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Zinc in PDB 6cnd: Yeast Rna Polymerase III Natural Open Complex (Noc)

Enzymatic activity of Yeast Rna Polymerase III Natural Open Complex (Noc)

All present enzymatic activity of Yeast Rna Polymerase III Natural Open Complex (Noc):
2.7.7.6;

Zinc Binding Sites:

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

Zinc binding site 1 out of 7 in 6cnd

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Zinc binding site 1 out of 7 in the Yeast Rna Polymerase III Natural Open Complex (Noc)


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Stereo pair view

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

b:0.0
occ:1.00
 NE2 A:HIS80 2.0 0.0 1.0
SG A:CYS67 2.5 0.0 1.0
OG1 A:THR69 2.5 0.0 1.0
SG A:CYS77 2.6 0.0 1.0
SG A:CYS70 2.6 0.0 1.0
N A:CYS70 2.7 0.0 1.0
CD2 A:HIS80 2.9 0.0 1.0
CE1 A:HIS80 2.9 0.0 1.0
O A:CYS70 3.2 0.0 1.0
CA A:CYS70 3.4 0.0 1.0
CB A:CYS67 3.5 0.0 1.0
CB A:CYS70 3.5 0.0 1.0
CB A:CYS77 3.5 0.0 1.0
C A:CYS70 3.6 0.0 1.0
CB A:THR69 3.7 0.0 1.0
C A:THR69 3.8 0.0 1.0
O A:CYS67 3.9 0.0 1.0
ND1 A:HIS80 4.0 0.0 1.0
CG A:HIS80 4.1 0.0 1.0
CA A:THR69 4.2 0.0 1.0
O A:LYS57 4.3 0.0 1.0
N A:THR69 4.4 0.0 1.0
C A:CYS67 4.5 0.0 1.0
CA A:CYS77 4.5 0.0 1.0
CA A:CYS67 4.6 0.0 1.0
N A:HIS71 4.8 0.0 1.0
CG2 A:THR69 4.9 0.0 1.0
O A:THR69 4.9 0.0 1.0
O A:GLY79 5.0 0.0 1.0
C A:ALA68 5.0 0.0 1.0

Zinc binding site 2 out of 7 in 6cnd

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Zinc binding site 2 out of 7 in the Yeast Rna Polymerase III Natural Open Complex (Noc)


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Stereo pair view

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

b:0.0
occ:1.00
 SG A:CYS110 2.0 0.0 1.0
SG A:CYS107 2.3 0.0 1.0
SG A:CYS154 2.3 0.0 1.0
SG A:CYS157 2.3 0.0 1.0
CB A:CYS157 2.8 0.0 1.0
CB A:CYS107 2.9 0.0 1.0
CB A:CYS154 2.9 0.0 1.0
CB A:CYS110 3.6 0.0 1.0
N A:CYS110 3.7 0.0 1.0
N A:CYS157 3.8 0.0 1.0
CA A:CYS157 3.9 0.0 1.0
CE1 A:HIS156 4.0 0.0 1.0
CA A:CYS110 4.0 0.0 1.0
NE2 A:HIS156 4.1 0.0 1.0
N A:SER111 4.3 0.0 1.0
C A:CYS110 4.3 0.0 1.0
CA A:CYS107 4.3 0.0 1.0
CA A:CYS154 4.4 0.0 1.0
ND1 A:HIS156 4.5 0.0 1.0
CD2 A:HIS156 4.7 0.0 1.0
C A:CYS107 4.7 0.0 1.0
O A:CYS107 4.7 0.0 1.0
C A:ASN109 4.8 0.0 1.0
CB A:ASN109 4.8 0.0 1.0
N A:ALA112 4.8 0.0 1.0
CG A:HIS156 4.9 0.0 1.0
C A:CYS157 4.9 0.0 1.0
N A:ASN109 4.9 0.0 1.0
C A:CYS154 4.9 0.0 1.0
N A:LEU155 5.0 0.0 1.0

Zinc binding site 3 out of 7 in 6cnd

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Zinc binding site 3 out of 7 in the Yeast Rna Polymerase III Natural Open Complex (Noc)


