1.0 CA A:CYS113 4.0 64.5 1.0 ND1 A:HIS126 4.0 54.0 1.0 C A:CYS113 4.3 64.5 1.0 CA A:LYS115 4.3 66.8 1.0 O A:LYS115 4.4 66.8 1.0 C A:CYS110 4.5 62.5 1.0 N A:CYS110 4.6 62.5 1.0 CE1 A:HIS130 4.7 46.8 1.0 C A:GLY114 4.7 64.4 1.0 CA A:GLY114 4.8 64.4 1.0 C A:LYS115 4.8 66.8 1.0 N A:TYR112 4.9 54.7 1.0 C A:TYR112 4.9 54.7 1.0

Zinc binding site 4 out of 9 in the Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:213.1 occ:1.00 SG A:CYS141 1.9 76.8 1.0 NE2 A:HIS159 2.0 76.7 1.0 SG A:CYS136 2.0 80.6 1.0 NE2 A:HIS154 2.2 69.7 1.0 CB A:CYS141 2.7 76.8 1.0 CE1 A:HIS159 2.9 76.7 1.0 CD2 A:HIS159 3.1 76.7 1.0 CD2 A:HIS154 3.1 69.7 1.0 CE1 A:HIS154 3.3 69.7 1.0 CB A:CYS136 3.4 80.6 1.0 CA A:CYS141 4.1 76.8 1.0 ND1 A:HIS159 4.1 76.7 1.0 CG A:HIS159 4.2 76.7 1.0 CG A:HIS154 4.3 69.7 1.0 ND1 A:HIS154 4.4 69.7 1.0 C A:CYS141 4.5 76.8 1.0 CG1 A:VAL158 4.6 68.8 1.0 CB A:GLU138 4.6 88.0 1.0 CA A:CYS136 4.7 80.6 1.0 CB A:VAL158 4.9 68.8 1.0

Zinc binding site 5 out of 9 in the Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:127.6 occ:1.00 SG A:CYS168 1.9 67.5 1.0 SG A:CYS165 1.9 70.5 1.0 NE2 A:HIS181 2.0 75.3 1.0 NE2 A:HIS186 2.2 69.8 1.0 CB A:CYS165 2.7 70.5 1.0 CB A:CYS168 2.9 67.5 1.0 CE1 A:HIS181 3.0 75.3 1.0 CD2 A:HIS186 3.0 69.8 1.0 CD2 A:HIS181 3.2 75.3 1.0 N A:CYS168 3.2 67.5 1.0 CE1 A:HIS186 3.4 69.8 1.0 CA A:CYS168 3.6 67.5 1.0 CA A:CYS165 4.1 70.5 1.0 ND1 A:HIS181 4.1 75.3 1.0 CG A:HIS186 4.2 69.8 1.0 CG A:HIS181 4.2 75.3 1.0 N A:ASN169 4.3 64.4 1.0 C A:CYS168 4.3 67.5 1.0 ND1 A:HIS186 4.3 69.8 1.0 C A:HIS167 4.4 68.8 1.0 N A:HIS167 4.6 68.8 1.0 CB A:HIS167 4.6 68.8 1.0 CA A:HIS167 4.7 68.8 1.0 C A:CYS165 4.8 70.5 1.0 N A:LYS170 4.8 69.0 1.0 CB A:LYS170 4.9 69.0 1.0 CZ A:PHE172 4.9 69.6 1.0

Zinc binding site 6 out of 9 in the Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:106.1 occ:1.00 NE2 A:HIS244 1.8 37.2 1.0 SG A:CYS227 1.9 45.5 1.0 SG A:CYS224 1.9 49.1 1.0 CE1 A:HIS244 2.7 37.2 1.0 CD2 A:HIS244 3.0 37.2 1.0 NE2 A:HIS240 3.0 38.8 1.0 CB A:CYS224 3.1 49.1 1.0 CB A:CYS227 3.2 45.5 1.0 CD2 A:HIS240 3.2 38.8 1.0 N A:CYS227 3.3 45.5 1.0 CA A:CYS227 3.8 45.5 1.0 ND1 A:HIS244 3.9 37.2 1.0 CG A:HIS244 4.0 37.2 1.0 CB A:ILE226 4.1 51.0 1.0 CE1 A:HIS240 4.3 38.8 1.0 C A:ILE226 4.3 51.0 1.0 CA A:CYS224 4.4 49.1 1.0 N A:ILE226 4.5 51.0 1.0 CA A:ILE226 4.5 51.0 1.0 CG A:HIS240 4.5 38.8 1.0 C A:CYS227 4.6 45.5 1.0 CG2 A:ILE226 4.7 51.0 1.0 C A:CYS224 4.8 49.1 1.0 N A:SER228 4.9 49.2 1.0

