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Zinc in PDB 5n61: Rna Polymerase I Initially Transcribing Complex

Enzymatic activity of Rna Polymerase I Initially Transcribing Complex

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

Other elements in 5n61:

The structure of Rna Polymerase I Initially Transcribing Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase I Initially Transcribing Complex (pdb code 5n61). 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 I Initially Transcribing Complex, PDB code: 5n61:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 5n61

Go back to Zinc Binding Sites List in 5n61
Zinc binding site 1 out of 7 in the Rna Polymerase I 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 I Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3001

b:0.0
occ:1.00
 CD2 A:HIS75 1.6 0.0 1.0
NE2 A:HIS75 2.1 0.0 1.0
SG A:CYS72 2.3 0.0 1.0
SG A:CYS62 2.3 0.0 1.0
SG A:CYS65 2.3 0.0 1.0
CA A:GLY55 2.7 0.0 1.0
CG A:HIS75 2.9 0.0 1.0
N A:GLY55 3.3 0.0 1.0
CE1 A:HIS75 3.3 0.0 1.0
CB A:CYS65 3.5 0.0 1.0
ND1 A:HIS75 3.7 0.0 1.0
CB A:CYS62 3.7 0.0 1.0
C A:GLY55 3.7 0.0 1.0
N A:CYS65 3.7 0.0 1.0
C A:LEU54 3.8 0.0 1.0
O A:LEU54 3.8 0.0 1.0
CB A:HIS75 3.9 0.0 1.0
CA A:GLY74 3.9 0.0 1.0
C A:GLY74 3.9 0.0 1.0
N A:HIS75 3.9 0.0 1.0
N A:GLY74 3.9 0.0 1.0
N A:ALA56 4.0 0.0 1.0
CB A:CYS72 4.1 0.0 1.0
CB A:THR64 4.2 0.0 1.0
CA A:CYS65 4.3 0.0 1.0
O A:GLY74 4.5 0.0 1.0
CA A:HIS75 4.6 0.0 1.0
O A:ALA53 4.6 0.0 1.0
O A:GLY55 4.6 0.0 1.0
C A:THR64 4.8 0.0 1.0
CA A:CYS62 4.8 0.0 1.0
CG2 A:THR64 4.8 0.0 1.0
O A:LEU52 4.9 0.0 1.0
CA A:THR64 4.9 0.0 1.0
N A:THR64 4.9 0.0 1.0
CA A:LEU54 5.0 0.0 1.0
CA A:CYS72 5.0 0.0 1.0
C A:CYS72 5.0 0.0 1.0

Zinc binding site 2 out of 7 in 5n61

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Zinc binding site 2 out of 7 in the Rna Polymerase I 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 I Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3002

b:0.0
occ:1.00
 CB A:CYS233 1.3 0.0 1.0
SG A:CYS233 2.3 0.0 1.0
SG A:CYS102 2.3 0.0 1.0
SG A:CYS236 2.3 0.0 1.0
SG A:CYS105 2.4 0.0 1.0
CA A:CYS233 2.8 0.0 1.0
CB A:CYS102 3.2 0.0 1.0
N A:CYS233 3.3 0.0 1.0
C A:CYS233 3.7 0.0 1.0
O A:CYS233 3.9 0.0 1.0
N A:MET238 3.9 0.0 1.0
O A:MET238 4.0 0.0 1.0
CA A:CYS102 4.0 0.0 1.0
CB A:CYS105 4.1 0.0 1.0
CB A:CYS236 4.1 0.0 1.0
CB A:MET238 4.1 0.0 1.0
C A:MET238 4.1 0.0 1.0
N A:CYS105 4.2 0.0 1.0
CA A:MET238 4.3 0.0 1.0
CG A:ARG109 4.5 0.0 1.0
N A:GLY237 4.5 0.0 1.0
N A:CYS236 4.6 0.0 1.0
C A:LYS232 4.7 0.0 1.0
N A:ASP234 4.7 0.0 1.0
N A:PHE239 4.8 0.0 1.0
CA A:CYS105 4.8 0.0 1.0
CA A:CYS236 4.8 0.0 1.0
C A:GLY237 4.8 0.0 1.0
CB A:PHE104 4.8 0.0 1.0
C A:CYS102 4.9 0.0 1.0
N A:PHE104 4.9 0.0 1.0
CD2 A:PHE104 5.0 0.0 1.0
N A:LEU103 5.0 0.0 1.0