Mono view


Stereo pair view

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

b:0.0
occ:1.00
 SG B:CYS1107 2.3 0.0 1.0
O B:LYS1097 2.4 0.0 1.0
SG B:CYS1098 2.4 0.0 1.0
SG B:CYS1095 2.6 0.0 1.0
SG B:CYS1110 2.8 0.0 1.0
CB B:CYS1095 3.0 0.0 1.0
O B:CYS1098 3.2 0.0 1.0
CB B:CYS1107 3.2 0.0 1.0
C B:LYS1097 3.3 0.0 1.0
CB B:CYS1098 3.8 0.0 1.0
C B:CYS1098 3.9 0.0 1.0
N B:CYS1098 4.1 0.0 1.0
CA B:CYS1098 4.1 0.0 1.0
CG2 B:THR1109 4.1 0.0 1.0
CB B:LYS1097 4.2 0.0 1.0
CA B:LYS1097 4.3 0.0 1.0
CA B:CYS1095 4.3 0.0 1.0
CB B:CYS1110 4.3 0.0 1.0
O B:CYS1095 4.4 0.0 1.0
C B:CYS1095 4.5 0.0 1.0
CG B:LYS1097 4.5 0.0 1.0
CA B:CYS1107 4.7 0.0 1.0
N B:LYS1097 4.7 0.0 1.0
N B:CYS1110 4.9 0.0 1.0
N B:GLY1099 4.9 0.0 1.0

Zinc binding site 4 out of 7 in 6cnd

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Zinc binding site 4 out of 7 in the Yeast Rna Polymerase III Natural Open Complex (Noc)


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Stereo pair view

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

b:0.0
occ:1.00
 SG I:CYS26 2.3 0.0 1.0
SG I:CYS8 2.6 0.0 1.0
CB I:CYS8 2.7 0.0 1.0
SG I:CYS29 2.8 0.0 1.0
SG I:CYS5 2.8 0.0 1.0
CB I:ASN10 3.0 0.0 1.0
CB I:CYS26 3.3 0.0 1.0
N I:ASN10 3.7 0.0 1.0
CB I:CYS29 3.8 0.0 1.0
CA I:ASN10 4.0 0.0 1.0
CA I:CYS8 4.1 0.0 1.0
CG I:ASN10 4.1 0.0 1.0
CB I:CYS5 4.2 0.0 1.0
N I:MET11 4.2 0.0 1.0
ND2 I:ASN10 4.3 0.0 1.0
O I:MET11 4.3 0.0 1.0
O I:ARG27 4.3 0.0 1.0
C I:CYS8 4.3 0.0 1.0
N I:ASN9 4.4 0.0 1.0
O I:SER28 4.5 0.0 1.0
CA I:CYS26 4.6 0.0 1.0
C I:ASN10 4.7 0.0 1.0
C I:ASN9 4.7 0.0 1.0
N I:CYS8 4.7 0.0 1.0
OH B:TYR296 4.9 0.0 1.0
N I:CYS29 4.9 0.0 1.0
C I:CYS26 4.9 0.0 1.0
O I:CYS8 4.9 0.0 1.0
C I:SER28 4.9 0.0 1.0
CA I:CYS29 5.0 0.0 1.0

Zinc binding site 5 out of 7 in 6cnd

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Zinc binding site 5 out of 7 in the Yeast Rna Polymerase III Natural Open Complex (Noc)


Mono view


Stereo pair view

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

b:0.0
occ:1.00
 N J:CYS46 2.1 0.0 1.0
SG J:CYS10 2.2 0.0 1.0
SG J:CYS46 2.2 0.0 1.0
SG J:CYS45 2.3 0.0 1.0
SG J:CYS7 2.5 0.0 1.0
CA J:CYS46 2.6 0.0 1.0
CB J:CYS10 2.7 0.0 1.0
CB J:CYS46 2.8 0.0 1.0
C J:CYS45 3.0 0.0 1.0
CB J:CYS45 3.3 0.0 1.0
N J:CYS10 3.7 0.0 1.0
CA J:CYS45 3.7 0.0 1.0
OG J:SER9 3.7 0.0 1.0
CB J:CYS7 3.7 0.0 1.0
CA J:CYS10 3.8 0.0 1.0
O J:CYS45 3.9 0.0 1.0
C J:CYS46 4.1 0.0 1.0
NE J:ARG43 4.1 0.0 1.0
N J:CYS45 4.4 0.0 1.0
O J:ARG43 4.5 0.0 1.0
CG J:ARG43 4.5 0.0 1.0
NH2 J:ARG43 4.5 0.0 1.0
CZ J:ARG43 4.6 0.0 1.0
N J:ARG47 4.7 0.0 1.0
CD J:ARG43 4.8 0.0 1.0
C J:CYS10 4.9 0.0 1.0
O J:CYS46 4.9 0.0 1.0
C J:SER9 4.9 0.0 1.0
N J:GLY11 5.0 0.0 1.0

