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Zinc in PDB 5n5y: Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)

Enzymatic activity of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)

All present enzymatic activity of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III):
2.7.7.6;

Other elements in 5n5y:

The structure of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) 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 Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) (pdb code 5n5y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III), PDB code: 5n5y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5n5y

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Zinc binding site 1 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)


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 Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:0.0
occ:1.00
 SG A:CYS65 1.8 0.0 1.0
NE2 A:HIS75 2.0 0.0 1.0
SG A:CYS62 2.1 0.0 1.0
SG A:CYS72 2.3 0.0 1.0
CD2 A:HIS75 2.8 0.0 1.0
CE1 A:HIS75 3.0 0.0 1.0
CB A:CYS62 3.2 0.0 1.0
CB A:CYS65 3.4 0.0 1.0
CB A:CYS72 3.6 0.0 1.0
N A:CYS65 3.9 0.0 1.0
CG A:HIS75 3.9 0.0 1.0
CD A:PRO73 3.9 0.0 1.0
ND1 A:HIS75 4.0 0.0 1.0
CA A:CYS65 4.3 0.0 1.0
CA A:CYS72 4.3 0.0 1.0
N A:GLY74 4.4 0.0 1.0
CA A:GLY55 4.5 0.0 1.0
N A:PRO73 4.5 0.0 1.0
C A:CYS72 4.6 0.0 1.0
CA A:CYS62 4.7 0.0 1.0
CB A:THR64 4.7 0.0 1.0
CG A:PRO73 4.7 0.0 1.0
CA A:GLY74 4.7 0.0 1.0
C A:THR64 4.9 0.0 1.0
C A:GLY74 4.9 0.0 1.0
N A:GLY66 5.0 0.0 1.0
C A:CYS65 5.0 0.0 1.0

Zinc binding site 2 out of 8 in 5n5y

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Zinc binding site 2 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)


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 Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:0.0
occ:1.00
 SG A:CYS105 2.1 0.0 1.0
SG A:CYS236 2.3 0.0 1.0
SG A:CYS233 2.4 0.0 1.0
SG A:CYS102 2.4 0.0 1.0
CB A:CYS105 3.1 0.0 1.0
CB A:CYS102 3.3 0.0 1.0
CB A:CYS233 3.3 0.0 1.0
CB A:CYS236 3.4 0.0 1.0
N A:CYS105 3.6 0.0 1.0
N A:CYS236 3.8 0.0 1.0
CA A:CYS105 3.9 0.0 1.0
CA A:CYS236 4.2 0.0 1.0
C A:CYS105 4.6 0.0 1.0
N A:HIS106 4.7 0.0 1.0
CB A:ASN235 4.7 0.0 1.0
C A:ASN235 4.7 0.0 1.0
CA A:CYS102 4.8 0.0 1.0
CA A:CYS233 4.8 0.0 1.0
C A:PHE104 4.8 0.0 1.0
C A:CYS236 4.9 0.0 1.0
CB A:PHE104 4.9 0.0 1.0
N A:GLY237 5.0 0.0 1.0

Zinc binding site 3 out of 8 in 5n5y

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Zinc binding site 3 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)


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 Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:0.0
occ:1.00
 SG B:CYS1104 2.2 0.0 1.0
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
CB B:CYS1104 3.0 0.0 1.0
CB B:CYS1107 3.1 0.0 1.0
CB B:CYS1128 3.3 0.0 1.0
CB B:CYS1131 3.3 0.0 1.0
N B:CYS1107 3.6 0.0 1.0
CA B:CYS1107 4.0 0.0 1.0
N B:CYS1131 4.0 0.0 1.0
CA B:CYS1131 4.3 0.0 1.0
CB B:ARG1130 4.3 0.0 1.0
CA B:CYS1104 4.5 0.0 1.0
CB B:GLU1106 4.5 0.0 1.0
OG1 B:THR1112 4.5 0.0 1.0
C B:GLU1106 4.6 0.0 1.0
CA B:CYS1128 4.7 0.0 1.0
CD B:ARG1130 4.7 0.0 1.0
C B:ARG1130 4.8 0.0 1.0
C B:CYS1107 4.8 0.0 1.0
N B:ARG1130 4.9 0.0 1.0
CA B:ARG1130 4.9 0.0 1.0
CG B:ARG1130 4.9 0.0 1.0
CA B:GLU1106 4.9 0.0 1.0
C B:CYS1104 4.9 0.0 1.0
O B:CYS1104 4.9 0.0 1.0
N B:GLU1106 5.0 0.0 1.0

Zinc binding site 4 out of 8 in 5n5y

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Zinc binding site 4 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)


