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Zinc in PDB 7pyj: Cryoem Structure of E.Coli Rna Polymerase Elongation Complex Bound to Nusa (Nusa Elongation Complex in Less-Swiveled Conformation)

Enzymatic activity of Cryoem Structure of E.Coli Rna Polymerase Elongation Complex Bound to Nusa (Nusa Elongation Complex in Less-Swiveled Conformation)

All present enzymatic activity of Cryoem Structure of E.Coli Rna Polymerase Elongation Complex Bound to Nusa (Nusa Elongation Complex in Less-Swiveled Conformation):
2.7.7.6;

Other elements in 7pyj:

The structure of Cryoem Structure of E.Coli Rna Polymerase Elongation Complex Bound to Nusa (Nusa Elongation Complex in Less-Swiveled Conformation) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryoem Structure of E.Coli Rna Polymerase Elongation Complex Bound to Nusa (Nusa Elongation Complex in Less-Swiveled Conformation) (pdb code 7pyj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryoem Structure of E.Coli Rna Polymerase Elongation Complex Bound to Nusa (Nusa Elongation Complex in Less-Swiveled Conformation), PDB code: 7pyj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7pyj

Go back to Zinc Binding Sites List in 7pyj
Zinc binding site 1 out of 2 in the Cryoem Structure of E.Coli Rna Polymerase Elongation Complex Bound to Nusa (Nusa Elongation Complex in Less-Swiveled Conformation)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryoem Structure of E.Coli Rna Polymerase Elongation Complex Bound to Nusa (Nusa Elongation Complex in Less-Swiveled Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1502

b:310.9
occ:1.00
N D:TYR75 2.2 253.2 1.0
O D:GLY73 2.3 262.9 1.0
C D:TYR75 2.3 253.2 1.0
C D:LYS74 2.4 252.9 1.0
CA D:TYR75 2.5 253.2 1.0
N D:LYS76 2.7 256.3 1.0
O D:LYS74 2.7 252.9 1.0
CG D:LYS76 2.8 256.3 1.0
C D:GLY73 2.8 262.9 1.0
O D:TYR75 2.8 253.2 1.0
N D:LYS74 3.3 252.9 1.0
CA D:LYS74 3.3 252.9 1.0
CB D:LYS76 3.4 256.3 1.0
NZ D:LYS76 3.5 256.3 1.0
CA D:LYS76 3.6 256.3 1.0
CA D:GLY73 3.7 262.9 1.0
CD D:LYS76 3.8 256.3 1.0
CE D:LYS76 4.0 256.3 1.0
CB D:TYR75 4.0 253.2 1.0
CB D:LYS74 4.7 252.9 1.0
SG D:CYS70 4.7 252.5 1.0
CG D:TYR75 4.9 253.2 1.0
C D:LYS76 4.9 256.3 1.0
N D:GLY73 4.9 262.9 1.0

Zinc binding site 2 out of 2 in 7pyj

Go back to Zinc Binding Sites List in 7pyj
Zinc binding site 2 out of 2 in the Cryoem Structure of E.Coli Rna Polymerase Elongation Complex Bound to Nusa (Nusa Elongation Complex in Less-Swiveled Conformation)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryoem Structure of E.Coli Rna Polymerase Elongation Complex Bound to Nusa (Nusa Elongation Complex in Less-Swiveled Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1503

b:288.1
occ:1.00
SG D:CYS898 2.3 222.6 1.0
SG D:CYS895 2.3 222.4 1.0
SG D:CYS814 2.3 241.7 1.0
SG D:CYS888 2.3 217.5 1.0
CB D:CYS814 2.5 241.7 1.0
CB D:CYS898 3.0 222.6 1.0
CB D:CYS888 3.2 217.5 1.0
CA D:CYS888 3.7 217.5 1.0
CB D:CYS895 3.7 222.4 1.0
CA D:CYS814 3.7 241.7 1.0
N D:CYS814 3.8 241.7 1.0
OG1 D:THR890 3.8 225.9 1.0
N D:ASP889 4.0 220.7 1.0
NH2 D:ARG883 4.0 215.2 1.0
CA D:CYS898 4.2 222.6 1.0
C D:CYS888 4.3 217.5 1.0
N D:CYS898 4.3 222.6 1.0
N D:CYS895 4.4 222.4 1.0
CA D:CYS895 4.5 222.4 1.0
O D:CYS895 4.6 222.4 1.0
CZ D:ARG883 4.6 215.2 1.0
C D:CYS814 4.7 241.7 1.0
N D:THR890 4.9 225.9 1.0
C D:CYS895 4.9 222.4 1.0
NE D:ARG883 4.9 215.2 1.0

Reference:

C.Zhu, X.Guo, P.Dumas, M.Takacs, M.Abdelkareem, A.Vanden Broeck, C.Saint-Andre, G.Papai, C.Crucifix, J.Ortiz, A.Weixlbaumer. Transcription Factors Modulate Rna Polymerase Conformational Equilibrium. Nat Commun V. 13 1546 2022.
ISSN: ESSN 2041-1723
PubMed: 35318334
DOI: 10.1038/S41467-022-29148-0
Page generated: Sat Apr 8 01:43:06 2023

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