Zinc in PDB 8rbo: Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation

Enzymatic activity of Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation

All present enzymatic activity of Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation:
2.7.7.6;

Other elements in 8rbo:

The structure of Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation (pdb code 8rbo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation, PDB code: 8rbo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 8rbo

Go back to Zinc Binding Sites List in 8rbo
Zinc binding site 1 out of 5 in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation


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 Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1000

b:30.0
occ:1.00
 NE2 A:HIS70 2.1 0.8 1.0
SG A:CYS57 2.3 0.7 1.0
SG A:CYS60 2.3 30.0 1.0
SG A:CYS67 2.3 0.8 1.0
CE1 A:HIS70 3.0 0.8 1.0
CD2 A:HIS70 3.1 0.8 1.0
CB A:CYS60 3.2 30.0 1.0
CB A:CYS67 3.5 0.8 1.0
CB A:CYS57 3.6 0.7 1.0
OG1 A:THR59 3.6 0.6 1.0
N A:CYS60 3.6 30.0 1.0
CA A:CYS60 3.8 30.0 1.0
N A:GLY61 3.8 0.6 1.0
O A:GLY61 4.0 0.6 1.0
C A:CYS60 4.0 30.0 1.0
CA A:CYS67 4.1 0.8 1.0
ND1 A:HIS70 4.1 0.8 1.0
CG A:HIS70 4.2 0.8 1.0
CD A:PRO68 4.4 0.8 1.0
CA A:GLY49 4.7 0.8 1.0
C A:THR59 4.7 0.6 1.0
CA A:GLY61 4.8 0.6 1.0
C A:GLY61 4.8 0.6 1.0
C A:CYS67 4.8 0.8 1.0
N A:PRO68 4.9 0.8 1.0
CA A:CYS57 4.9 0.7 1.0
O A:CYS60 4.9 30.0 1.0
CB A:THR59 4.9 0.6 1.0

Zinc binding site 2 out of 5 in 8rbo

Go back to Zinc Binding Sites List in 8rbo
Zinc binding site 2 out of 5 in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation


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 Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:30.0
occ:1.00
 SG A:CYS97 2.3 0.8 1.0
SG A:CYS100 2.3 0.7 1.0
SG A:CYS147 2.3 0.8 1.0
SG A:CYS144 2.3 0.7 1.0
CB A:CYS144 3.1 0.7 1.0
CB A:CYS97 3.2 0.8 1.0
CB A:CYS147 3.6 0.8 1.0
OE2 A:GLU99 3.8 0.7 1.0
N A:CYS147 3.9 0.8 1.0
N A:CYS100 3.9 0.7 1.0
CB A:CYS100 3.9 0.7 1.0
O A:CYS147 4.2 0.8 1.0
CA A:CYS147 4.2 0.8 1.0
CB A:GLU99 4.5 0.7 1.0
CA A:CYS100 4.5 0.7 1.0
CA A:CYS144 4.6 0.7 1.0
CB A:HIS146 4.6 0.7 1.0
CD2 A:HIS146 4.6 0.7 1.0
N A:GLU99 4.7 0.7 1.0
C A:CYS147 4.7 0.8 1.0
CA A:CYS97 4.7 0.8 1.0
C A:HIS146 4.8 0.7 1.0
C A:GLU99 4.9 0.7 1.0
CA A:GLU99 4.9 0.7 1.0
NE2 A:GLN151 4.9 0.7 1.0
CD A:GLU99 4.9 0.7 1.0
N A:HIS146 5.0 0.7 1.0
CG A:HIS146 5.0 0.7 1.0