Zinc binding site 6 out of 7 in 6cnd

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Zinc binding site 6 out of 7 in the Yeast Rna Polymerase III Natural Open Complex (Noc)


Mono view


Stereo pair view

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

b:0.0
occ:1.00
 CB L:CYS51 1.9 0.0 1.0
SG L:CYS51 2.0 0.0 1.0
SG L:CYS34 2.4 0.0 1.0
SG L:CYS48 2.5 0.0 1.0
SG L:CYS31 2.5 0.0 1.0
CA L:CYS51 2.9 0.0 1.0
CB L:CYS34 3.0 0.0 1.0
OD1 L:ASP50 3.0 0.0 1.0
N L:CYS51 3.0 0.0 1.0
CB L:CYS31 3.5 0.0 1.0
CB L:CYS48 3.7 0.0 1.0
OG L:SER36 3.9 0.0 1.0
CG L:ASP50 4.0 0.0 1.0
N L:CYS34 4.1 0.0 1.0
C L:CYS51 4.1 0.0 1.0
CA L:CYS34 4.1 0.0 1.0
C L:ASP50 4.2 0.0 1.0
O L:CYS51 4.5 0.0 1.0
OD2 L:ASP50 4.5 0.0 1.0
CA L:CYS31 4.7 0.0 1.0
CB L:HIS53 4.8 0.0 1.0
N L:ASP50 4.8 0.0 1.0
O L:HIS53 4.8 0.0 1.0
CA L:ASP50 4.9 0.0 1.0
O L:ASP50 4.9 0.0 1.0
CB L:ASP50 5.0 0.0 1.0

Zinc binding site 7 out of 7 in 6cnd

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Zinc binding site 7 out of 7 in the Yeast Rna Polymerase III Natural Open Complex (Noc)


Mono view


Stereo pair view

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

b:0.0
occ:1.00
 CB R:CYS4 1.8 0.0 1.0
SG R:CYS4 2.3 0.0 1.0
SG R:CYS25 2.3 0.0 1.0
SG R:CYS7 2.3 0.0 1.0
SG R:CYS28 2.9 0.0 1.0
CB R:CYS28 3.0 0.0 1.0
CA R:CYS4 3.0 0.0 1.0
N R:CYS4 3.8 0.0 1.0
CB R:CYS25 3.9 0.0 1.0
CB R:CYS7 4.0 0.0 1.0
N R:GLY9 4.0 0.0 1.0
C R:CYS4 4.2 0.0 1.0
CA R:CYS28 4.2 0.0 1.0
O R:GLY9 4.2 0.0 1.0
N R:CYS28 4.3 0.0 1.0
CA R:GLY9 4.3 0.0 1.0
N R:CYS7 4.4 0.0 1.0
N R:HIS8 4.5 0.0 1.0
CA R:CYS7 4.6 0.0 1.0
N R:LYS5 4.7 0.0 1.0
C R:GLY9 4.7 0.0 1.0
C R:ALA27 4.7 0.0 1.0
C R:CYS7 4.8 0.0 1.0
CE1 R:PHE12 4.8 0.0 1.0
O R:CYS4 4.9 0.0 1.0
O R:VAL30 5.0 0.0 1.0

Reference:

Y.Han, C.Yan, S.Fishbain, I.Ivanov, Y.He. Structural Visualization of Rna Polymerase III Transcription Machineries. Cell Discov V. 4 40 2018.
ISSN: ESSN 2056-5968
PubMed: 30083386
DOI: 10.1038/S41421-018-0044-Z
Page generated: Mon Oct 28 19:00:46 2024

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