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Zinc in PDB 6f41: Rna Polymerase III Initially Transcribing Complex

Enzymatic activity of Rna Polymerase III Initially Transcribing Complex

All present enzymatic activity of Rna Polymerase III Initially Transcribing Complex:
2.7.7.6;

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase III Initially Transcribing Complex (pdb code 6f41). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Rna Polymerase III Initially Transcribing Complex, PDB code: 6f41:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6f41

Go back to Zinc Binding Sites List in 6f41
Zinc binding site 1 out of 7 in the Rna Polymerase III Initially Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase III Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1501

b:0.8
occ:1.00
 NE2 A:HIS80 2.2 84.1 1.0
N A:CYS70 2.2 94.1 1.0
SG A:CYS67 2.5 99.3 1.0
SG A:CYS70 2.6 94.1 1.0
CB A:CYS70 2.6 94.1 1.0
CD2 A:HIS80 2.7 84.1 1.0
CA A:CYS70 2.9 94.1 1.0
CB A:THR69 3.1 93.7 1.0
C A:THR69 3.2 93.7 1.0
CE1 A:HIS80 3.4 84.1 1.0
CA A:THR69 3.5 93.7 1.0
CG2 A:THR69 3.7 93.7 1.0
N A:THR69 3.7 93.7 1.0
CB A:CYS67 3.8 99.3 1.0
CG A:HIS80 4.0 84.1 1.0
C A:CYS70 4.1 94.1 1.0
N A:HIS71 4.2 0.1 1.0
OG1 A:THR69 4.3 93.7 1.0
ND1 A:HIS80 4.3 84.1 1.0
O A:THR69 4.3 93.7 1.0
SG A:CYS77 4.4 98.8 1.0
O A:CYS67 4.6 99.3 1.0
C A:CYS67 4.7 99.3 1.0
CA A:CYS67 4.9 99.3 1.0

Zinc binding site 2 out of 7 in 6f41

Go back to Zinc Binding Sites List in 6f41
Zinc binding site 2 out of 7 in the Rna Polymerase III Initially Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase III Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1502

b:0.8
occ:1.00
 SG A:CYS157 2.5 0.4 1.0
SG A:CYS110 2.5 95.0 1.0
SG A:CYS107 2.5 90.0 1.0
SG A:CYS154 2.5 98.3 1.0
CB A:CYS110 3.2 95.0 1.0
CB A:CYS154 3.3 98.3 1.0
N A:CYS110 3.5 95.0 1.0
CB A:CYS107 3.6 90.0 1.0
CA A:CYS110 3.9 95.0 1.0
CB A:CYS157 4.0 0.4 1.0
N A:CYS157 4.0 0.4 1.0
CB A:ASN109 4.1 92.6 1.0
CB A:ALA159 4.3 0.3 1.0
CA A:CYS157 4.4 0.4 1.0
N A:ALA159 4.4 0.3 1.0
C A:ASN109 4.5 92.6 1.0
N A:GLY158 4.6 0.2 1.0
CA A:ASN109 4.7 92.6 1.0
C A:CYS157 4.7 0.4 1.0
CA A:CYS154 4.7 98.3 1.0
N A:ASN109 4.8 92.6 1.0
C A:CYS110 4.8 95.0 1.0
N A:HIS156 4.9 0.2 1.0
CA A:ALA159 4.9 0.3 1.0
N A:SER111 5.0 88.0 1.0
CG A:ASN109 5.0 92.6 1.0

Zinc binding site 3 out of 7 in 6f41

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Zinc binding site 3 out of 7 in the Rna Polymerase III Initially Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase III Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2000

b:0.4
occ:1.00
 O B:LYS1097 2.4 78.8 1.0
SG B:CYS1107 2.6 75.6 1.0
SG B:CYS1095 2.8 77.0 1.0
SG B:CYS1098 2.8 79.0 1.0
O B:CYS1098 3.0 79.0 1.0
CB B:CYS1095 3.2 77.0 1.0
SG B:CYS1110 3.5 80.8 1.0
C B:LYS1097 3.6 78.8 1.0
C B:CYS1098 3.7 79.0 1.0
CB B:CYS1098 4.1 79.0 1.0
CB B:CYS1107 4.2 75.6 1.0
CA B:CYS1098 4.2 79.0 1.0
CG2 B:THR1109 4.3 78.1 1.0
N B:CYS1098 4.4 79.0 1.0
CA B:CYS1095 4.6 77.0 1.0
CG B:LYS1097 4.6 78.8 1.0
N B:GLY1099 4.6 71.5 1.0
CD2 B:LEU1100 4.6 69.0 1.0
CA B:GLY1099 4.7 71.5 1.0
CA B:LYS1097 4.8 78.8 1.0
N B:LEU1100 4.8 69.0 1.0
O B:LEU1100 4.8 69.0 1.0
N B:LYS1097 4.8 78.8 1.0
C B:CYS1095 4.9 77.0 1.0
N B:ASP1096 5.0 79.5 1.0