Zinc binding site 3 out of 7 in 5n61

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Zinc binding site 3 out of 7 in the Rna Polymerase I 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 I Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1302

b:0.0
occ:1.00
 SG B:CYS1128 2.3 0.0 1.0
SG B:CYS1131 2.3 0.0 1.0
SG B:CYS1107 2.3 0.0 1.0
SG B:CYS1104 2.3 0.0 1.0
CB B:CYS1131 2.5 0.0 1.0
CB B:CYS1107 2.8 0.0 1.0
CB B:CYS1128 2.8 0.0 1.0
N B:CYS1131 3.1 0.0 1.0
CB B:CYS1104 3.3 0.0 1.0
CA B:CYS1131 3.4 0.0 1.0
N B:CYS1107 3.5 0.0 1.0
CA B:CYS1107 3.8 0.0 1.0
CA B:CYS1128 4.1 0.0 1.0
O B:CYS1128 4.2 0.0 1.0
C B:ARG1130 4.2 0.0 1.0
C B:CYS1128 4.2 0.0 1.0
CA B:GLY1170 4.4 0.0 1.0
CB B:ARG1130 4.4 0.0 1.0
C B:CYS1131 4.4 0.0 1.0
N B:ARG1130 4.5 0.0 1.0
CA B:ARG1130 4.6 0.0 1.0
CB B:GLU1106 4.7 0.0 1.0
CA B:CYS1104 4.7 0.0 1.0
OG1 B:THR1112 4.7 0.0 1.0
C B:GLU1106 4.7 0.0 1.0
OE1 B:GLU1106 4.8 0.0 1.0
C B:CYS1107 4.9 0.0 1.0

Zinc binding site 4 out of 7 in 5n61

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Zinc binding site 4 out of 7 in the Rna Polymerase I 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 I Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3001

b:0.0
occ:1.00
 CB I:CYS30 1.4 0.0 1.0
SG I:CYS33 2.3 0.0 1.0
SG I:CYS10 2.3 0.0 1.0
SG I:CYS30 2.3 0.0 1.0
SG I:CYS13 2.3 0.0 1.0
CB I:CYS10 2.6 0.0 1.0
CA I:CYS30 2.7 0.0 1.0
N I:CYS30 3.3 0.0 1.0
CB I:ALA35 3.3 0.0 1.0
N I:ALA35 3.4 0.0 1.0
O I:ALA35 3.4 0.0 1.0
CA I:ALA35 3.7 0.0 1.0
C I:CYS30 3.9 0.0 1.0
CA I:CYS10 3.9 0.0 1.0
C I:ALA35 4.0 0.0 1.0
CB I:CYS33 4.1 0.0 1.0
CB I:CYS13 4.1 0.0 1.0
N I:LYS34 4.2 0.0 1.0
C I:LYS34 4.4 0.0 1.0
N I:CYS13 4.5 0.0 1.0
N I:CYS33 4.5 0.0 1.0
N I:SER31 4.5 0.0 1.0
CE2 I:TYR37 4.5 0.0 1.0
C I:GLU29 4.6 0.0 1.0
C I:CYS33 4.6 0.0 1.0
O I:CYS30 4.6 0.0 1.0
CA I:CYS33 4.6 0.0 1.0
N I:CYS10 4.7 0.0 1.0
CA I:LYS34 4.8 0.0 1.0
CA I:CYS13 4.8 0.0 1.0
C I:CYS10 4.9 0.0 1.0

Zinc binding site 5 out of 7 in 5n61

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Zinc binding site 5 out of 7 in the Rna Polymerase I 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 I Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3001

b:0.0
occ:1.00
 CB J:CYS10 1.3 0.0 1.0
CA J:CYS10 2.0 0.0 1.0
N J:CYS10 2.1 0.0 1.0
SG J:CYS10 2.3 0.0 1.0
SG J:CYS7 2.3 0.0 1.0
SG J:CYS46 2.3 0.0 1.0
SG J:CYS45 2.4 0.0 1.0
CB J:CYS7 2.5 0.0 1.0
C J:CYS10 2.8 0.0 1.0
N J:GLY11 2.9 0.0 1.0
C J:SER9 3.4 0.0 1.0
O J:CYS7 3.6 0.0 1.0
N J:LYS12 3.6 0.0 1.0
CA J:CYS7 3.7 0.0 1.0
C J:CYS7 3.8 0.0 1.0
O J:CYS10 3.9 0.0 1.0
CB J:CYS45 4.0 0.0 1.0
CB J:CYS46 4.0 0.0 1.0
CA J:GLY11 4.1 0.0 1.0
O J:SER9 4.2 0.0 1.0
CB J:LYS12 4.2 0.0 1.0
N J:CYS46 4.2 0.0 1.0
CA J:SER9 4.3 0.0 1.0
C J:GLY11 4.3 0.0 1.0
N J:SER9 4.3 0.0 1.0
CA J:CYS46 4.4 0.0 1.0
N J:CYS7 4.4 0.0 1.0
CA J:LYS12 4.5 0.0 1.0
CB J:SER9 4.6 0.0 1.0
N J:PHE8 4.6 0.0 1.0
C J:CYS45 4.7 0.0 1.0
C J:PHE8 4.7 0.0 1.0
O J:LYS12 4.8 0.0 1.0
O C:SER223 4.8 0.0 1.0

