Zinc in PDB 6m6a: Cryo-Em Structure of Thermus Thermophilus Mfd in Complex with Rna Polymerase

All present enzymatic activity of Cryo-Em Structure of Thermus Thermophilus Mfd in Complex with Rna Polymerase:
2.7.7.6;

The structure of Cryo-Em Structure of Thermus Thermophilus Mfd in Complex with Rna Polymerase also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Cryo-Em Structure of Thermus Thermophilus Mfd in Complex with Rna Polymerase (pdb code 6m6a). 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 Thermus Thermophilus Mfd in Complex with Rna Polymerase, PDB code: 6m6a:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of Thermus Thermophilus Mfd in Complex with Rna Polymerase


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 Thermus Thermophilus Mfd in Complex with Rna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2001 b:0.1 occ:1.00 SG D:CYS1194 2.4 0.3 1.0 SG D:CYS1112 2.5 0.2 1.0 SG D:CYS1201 2.5 0.5 1.0 CB D:CYS1204 2.5 0.5 1.0 SG D:CYS1204 2.5 0.5 1.0 CB D:CYS1194 2.7 0.3 1.0 CA D:CYS1194 2.9 0.3 1.0 CB D:CYS1112 3.1 0.2 1.0 NH2 D:ARG1189 3.3 0.1 1.0 CB D:CYS1201 3.5 0.5 1.0 N D:CYS1204 3.6 0.5 1.0 CA D:CYS1204 3.7 0.5 1.0 C D:CYS1194 3.9 0.3 1.0 N D:CYS1194 3.9 0.3 1.0 N D:CYS1112 4.1 0.2 1.0 N D:CYS1201 4.2 0.5 1.0 N D:GLN1195 4.2 0.1 1.0 CA D:CYS1112 4.2 0.2 1.0 CZ D:ARG1189 4.3 0.1 1.0 CA D:CYS1201 4.4 0.5 1.0 NE D:ARG1189 4.4 0.1 1.0 OG1 D:THR1196 4.4 0.8 1.0 O D:THR1193 4.5 0.9 1.0 O D:CYS1201 4.6 0.5 1.0 C D:THR1193 4.6 0.9 1.0 O D:SER1190 4.7 0.7 1.0 C D:CYS1204 4.7 0.5 1.0 O D:CYS1194 4.7 0.3 1.0 C D:CYS1201 4.8 0.5 1.0 C D:LYS1203 4.9 0.4 1.0 CG2 D:THR1114 5.0 0.2 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Thermus Thermophilus Mfd in Complex with Rna Polymerase


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 Thermus Thermophilus Mfd in Complex with Rna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:0.6 occ:1.00 N D:PHE45 2.2 0.8 1.0 O D:GLU40 2.3 1.0 1.0 C D:PHE45 2.5 0.8 1.0 N D:ASP46 2.5 0.1 1.0 CA D:PHE45 2.6 0.8 1.0 N D:GLU40 2.8 1.0 1.0 CB D:PHE45 3.0 0.8 1.0 C D:GLU40 3.1 1.0 1.0 CA D:ASP46 3.2 0.1 1.0 O D:PHE45 3.2 0.8 1.0 O D:GLY43 3.3 0.7 1.0 C D:GLY43 3.3 0.7 1.0 CA D:GLU40 3.4 1.0 1.0 C D:LEU44 3.4 0.4 1.0 N D:LEU44 3.5 0.4 1.0 O D:THR31 3.6 0.8 1.0 C D:PRO39 3.7 0.8 1.0 CB D:PRO39 3.8 0.8 1.0 CB D:ASP46 3.8 0.1 1.0 CB D:GLU40 3.8 1.0 1.0 CA D:PRO39 4.0 0.8 1.0 CA D:GLY43 4.0 0.7 1.0 CA D:LEU44 4.0 0.4 1.0 CG D:PHE45 4.2 0.8 1.0 N D:GLY43 4.3 0.7 1.0 N D:ARG41 4.4 0.5 1.0 O D:LEU44 4.4 0.4 1.0 CD2 D:PHE45 4.5 0.8 1.0 C D:ASP46 4.6 0.1 1.0 O D:PRO39 4.8 0.8 1.0 C D:THR31 4.9 0.8 1.0 CG D:GLU40 4.9 1.0 1.0 CA D:ARG41 5.0 0.5 1.0

J.Shi, A.Wen, M.Zhao, S.Jin, L.You, Y.Shi, S.Dong, X.Hua, Y.Zhang, Y.Feng. Structural Basis of Mfd-Dependent Transcription Termination. Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962