Zinc binding site 4 out of 7 in 6f41

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Zinc binding site 4 out of 7 in the Rna Polymerase III Initially Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase III Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn2000

b:0.3
occ:1.00
 SG I:CYS5 2.4 0.1 1.0
SG I:CYS26 2.4 0.3 1.0
CB I:CYS29 2.4 67.3 1.0
SG I:CYS8 2.5 88.2 1.0
SG I:CYS29 2.7 67.3 1.0
CB I:CYS5 3.4 0.1 1.0
CB I:CYS8 3.7 88.2 1.0
CA I:CYS29 3.8 67.3 1.0
O I:CYS29 4.1 67.3 1.0
CB I:CYS26 4.1 0.3 1.0
C I:CYS29 4.2 67.3 1.0
CB I:TYR31 4.3 71.7 1.0
N I:CYS29 4.4 67.3 1.0
O I:PRO6 4.6 89.8 1.0
O I:ARG27 4.7 76.9 1.0
CA I:CYS5 4.7 0.1 1.0
O I:CYS5 4.8 0.1 1.0
C I:CYS5 4.8 0.1 1.0
CA I:CYS8 4.9 88.2 1.0
O I:MET11 5.0 0.1 1.0
N I:CYS8 5.0 88.2 1.0

Zinc binding site 5 out of 7 in 6f41

Go back to Zinc Binding Sites List in 6f41
Zinc binding site 5 out of 7 in the Rna Polymerase III Initially Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase III Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2000

b:0.6
occ:1.00
 SG J:CYS46 2.4 87.2 1.0
SG J:CYS7 2.4 66.8 1.0
SG J:CYS45 2.4 84.1 1.0
SG J:CYS10 2.6 70.3 1.0
N J:CYS46 2.9 87.2 1.0
C J:CYS45 3.2 84.1 1.0
CB J:CYS7 3.3 66.8 1.0
CA J:CYS46 3.3 87.2 1.0
CB J:CYS46 3.5 87.2 1.0
CB J:CYS45 3.5 84.1 1.0
O J:CYS45 3.6 84.1 1.0
CB J:CYS10 3.6 70.3 1.0
CA J:CYS45 3.9 84.1 1.0
N J:CYS10 4.0 70.3 1.0
N J:CYS45 4.4 84.1 1.0
CA J:CYS10 4.5 70.3 1.0
CA J:CYS7 4.8 66.8 1.0
C J:CYS46 4.9 87.2 1.0
CB J:ARG43 4.9 84.7 1.0
CG J:LYS12 5.0 69.5 1.0
N J:GLY11 5.0 71.5 1.0

Zinc binding site 6 out of 7 in 6f41

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Zinc binding site 6 out of 7 in the Rna Polymerase III Initially Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase III Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn2000

b:99.1
occ:1.00
 SG L:CYS48 2.6 63.5 1.0
CB L:CYS51 2.6 63.6 1.0
CB L:CYS34 2.6 63.3 1.0
SG L:CYS31 2.7 57.9 1.0
CB L:CYS31 3.4 57.9 1.0
SG L:CYS34 3.5 63.3 1.0
O L:LYS49 3.5 63.2 1.0
SG L:CYS51 3.6 63.6 1.0
CA L:CYS51 3.7 63.6 1.0
CB L:CYS48 3.9 63.5 1.0
N L:CYS51 3.9 63.6 1.0
CA L:CYS34 4.0 63.3 1.0
C L:CYS51 4.2 63.6 1.0
N L:CYS34 4.2 63.3 1.0
O L:CYS51 4.2 63.6 1.0
CB L:HIS53 4.2 57.2 1.0
C L:ASP50 4.4 65.2 1.0
C L:LYS49 4.6 63.2 1.0
O L:ASP50 4.6 65.2 1.0
N L:HIS53 4.7 57.2 1.0
CA L:CYS31 4.8 57.9 1.0
C L:CYS34 4.9 63.3 1.0

Zinc binding site 7 out of 7 in 6f41

Go back to Zinc Binding Sites List in 6f41
Zinc binding site 7 out of 7 in the Rna Polymerase III Initially Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase III Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Zn1001

b:0.0
occ:1.00
 SG V:CYS7 2.5 0.3 1.0
SG V:CYS25 2.5 0.3 1.0
SG V:CYS4 2.5 0.4 1.0
SG V:CYS28 2.5 0.8 1.0
CB V:CYS4 3.1 0.4 1.0
OD1 V:ASN6 3.5 0.4 1.0
CB V:CYS28 3.8 0.8 1.0
CB V:CYS25 3.9 0.3 1.0
N V:CYS28 4.0 0.8 1.0
CB V:CYS7 4.1 0.3 1.0
CB V:ALA27 4.4 0.1 1.0
CA V:CYS28 4.5 0.8 1.0
N V:CYS7 4.5 0.3 1.0
CG V:ASN6 4.6 0.4 1.0
CA V:CYS4 4.6 0.4 1.0
N V:GLY9 4.6 0.5 1.0
N V:GLY29 4.7 0.6 1.0
CA V:CYS7 4.7 0.3 1.0
N V:HIS8 4.8 0.5 1.0
C V:CYS7 5.0 0.3 1.0
C V:ALA27 5.0 0.1 1.0

Reference:

M.K.Vorlander, H.Khatter, R.Wetzel, W.J.H.Hagen, C.W.Muller. Molecular Mechanism of Promoter Opening By Rna Polymerase III. Nature V. 553 295 2018.
ISSN: ESSN 1476-4687
PubMed: 29345638
DOI: 10.1038/NATURE25440
Page generated: Mon Oct 28 20:40:13 2024

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