Zinc binding site 7 out of 9 in the Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:148.4 occ:1.00 NE2 A:HIS272 1.9 77.2 1.0 SG A:CYS255 1.9 72.4 1.0 SG A:CYS258 1.9 88.5 1.0 CB A:CYS258 2.6 88.5 1.0 CE1 A:HIS272 2.8 77.2 1.0 CB A:CYS255 2.8 72.4 1.0 CD2 A:HIS272 2.9 77.2 1.0 NE2 A:HIS277 3.2 85.7 1.0 N A:CYS258 3.4 88.5 1.0 CA A:CYS258 3.6 88.5 1.0 CE1 A:HIS277 3.8 85.7 1.0 ND1 A:HIS272 3.9 77.2 1.0 CG A:HIS272 4.0 77.2 1.0 CD2 A:HIS277 4.1 85.7 1.0 CA A:CYS255 4.2 72.4 1.0 CG2 A:ILE276 4.4 80.6 1.0 C A:ILE257 4.5 83.0 1.0 O A:CYS258 4.6 88.5 1.0 C A:CYS258 4.7 88.5 1.0 N A:ILE257 4.7 83.0 1.0 CG A:MET261 4.8 73.1 1.0 CB A:ILE276 4.8 80.6 1.0 C A:CYS255 4.9 72.4 1.0 ND1 A:HIS277 4.9 85.7 1.0 CB A:ILE257 4.9 83.0 1.0 CA A:ILE257 4.9 83.0 1.0

Zinc binding site 8 out of 9 in the Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:212.4 occ:1.00 SG A:CYS367 1.9 144.5 1.0 SG A:CYS372 1.9 139.6 1.0 NE2 A:HIS389 2.1 139.7 1.0 NE2 A:HIS385 2.2 144.4 1.0 CB A:CYS367 2.6 144.5 1.0 CB A:CYS372 2.7 139.6 1.0 CD2 A:HIS389 3.0 139.7 1.0 CE1 A:HIS389 3.1 139.7 1.0 CE1 A:HIS385 3.1 144.4 1.0 CD2 A:HIS385 3.2 144.4 1.0 CA A:CYS367 4.0 144.5 1.0 CA A:CYS372 4.0 139.6 1.0 CG A:HIS389 4.1 139.7 1.0 ND1 A:HIS389 4.2 139.7 1.0 ND1 A:HIS385 4.3 144.4 1.0 CG A:HIS385 4.3 144.4 1.0 NH1 A:ARG374 4.3 160.6 1.0 C A:CYS372 4.3 139.6 1.0 CB A:TYR369 4.4 135.6 1.0 NE A:ARG374 4.6 160.6 1.0 N A:SER373 4.6 143.7 1.0 C A:CYS367 4.8 144.5 1.0 N A:TYR369 4.8 135.6 1.0 O A:CYS372 4.9 139.6 1.0 N A:PHE368 4.9 133.0 1.0 CZ A:ARG374 4.9 160.6 1.0 N A:ARG374 5.0 160.6 1.0

Zinc binding site 9 out of 9 in the Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Tfiiia-Tfiiic-BRF1-Tbp Complex Bound to 5S Rrna Gene within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn509 b:96.3 occ:1.00 NE2 A:HIS219 1.9 38.8 1.0 SG A:CYS201 1.9 42.8 1.0 SG A:CYS196 1.9 42.2 1.0 NE2 A:HIS214 2.1 43.8 1.0 CB A:CYS201 2.8 42.8 1.0 CE1 A:HIS219 2.9 38.8 1.0 CD2 A:HIS219 2.9 38.8 1.0 CD2 A:HIS214 3.0 43.8 1.0 CB A:CYS196 3.2 42.2 1.0 CE1 A:HIS214 3.3 43.8 1.0 ND1 A:HIS219 4.0 38.8 1.0 CG A:HIS219 4.0 38.8 1.0 CA A:CYS201 4.2 42.8 1.0 CG A:HIS214 4.2 43.8 1.0 ND1 A:HIS214 4.4 43.8 1.0 CA A:CYS196 4.5 42.2 1.0 C A:CYS201 4.7 42.8 1.0 CB A:PHE198 4.8 41.2 1.0

A.Talyzina, Y.Han, C.Banerjee, S.Fishbain, A.Reyes, R.Vafabakhsh, Y.He. Structural Basis of Tfiiic-Dependent Rna Polymerase III Transcription Initiation. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 37292922
DOI: 10.1101/2023.05.16.540967