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

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

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

Other elements in 8orq:

The structure of Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Open 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 Open Clamp Conformation (pdb code 8orq). 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 Open Clamp Conformation, PDB code: 8orq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 8orq

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Zinc binding site 1 out of 5 in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Open 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 Open Clamp Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:30.0
occ:1.00
 NE2 A:HIS70 2.1 92.2 1.0
SG A:CYS60 2.3 88.9 1.0
SG A:CYS67 2.3 83.4 1.0
SG A:CYS57 2.3 92.1 1.0
CD2 A:HIS70 2.9 92.2 1.0
CB A:CYS57 3.1 92.1 1.0
CE1 A:HIS70 3.2 92.2 1.0
CB A:CYS60 3.2 88.9 1.0
CB A:CYS67 3.3 83.4 1.0
N A:CYS60 3.7 88.9 1.0
CA A:CYS60 3.9 88.9 1.0
CG A:HIS70 4.1 92.2 1.0
CA A:CYS67 4.2 83.4 1.0
ND1 A:HIS70 4.2 92.2 1.0
CA A:GLY49 4.3 89.6 1.0
N A:GLY61 4.5 89.8 1.0
N A:GLY69 4.5 86.5 1.0
N A:GLY62 4.5 86.5 1.0
C A:CYS60 4.5 88.9 1.0
CA A:CYS57 4.5 92.1 1.0
CD A:PRO68 4.6 79.5 1.0
C A:CYS67 4.6 83.4 1.0
N A:PRO68 4.8 79.5 1.0
CA A:GLY69 4.8 86.5 1.0
C A:THR59 4.8 92.3 1.0
CB A:THR59 4.9 92.3 1.0
N A:GLY49 5.0 89.6 1.0
C A:GLY69 5.0 86.5 1.0

Zinc binding site 2 out of 5 in 8orq

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Zinc binding site 2 out of 5 in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Open 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 Open Clamp Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:30.0
occ:1.00
 SG A:CYS100 2.3 96.0 1.0
SG A:CYS147 2.3 95.1 1.0
SG A:CYS97 2.3 97.3 1.0
SG A:CYS144 2.3 95.8 1.0
CB A:CYS97 2.6 97.3 1.0
CB A:CYS100 3.0 96.0 1.0
CB A:CYS144 3.3 95.8 1.0
CB A:CYS147 3.5 95.1 1.0
N A:CYS100 3.6 96.0 1.0
CA A:CYS100 3.9 96.0 1.0
N A:CYS147 4.0 95.1 1.0
CA A:CYS97 4.2 97.3 1.0
CA A:CYS147 4.4 95.1 1.0
CD2 A:HIS146 4.4 95.4 1.0
N A:GLY101 4.5 96.4 1.0
CB A:HIS146 4.5 95.4 1.0
C A:CYS100 4.6 96.0 1.0
C A:GLU99 4.8 95.2 1.0
CA A:CYS144 4.8 95.8 1.0
NE2 A:GLN151 4.8 93.7 1.0
CG A:HIS146 4.8 95.4 1.0
C A:CYS97 4.8 97.3 1.0
C A:HIS146 4.9 95.4 1.0
CB A:GLU99 4.9 95.2 1.0
N A:CYS97 5.0 97.3 1.0
N A:GLU99 5.0 95.2 1.0

Zinc binding site 3 out of 5 in 8orq

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Zinc binding site 3 out of 5 in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Open 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 Open Clamp Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:30.0
occ:1.00
 SG B:CYS1062 2.3 91.7 1.0
SG B:CYS1080 2.3 89.8 1.0
SG B:CYS1059 2.3 93.5 1.0
SG B:CYS1077 2.3 91.8 1.0
CB B:CYS1062 3.1 91.7 1.0
CB B:CYS1059 3.2 93.5 1.0
N B:CYS1062 3.4 91.7 1.0
CB B:CYS1077 3.5 91.8 1.0
CB B:CYS1080 3.8 89.8 1.0
CA B:CYS1062 3.9 91.7 1.0
N B:CYS1080 4.1 89.8 1.0
N B:GLY1063 4.3 92.3 1.0
CB B:ASN1061 4.4 90.9 1.0
CB B:VAL1079 4.4 90.2 1.0
CA B:CYS1080 4.4 89.8 1.0
C B:ASN1061 4.5 90.9 1.0
C B:CYS1062 4.6 91.7 1.0
CA B:CYS1059 4.6 93.5 1.0
CG1 B:VAL1079 4.7 90.2 1.0
N B:ASN1061 4.8 90.9 1.0
N B:HIS1064 4.8 92.7 1.0
CA B:ASN1061 4.8 90.9 1.0
C B:CYS1080 4.8 89.8 1.0
CG B:GLU1084 4.8 75.7 1.0
CA B:CYS1077 4.9 91.8 1.0
CB B:GLU1084 5.0 75.7 1.0
O B:CYS1080 5.0 89.8 1.0

Zinc binding site 4 out of 5 in 8orq

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Zinc binding site 4 out of 5 in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Open 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 Open Clamp Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn101

b:30.0
occ:1.00
 SG N:CYS10 2.3 30.0 1.0
SG N:CYS45 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 3.2 0.6 1.0
N N:CYS45 3.3 0.6 1.0
CB N:CYS10 3.5 30.0 1.0
CB N:CYS45 3.6 0.6 1.0
CA N:CYS45 3.6 0.6 1.0
CB N:CYS44 3.8 0.6 1.0
C N:CYS44 3.8 0.6 1.0
N N:CYS10 3.8 30.0 1.0
CA N:CYS10 4.2 30.0 1.0
O N:CYS44 4.2 0.6 1.0
CA N:CYS44 4.4 0.6 1.0
NE N:ARG42 4.5 0.5 1.0
CA N:CYS7 4.7 0.6 1.0
CB N:LYS12 4.7 0.6 1.0
CB N:THR9 4.7 0.5 1.0
C N:CYS10 4.7 30.0 1.0
NH2 N:ARG42 4.7 0.5 1.0
N N:GLY11 4.8 0.5 1.0
N N:LYS12 4.9 0.6 1.0
C N:THR9 4.9 0.5 1.0
N N:THR9 5.0 0.5 1.0

Zinc binding site 5 out of 5 in 8orq

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Zinc binding site 5 out of 5 in the Cryo-Em Structure of Pyrococcus Furiosus Apo Form Rna Polymerase Open 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 Open 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 82.8 1.0
SG P:CYS27 2.3 79.7 1.0
CB P:CYS8 3.0 86.8 1.0
CB P:CYS27 3.4 79.7 1.0
CB P:CYS11 3.4 84.7 1.0
CB P:CYS30 3.6 82.8 1.0
N P:CYS11 3.9 84.7 1.0
N P:CYS30 4.1 82.8 1.0
CA P:CYS11 4.2 84.7 1.0
CB P:SER32 4.3 83.0 1.0
CA P:CYS30 4.4 82.8 1.0
CA P:CYS8 4.5 86.8 1.0
N P:SER32 4.8 83.0 1.0
CA P:CYS27 4.8 79.7 1.0
CB P:TYR29 4.8 81.8 1.0
C P:CYS30 4.9 82.8 1.0
C P:CYS11 4.9 84.7 1.0
N P:GLY12 4.9 83.3 1.0
N P:GLY31 5.0 80.6 1.0
C P:TYR29 5.0 81.8 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 08:55:44 2024

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