Zinc in PDB 6f40: Rna Polymerase III Open Complex

Enzymatic activity of Rna Polymerase III Open Complex

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase III Open Complex (pdb code 6f40). 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 Open Complex, PDB code: 6f40:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6f40

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Zinc binding site 1 out of 7 in the Rna Polymerase III Open 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 Open Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1501

b:0.5
occ:1.00
 NE2 A:HIS80 2.2 40.0 1.0
N A:CYS70 2.2 67.1 1.0
SG A:CYS67 2.5 66.9 1.0
SG A:CYS70 2.7 67.1 1.0
CB A:CYS70 2.8 67.1 1.0
CD2 A:HIS80 2.8 40.0 1.0
CA A:CYS70 3.1 67.1 1.0
CB A:THR69 3.1 60.9 1.0
CE1 A:HIS80 3.2 40.0 1.0
C A:THR69 3.2 60.9 1.0
CA A:THR69 3.4 60.9 1.0
N A:THR69 3.6 60.9 1.0
CB A:CYS67 3.8 66.9 1.0
CG2 A:THR69 3.8 60.9 1.0
CG A:HIS80 3.9 40.0 1.0
ND1 A:HIS80 4.0 40.0 1.0
C A:CYS70 4.1 67.1 1.0
N A:HIS71 4.2 69.2 1.0
OG1 A:THR69 4.2 60.9 1.0
O A:THR69 4.3 60.9 1.0
O A:CYS67 4.5 66.9 1.0
C A:CYS67 4.6 66.9 1.0
SG A:CYS77 4.6 58.5 1.0
CA A:CYS67 4.8 66.9 1.0
C A:ALA68 4.9 66.2 1.0
N A:ALA68 5.0 66.2 1.0

Zinc binding site 2 out of 7 in 6f40

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Zinc binding site 2 out of 7 in the Rna Polymerase III Open 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 Open Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1502

b:0.5
occ:1.00
 SG A:CYS157 2.4 75.2 1.0
SG A:CYS107 2.4 59.9 1.0
SG A:CYS110 2.4 66.1 1.0
SG A:CYS154 2.4 69.5 1.0
N A:CYS110 3.4 66.1 1.0
CB A:CYS110 3.4 66.1 1.0
CB A:CYS107 3.4 59.9 1.0
CB A:CYS154 3.5 69.5 1.0
CB A:CYS157 3.9 75.2 1.0
CA A:CYS110 3.9 66.1 1.0
N A:CYS157 4.0 75.2 1.0
CB A:ASN109 4.1 64.9 1.0
C A:ASN109 4.4 64.9 1.0
CA A:CYS157 4.4 75.2 1.0
N A:ASN109 4.5 64.9 1.0
N A:SER111 4.5 54.8 1.0
CA A:ASN109 4.6 64.9 1.0
C A:CYS110 4.6 66.1 1.0
N A:GLY158 4.6 73.9 1.0
N A:ALA159 4.7 67.7 1.0
C A:CYS157 4.8 75.2 1.0
CB A:ALA159 4.8 67.7 1.0
CA A:CYS107 4.8 59.9 1.0
CA A:CYS154 4.9 69.5 1.0
C A:HIS156 4.9 84.3 1.0

Zinc binding site 3 out of 7 in 6f40

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Zinc binding site 3 out of 7 in the Rna Polymerase III Open 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 Open Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2000

b:0.2
occ:1.00
 SG B:CYS1107 2.5 56.2 1.0
SG B:CYS1095 2.6 57.4 1.0
SG B:CYS1098 2.6 59.0 1.0
SG B:CYS1110 2.7 63.1 1.0
O B:LYS1097 2.8 60.9 1.0
CB B:CYS1095 3.2 57.4 1.0
O B:CYS1098 3.2 59.0 1.0
CB B:CYS1107 3.9 56.2 1.0
C B:CYS1098 4.0 59.0 1.0
C B:LYS1097 4.0 60.9 1.0
CB B:CYS1098 4.0 59.0 1.0
CB B:CYS1110 4.2 63.1 1.0
CG2 B:THR1109 4.2 59.0 1.0
CA B:CYS1098 4.4 59.0 1.0
N B:CYS1110 4.6 63.1 1.0
N B:CYS1098 4.6 59.0 1.0
CA B:CYS1095 4.7 57.4 1.0
CD2 B:LEU1100 4.8 46.3 1.0
N B:GLY1099 4.9 51.0 1.0

