Zinc in PDB 8r3m: Mycobacterium Smegnatis Rna Polymerase Transcription Initiation Complex with Sigmaa, Rbpa, Held N-Terminal, Co and Pch Loop Domain, and An Upstream-Fork Promoter Fragment; State III Conformation

Enzymatic activity of Mycobacterium Smegnatis Rna Polymerase Transcription Initiation Complex with Sigmaa, Rbpa, Held N-Terminal, Co and Pch Loop Domain, and An Upstream-Fork Promoter Fragment; State III Conformation

All present enzymatic activity of Mycobacterium Smegnatis Rna Polymerase Transcription Initiation Complex with Sigmaa, Rbpa, Held N-Terminal, Co and Pch Loop Domain, and An Upstream-Fork Promoter Fragment; State III Conformation:
2.7.7.6;

Other elements in 8r3m:

The structure of Mycobacterium Smegnatis Rna Polymerase Transcription Initiation Complex with Sigmaa, Rbpa, Held N-Terminal, Co and Pch Loop Domain, and An Upstream-Fork Promoter Fragment; State III Conformation also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Mycobacterium Smegnatis Rna Polymerase Transcription Initiation Complex with Sigmaa, Rbpa, Held N-Terminal, Co and Pch Loop Domain, and An Upstream-Fork Promoter Fragment; State III Conformation (pdb code 8r3m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Mycobacterium Smegnatis Rna Polymerase Transcription Initiation Complex with Sigmaa, Rbpa, Held N-Terminal, Co and Pch Loop Domain, and An Upstream-Fork Promoter Fragment; State III Conformation, PDB code: 8r3m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8r3m

Go back to Zinc Binding Sites List in 8r3m
Zinc binding site 1 out of 2 in the Mycobacterium Smegnatis Rna Polymerase Transcription Initiation Complex with Sigmaa, Rbpa, Held N-Terminal, Co and Pch Loop Domain, and An Upstream-Fork Promoter Fragment; State III Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mycobacterium Smegnatis Rna Polymerase Transcription Initiation Complex with Sigmaa, Rbpa, Held N-Terminal, Co and Pch Loop Domain, and An Upstream-Fork Promoter Fragment; State III Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:33.0
occ:1.00
SG D:CYS974 2.3 19.7 1.0
SG D:CYS977 2.3 23.0 1.0
SG D:CYS967 2.3 22.7 1.0
SG D:CYS890 2.3 19.6 1.0
CB D:CYS977 3.2 23.0 1.0
CB D:CYS967 3.3 22.7 1.0
CB D:CYS890 3.4 19.6 1.0
CB D:CYS974 3.5 19.7 1.0
CA D:CYS967 3.8 22.7 1.0
NH2 D:ARG962 3.8 25.0 1.0
N D:CYS890 4.2 19.6 1.0
N D:CYS977 4.2 23.0 1.0
CA D:CYS977 4.3 23.0 1.0
N D:CYS974 4.3 19.7 1.0
N D:THR968 4.4 20.2 1.0
CA D:CYS974 4.4 19.7 1.0
CA D:CYS890 4.4 19.6 1.0
CG2 D:THR892 4.5 21.1 1.0
C D:CYS967 4.6 22.7 1.0
O D:CYS974 4.8 19.7 1.0
CZ D:ARG962 4.8 25.0 1.0
C D:CYS974 4.9 19.7 1.0
N D:CYS967 4.9 22.7 1.0
OD1 D:ASP889 5.0 21.4 1.0

Zinc binding site 2 out of 2 in 8r3m

Go back to Zinc Binding Sites List in 8r3m
Zinc binding site 2 out of 2 in the Mycobacterium Smegnatis Rna Polymerase Transcription Initiation Complex with Sigmaa, Rbpa, Held N-Terminal, Co and Pch Loop Domain, and An Upstream-Fork Promoter Fragment; State III Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mycobacterium Smegnatis Rna Polymerase Transcription Initiation Complex with Sigmaa, Rbpa, Held N-Terminal, Co and Pch Loop Domain, and An Upstream-Fork Promoter Fragment; State III Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:63.1
occ:1.00
SG D:CYS62 2.2 52.3 1.0
SG D:CYS78 2.2 46.5 1.0
SG D:CYS75 2.3 49.8 1.0
SG D:CYS60 2.4 43.6 1.0
CB D:CYS75 3.2 49.8 1.0
CB D:CYS60 3.4 43.6 1.0
N D:CYS62 3.5 52.3 1.0
CB D:CYS62 3.5 52.3 1.0
CB D:CYS78 3.6 46.5 1.0
CA D:CYS62 3.9 52.3 1.0
N D:LYS64 3.9 50.9 1.0
CB D:LYS64 4.0 50.9 1.0
N D:GLY63 4.0 50.4 1.0
N D:TYR61 4.2 43.1 1.0
N D:CYS78 4.2 46.5 1.0
C D:CYS62 4.3 52.3 1.0
CA D:CYS78 4.6 46.5 1.0
CA D:LYS64 4.6 50.9 1.0
C D:TYR61 4.6 43.1 1.0
C D:CYS60 4.6 43.6 1.0
CA D:CYS60 4.6 43.6 1.0
CA D:CYS75 4.7 49.8 1.0
CB D:ARG77 4.8 48.8 1.0
CA D:TYR61 4.9 43.1 1.0
N D:TYR65 4.9 50.6 1.0
C D:GLY63 4.9 50.4 1.0
CA D:GLY63 5.0 50.4 1.0

Reference:

T.Koval, L.Dohnalek, K.Libor, T.Kouba. Molecular Insights Into Rna Polymerase Recycling By Mycobacterial Held To Be Published.
Page generated: Thu Oct 31 10:23:13 2024

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