Zinc binding site 3 out of 5 in 8rbo

Go back to Zinc Binding Sites List in 8rbo
Zinc binding site 3 out of 5 in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:30.0
occ:1.00
 CB B:CYS1080 2.0 0.7 1.0
SG B:CYS1062 2.3 30.0 1.0
SG B:CYS1077 2.3 0.8 1.0
SG B:CYS1059 2.3 0.8 1.0
SG B:CYS1080 2.4 0.7 1.0
OD1 B:ASN1061 3.0 0.8 1.0
CB B:CYS1062 3.3 30.0 1.0
CB B:CYS1077 3.3 0.8 1.0
CA B:CYS1080 3.5 0.7 1.0
CB B:CYS1059 3.7 0.8 1.0
N B:CYS1062 3.9 30.0 1.0
N B:CYS1080 4.0 0.7 1.0
CG B:ASN1061 4.0 0.8 1.0
CA B:CYS1062 4.2 30.0 1.0
CB B:GLU1082 4.2 0.7 1.0
C B:CYS1080 4.3 0.7 1.0
ND2 B:ASN1061 4.4 0.8 1.0
CA B:CYS1077 4.7 0.8 1.0
O B:CYS1080 4.9 0.7 1.0
N B:GLY1081 4.9 0.8 1.0
ND1 B:HIS1064 4.9 0.8 1.0

Zinc binding site 4 out of 5 in 8rbo

Go back to Zinc Binding Sites List in 8rbo
Zinc binding site 4 out of 5 in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn101

b:30.0
occ:1.00
 SG N:CYS45 2.3 0.6 1.0
SG N:CYS10 2.3 0.6 1.0
SG N:CYS44 2.3 0.6 1.0
SG N:CYS7 2.3 0.6 1.0
N N:CYS45 3.3 0.6 1.0
CB N:CYS7 3.3 0.6 1.0
CB N:CYS10 3.4 0.6 1.0
CB N:CYS45 3.5 0.6 1.0
CA N:CYS45 3.6 0.6 1.0
CB N:CYS44 3.7 0.6 1.0
C N:CYS44 3.7 0.6 1.0
N N:CYS10 3.8 0.6 1.0
NH2 N:ARG42 4.2 0.5 1.0
CA N:CYS10 4.2 0.6 1.0
O N:CYS44 4.3 0.6 1.0
CA N:CYS44 4.3 0.6 1.0
NE N:ARG42 4.6 0.5 1.0
N N:GLY11 4.6 0.5 1.0
CB N:THR9 4.7 0.5 1.0
CA N:CYS7 4.7 0.6 1.0
C N:CYS10 4.8 0.6 1.0
CZ N:ARG42 4.9 0.5 1.0
C N:THR9 4.9 0.5 1.0
N N:CYS44 5.0 0.6 1.0
N N:LYS12 5.0 0.6 1.0
N N:THR9 5.0 0.5 1.0

Zinc binding site 5 out of 5 in 8rbo

Go back to Zinc Binding Sites List in 8rbo
Zinc binding site 5 out of 5 in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn101

b:30.0
occ:1.00
 SG P:CYS8 2.3 86.8 1.0
SG P:CYS11 2.3 84.7 1.0
SG P:CYS30 2.3 30.0 1.0
SG P:CYS27 2.3 79.7 1.0
CB P:CYS27 3.2 79.7 1.0
CB P:CYS8 3.2 86.8 1.0
CB P:CYS30 3.6 30.0 1.0
CB P:CYS11 3.8 84.7 1.0
N P:CYS30 3.9 30.0 1.0
N P:CYS11 4.0 84.7 1.0
CA P:CYS30 4.3 30.0 1.0
CB P:SER32 4.4 83.0 1.0
CA P:CYS11 4.5 84.7 1.0
CA P:CYS27 4.7 79.7 1.0
CA P:CYS8 4.7 86.8 1.0
CB P:TYR29 4.7 81.8 1.0
N P:SER32 4.8 83.0 1.0
C P:CYS30 4.8 30.0 1.0
C P:TYR29 5.0 81.8 1.0
N P:GLY31 5.0 80.6 1.0
CB P:LYS10 5.0 83.7 1.0

Reference:

D.M.Tarau, F.Grunberger, M.Pilsl, R.Reichelt, F.B.Heiss, S.Koenig, H.Urlaub, W.Hausner, C.Engel, D.Grohmann. Structural Basis of Archaeal Rna Polymerase Transcription Elongation and SPT4/5 Recruitment Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
Page generated: Thu Oct 31 10:26:48 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy