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Zinc in PDB 8p2i: Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation with SPT4/5

Enzymatic activity of Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation with SPT4/5

All present enzymatic activity of Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation with SPT4/5:
2.7.7.6;

Other elements in 8p2i:

The structure of Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation with SPT4/5 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 with SPT4/5 (pdb code 8p2i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation with SPT4/5, PDB code: 8p2i:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8p2i

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Zinc binding site 1 out of 6 in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation with SPT4/5


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 with SPT4/5 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:CYS67 2.3 0.8 1.0
SG A:CYS60 2.3 30.0 1.0
SG A:CYS57 2.3 0.7 1.0
CD2 A:HIS70 2.9 0.8 1.0
CE1 A:HIS70 3.1 0.8 1.0
CB A:CYS57 3.2 0.7 1.0
CB A:CYS67 3.5 0.8 1.0
CB A:CYS60 3.7 30.0 1.0
N A:CYS60 3.9 30.0 1.0
CG A:HIS70 4.1 0.8 1.0
ND1 A:HIS70 4.1 0.8 1.0
CA A:GLY49 4.2 0.8 1.0
CA A:CYS60 4.3 30.0 1.0
CA A:CYS67 4.3 0.8 1.0
CB A:THR59 4.5 0.6 1.0
CD A:PRO68 4.6 0.8 1.0
N A:GLY69 4.6 0.9 1.0
CA A:CYS57 4.6 0.7 1.0
C A:CYS60 4.6 30.0 1.0
O A:GLY61 4.7 0.6 1.0
N A:GLY49 4.8 0.8 1.0
O A:CYS57 4.8 0.7 1.0
C A:CYS67 4.8 0.8 1.0
C A:THR59 4.8 0.6 1.0
N A:PRO68 4.8 0.8 1.0
CG2 A:THR59 4.9 0.6 1.0
O A:MET48 4.9 0.8 1.0
CA A:GLY69 4.9 0.9 1.0
C A:CYS57 4.9 0.7 1.0
O A:CYS60 5.0 30.0 1.0
O A:ARG47 5.0 0.7 1.0

Zinc binding site 2 out of 6 in 8p2i

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation with SPT4/5


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 with SPT4/5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:30.0
occ:1.00
 SG A:CYS100 2.3 0.7 1.0
SG A:CYS97 2.3 0.8 1.0
SG A:CYS147 2.3 0.8 1.0
SG A:CYS144 2.3 0.7 1.0
CB A:CYS97 2.9 0.8 1.0
CB A:CYS144 3.1 0.7 1.0
CB A:CYS147 3.5 0.8 1.0
CB A:CYS100 3.6 0.7 1.0
N A:CYS100 3.9 0.7 1.0
N A:CYS147 3.9 0.8 1.0
O A:CYS147 4.0 0.8 1.0
CA A:CYS147 4.1 0.8 1.0
CA A:CYS100 4.3 0.7 1.0
C A:CYS147 4.4 0.8 1.0
CA A:CYS97 4.4 0.8 1.0
CA A:CYS144 4.6 0.7 1.0
CB A:GLU99 4.7 0.7 1.0
C A:HIS146 4.9 0.7 1.0
CB A:HIS146 4.9 0.7 1.0
N A:GLU99 4.9 0.7 1.0
C A:GLU99 5.0 0.7 1.0

Zinc binding site 3 out of 6 in 8p2i

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Zinc binding site 3 out of 6 in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation with SPT4/5


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 with SPT4/5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:30.0
occ:1.00
 SG B:CYS1062 2.3 30.0 1.0
SG B:CYS1077 2.3 0.8 1.0
SG B:CYS1080 2.3 0.7 1.0
SG B:CYS1059 2.3 0.8 1.0
CB B:CYS1059 3.1 0.8 1.0
CB B:CYS1077 3.4 0.8 1.0
CB B:CYS1080 3.5 0.7 1.0
CB B:CYS1062 3.7 30.0 1.0
CG1 B:VAL1079 4.1 0.8 1.0
CB B:GLU1082 4.1 0.7 1.0
N B:CYS1062 4.2 30.0 1.0
N B:CYS1080 4.3 0.7 1.0
CA B:CYS1080 4.3 0.7 1.0
CA B:CYS1062 4.5 30.0 1.0
CA B:CYS1059 4.5 0.8 1.0
O B:CYS1059 4.6 0.8 1.0
CB B:ASN1061 4.7 0.8 1.0
CA B:CYS1077 4.8 0.8 1.0
C B:CYS1080 4.8 0.7 1.0
N B:GLU1082 4.8 0.7 1.0
C B:CYS1059 4.8 0.8 1.0

Zinc binding site 4 out of 6 in 8p2i

Go back to Zinc Binding Sites List in 8p2i
Zinc binding site 4 out of 6 in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation with SPT4/5


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 with SPT4/5 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
CB N:CYS7 3.1 0.6 1.0
N N:CYS45 3.2 0.6 1.0
CB N:CYS44 3.5 0.6 1.0
CB N:CYS10 3.5 0.6 1.0
CB N:CYS45 3.5 0.6 1.0
CA N:CYS45 3.6 0.6 1.0
C N:CYS44 3.6 0.6 1.0
N N:CYS10 3.9 0.6 1.0
CA N:CYS44 4.1 0.6 1.0
O N:CYS44 4.3 0.6 1.0
CA N:CYS10 4.3 0.6 1.0
CA N:CYS7 4.6 0.6 1.0
NH2 N:ARG42 4.7 0.5 1.0
N N:CYS44 4.8 0.6 1.0
N N:GLY11 4.8 0.5 1.0
CB N:THR9 4.8 0.5 1.0
C N:CYS10 5.0 0.6 1.0

Zinc binding site 5 out of 6 in 8p2i

Go back to Zinc Binding Sites List in 8p2i
Zinc binding site 5 out of 6 in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation with SPT4/5


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 with SPT4/5 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 3.1 79.7 1.0
CB P:CYS8 3.1 86.8 1.0
OG P:SER32 3.6 83.0 1.0
CB P:CYS30 3.8 30.0 1.0
CB P:CYS11 3.9 84.7 1.0
N P:CYS30 4.0 30.0 1.0
O P:CYS30 4.1 30.0 1.0
N P:CYS11 4.2 84.7 1.0
CA P:CYS30 4.3 30.0 1.0
CA P:CYS27 4.6 79.7 1.0
C P:CYS30 4.6 30.0 1.0
CA P:CYS11 4.6 84.7 1.0
CA P:CYS8 4.6 86.8 1.0
CB P:SER32 4.7 83.0 1.0
CB P:TYR29 4.7 81.8 1.0
C P:TYR29 4.9 81.8 1.0

Zinc binding site 6 out of 6 in 8p2i

Go back to Zinc Binding Sites List in 8p2i
Zinc binding site 6 out of 6 in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation with SPT4/5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Contracted Clamp Conformation with SPT4/5 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn101

b:30.0
occ:1.00
 SG I:CYS21 2.3 203.7 1.0
SG I:CYS18 2.3 202.0 1.0
SG I:CYS6 2.3 204.5 1.0
SG I:CYS9 2.3 190.1 1.0
CB I:CYS18 2.9 200.5 1.0
CB I:CYS21 3.1 201.9 1.0
CB I:CYS6 3.1 194.8 1.0
CB I:CYS9 3.4 186.2 1.0
N I:CYS21 3.7 198.0 1.0
CA I:CYS21 3.9 202.3 1.0
CG2 I:VAL20 4.0 190.2 1.0
NE2 I:HIS8 4.2 222.9 1.0
CA I:CYS18 4.4 200.8 1.0
O I:CYS21 4.5 211.1 1.0
CE1 I:HIS8 4.5 222.1 1.0
CA I:CYS6 4.6 194.6 1.0
C I:CYS21 4.6 208.9 1.0
CA I:CYS9 4.7 185.1 1.0
N I:CYS9 4.7 188.9 1.0
CD2 I:HIS8 4.7 217.2 1.0
C I:VAL20 4.8 201.5 1.0
O I:SER23 4.9 202.3 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: Fri Aug 22 11:58:05 2025

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