Zinc binding site 4 out of 7 in 6f40

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Zinc binding site 4 out of 7 in the Rna Polymerase III Open 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 Open Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn2000

b:0.5
occ:1.00
 SG I:CYS26 2.5 59.4 1.0
SG I:CYS8 2.5 55.0 1.0
SG I:CYS5 2.5 54.0 1.0
CB I:CYS29 2.6 59.8 1.0
SG I:CYS29 2.9 59.8 1.0
CB I:CYS5 3.3 54.0 1.0
CA I:CYS29 4.0 59.8 1.0
CB I:CYS26 4.1 59.4 1.0
CB I:CYS8 4.1 55.0 1.0
O I:ARG27 4.3 59.9 1.0
CB I:ASN10 4.3 54.3 1.0
N I:CYS29 4.5 59.8 1.0
O I:CYS5 4.6 54.0 1.0
O I:MET11 4.6 56.1 1.0
CA I:CYS5 4.7 54.0 1.0
C I:CYS29 4.7 59.8 1.0
O I:CYS29 4.7 59.8 1.0
CB I:TYR31 4.8 59.1 1.0
O I:SER28 4.9 59.4 1.0
C I:CYS5 4.9 54.0 1.0
C I:SER28 4.9 59.4 1.0

Zinc binding site 5 out of 7 in 6f40

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Zinc binding site 5 out of 7 in the Rna Polymerase III Open 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 Open Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2000

b:96.1
occ:1.00
 SG J:CYS7 2.4 35.7 1.0
SG J:CYS45 2.5 41.3 1.0
SG J:CYS10 2.5 33.1 1.0
SG J:CYS46 2.5 40.2 1.0
N J:CYS46 3.3 40.2 1.0
CB J:CYS7 3.4 35.7 1.0
CB J:CYS10 3.4 33.1 1.0
C J:CYS45 3.4 41.3 1.0
O J:CYS45 3.6 41.3 1.0
CA J:CYS46 3.6 40.2 1.0
CB J:CYS45 3.6 41.3 1.0
CB J:CYS46 3.7 40.2 1.0
OG J:SER9 3.9 33.3 1.0
N J:CYS10 4.0 33.1 1.0
CA J:CYS45 4.1 41.3 1.0
CA J:CYS10 4.3 33.1 1.0
CD J:ARG43 4.7 41.5 1.0
N J:GLY11 4.7 33.6 1.0
CG J:ARG43 4.8 41.5 1.0
CA J:CYS7 4.8 35.7 1.0
N J:CYS45 4.8 41.3 1.0
NH1 J:ARG43 4.9 41.5 1.0
CG J:LYS12 4.9 34.8 1.0

Zinc binding site 6 out of 7 in 6f40

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Zinc binding site 6 out of 7 in the Rna Polymerase III Open 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 Open Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn2000

b:0.1
occ:1.00
 SG L:CYS48 2.6 44.9 1.0
CB L:CYS34 2.6 49.0 1.0
O L:LYS49 2.9 47.4 1.0
SG L:CYS34 3.0 49.0 1.0
CB L:CYS51 3.1 45.9 1.0
SG L:CYS31 3.1 42.0 1.0
CB L:CYS31 3.6 42.0 1.0
CB L:CYS48 3.8 44.9 1.0
N L:CYS51 3.9 45.9 1.0
CA L:CYS51 3.9 45.9 1.0
O L:CYS51 4.0 45.9 1.0
CA L:CYS34 4.1 49.0 1.0
C L:LYS49 4.1 47.4 1.0
SG L:CYS51 4.2 45.9 1.0
C L:CYS51 4.3 45.9 1.0
C L:ASP50 4.3 46.5 1.0
CB L:ASP50 4.5 46.5 1.0
N L:CYS34 4.5 49.0 1.0
C L:CYS48 4.8 44.9 1.0
C L:CYS34 4.8 49.0 1.0
N L:LYS49 4.8 47.4 1.0
CA L:ASP50 4.8 46.5 1.0
O L:ASP50 4.8 46.5 1.0
OG L:SER36 4.9 45.7 1.0
N L:ASP50 4.9 46.5 1.0
CB L:SER36 4.9 45.7 1.0
CA L:CYS48 4.9 44.9 1.0

Zinc binding site 7 out of 7 in 6f40

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Zinc binding site 7 out of 7 in the Rna Polymerase III Open 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 Open Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Zn1001

b:0.8
occ:1.00
 SG V:CYS25 2.4 72.0 1.0
SG V:CYS4 2.4 80.0 1.0
SG V:CYS7 2.5 80.5 1.0
CB V:CYS4 2.6 80.0 1.0
SG V:CYS28 3.0 71.5 1.0
CB V:CYS25 3.7 72.0 1.0
CB V:CYS7 4.0 80.5 1.0
CA V:CYS4 4.1 80.0 1.0
N V:CYS7 4.3 80.5 1.0
CB V:CYS28 4.5 71.5 1.0
O V:VAL30 4.7 66.1 1.0
CA V:CYS7 4.7 80.5 1.0
CE1 V:PHE12 4.8 80.0 1.0
N V:CYS28 4.8 71.5 1.0
N V:HIS8 4.8 82.8 1.0
N V:CYS4 4.8 80.0 1.0
CB V:VAL30 4.8 66.1 1.0
N V:VAL30 4.9 66.1 1.0
N V:GLY9 4.9 86.9 1.0
CA V:CYS25 5.0 72.0 1.0
C V:CYS4 5.0 80.0 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: Wed Dec 16 11:46:03 2020

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