Zinc binding site 6 out of 7 in 5n61

Go back to Zinc Binding Sites List in 5n61
Zinc binding site 6 out of 7 in the Rna Polymerase I 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 I Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn3001

b:0.0
occ:1.00
 SG L:CYS48 2.3 0.0 1.0
SG L:CYS31 2.3 0.0 1.0
SG L:CYS34 2.4 0.0 1.0
CB L:CYS51 2.5 0.0 1.0
CB L:CYS48 2.6 0.0 1.0
SG L:CYS51 2.8 0.0 1.0
N L:CYS51 3.2 0.0 1.0
CB L:CYS31 3.3 0.0 1.0
CA L:CYS51 3.4 0.0 1.0
CB L:CYS34 3.4 0.0 1.0
N L:CYS34 3.7 0.0 1.0
OG L:SER36 4.1 0.0 1.0
N L:GLY52 4.1 0.0 1.0
CA L:CYS48 4.1 0.0 1.0
CA L:CYS34 4.2 0.0 1.0
C L:CYS51 4.2 0.0 1.0
CD2 L:HIS53 4.2 0.0 1.0
C L:ASP50 4.4 0.0 1.0
CB L:ASP50 4.6 0.0 1.0
CB L:GLU33 4.6 0.0 1.0
CA L:CYS31 4.7 0.0 1.0
N L:HIS53 4.7 0.0 1.0
C L:CYS48 4.8 0.0 1.0
C L:GLU33 4.9 0.0 1.0
CA L:ASP50 4.9 0.0 1.0
CB L:HIS53 4.9 0.0 1.0
CG L:HIS53 4.9 0.0 1.0
O L:CYS48 5.0 0.0 1.0
N L:CYS48 5.0 0.0 1.0
C L:CYS34 5.0 0.0 1.0

Zinc binding site 7 out of 7 in 5n61

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Zinc binding site 7 out of 7 in the Rna Polymerase I 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 I Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn1001

b:0.0
occ:1.00
 SG Q:CYS10 2.2 0.0 1.0
SG Q:CYS15 2.7 0.0 1.0
SG Q:CYS29 2.8 0.0 1.0
ND1 Q:HIS33 2.8 0.0 1.0
CB Q:THR12 3.3 0.0 1.0
CE1 Q:HIS33 3.5 0.0 1.0
CB Q:CYS15 3.6 0.0 1.0
CG Q:HIS33 3.6 0.0 1.0
CG2 Q:THR12 3.7 0.0 1.0
CB Q:CYS10 3.8 0.0 1.0
CB Q:CYS29 3.9 0.0 1.0
CB Q:HIS33 4.0 0.0 1.0
O Q:THR12 4.1 0.0 1.0
OG1 Q:THR12 4.1 0.0 1.0
O Q:SER17 4.3 0.0 1.0
CA Q:THR12 4.3 0.0 1.0
NE2 Q:HIS33 4.4 0.0 1.0
N Q:THR12 4.4 0.0 1.0
OD1 Q:ASN14 4.5 0.0 1.0
CD2 Q:HIS33 4.5 0.0 1.0
C Q:THR12 4.6 0.0 1.0
N Q:CYS15 4.7 0.0 1.0
N Q:SER17 4.7 0.0 1.0
CA Q:CYS15 4.8 0.0 1.0
CB Q:SER17 4.8 0.0 1.0
CD2 Q:TYR31 4.9 0.0 1.0
CA Q:CYS10 5.0 0.0 1.0

Reference:

C.Engel, T.Gubbey, S.Neyer, S.Sainsbury, C.Oberthuer, C.Baejen, C.Bernecky, P.Cramer. Structural Basis of Rna Polymerase I Transcription Initiation. Cell V. 169 120 2017.
ISSN: ISSN 1097-4172
PubMed: 28340337
DOI: 10.1016/J.CELL.2017.03.003
Page generated: Sun Oct 27 22:37:27 2024

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