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 Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1001

b:0.0
occ:1.00
 SG I:CYS10 2.2 0.0 1.0
SG I:CYS13 2.2 0.0 1.0
SG I:CYS33 2.3 0.0 1.0
SG I:CYS30 2.4 0.0 1.0
CB I:CYS10 3.1 0.0 1.0
CB I:CYS30 3.4 0.0 1.0
CB I:CYS13 3.4 0.0 1.0
N I:CYS13 3.5 0.0 1.0
CB I:CYS33 3.7 0.0 1.0
CA I:CYS13 3.9 0.0 1.0
N I:CYS33 4.0 0.0 1.0
C I:CYS13 4.3 0.0 1.0
CB I:ASP12 4.4 0.0 1.0
CA I:CYS33 4.4 0.0 1.0
CB I:ALA35 4.4 0.0 1.0
O I:CYS13 4.5 0.0 1.0
CB I:GLN32 4.5 0.0 1.0
CA I:CYS10 4.5 0.0 1.0
C I:ASP12 4.6 0.0 1.0
N I:ASP12 4.8 0.0 1.0
CA I:ASP12 4.8 0.0 1.0
CA I:CYS30 4.8 0.0 1.0
N I:ASP15 4.9 0.0 1.0
C I:CYS10 5.0 0.0 1.0

Zinc binding site 5 out of 8 in 5n5y

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Zinc binding site 5 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)


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 Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1002

b:0.0
occ:0.75
 SG I:CYS114 2.2 0.0 1.0
SG I:CYS117 2.2 0.0 1.0
SG I:CYS89 2.2 0.0 1.0
SG I:CYS86 2.5 0.0 1.0
CB I:CYS117 3.1 0.0 1.0
CB I:CYS86 3.1 0.0 1.0
CB I:CYS89 3.1 0.0 1.0
CB I:CYS114 3.2 0.0 1.0
N I:CYS89 3.7 0.0 1.0
CA I:CYS89 3.9 0.0 1.0
N I:CYS117 3.9 0.0 1.0
CA I:CYS117 4.0 0.0 1.0
CB I:ASN91 4.1 0.0 1.0
OG I:SER116 4.6 0.0 1.0
N I:GLY90 4.6 0.0 1.0
C I:CYS89 4.6 0.0 1.0
CA I:CYS114 4.6 0.0 1.0
CA I:CYS86 4.6 0.0 1.0
N I:ASN91 4.6 0.0 1.0
C I:CYS117 4.7 0.0 1.0
CB I:GLN88 4.8 0.0 1.0
C I:GLN88 4.9 0.0 1.0
N I:GLY118 4.9 0.0 1.0
CB I:TYR119 5.0 0.0 1.0

Zinc binding site 6 out of 8 in 5n5y

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Zinc binding site 6 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1001

b:0.0
occ:1.00
 CA J:CYS46 1.7 0.0 1.0
N J:CYS46 1.8 0.0 1.0
SG J:CYS7 2.2 0.0 1.0
SG J:CYS46 2.3 0.0 1.0
CB J:CYS46 2.3 0.0 1.0
SG J:CYS45 2.3 0.0 1.0
C J:CYS45 2.3 0.0 1.0
SG J:CYS10 2.4 0.0 1.0
O J:CYS45 2.8 0.0 1.0
CB J:CYS7 3.1 0.0 1.0
C J:CYS46 3.2 0.0 1.0
CB J:CYS45 3.4 0.0 1.0
CA J:CYS45 3.4 0.0 1.0
O J:CYS46 3.8 0.0 1.0
CG J:MET49 4.0 0.0 1.0
N J:ARG47 4.1 0.0 1.0
CB J:CYS10 4.1 0.0 1.0
NH1 J:ARG48 4.4 0.0 1.0
CA J:CYS7 4.4 0.0 1.0
N J:CYS45 4.4 0.0 1.0
O J:ARG43 4.5 0.0 1.0
CB J:MET49 4.9 0.0 1.0
N J:CYS10 4.9 0.0 1.0
C J:TYR44 4.9 0.0 1.0
O J:TYR44 4.9 0.0 1.0

Zinc binding site 7 out of 8 in 5n5y

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Zinc binding site 7 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1001

b:0.0
occ:1.00
 SG L:CYS34 2.2 0.0 1.0
SG L:CYS48 2.2 0.0 1.0
SG L:CYS51 2.3 0.0 1.0
SG L:CYS31 2.5 0.0 1.0
CB L:CYS51 2.7 0.0 1.0
CB L:CYS48 2.9 0.0 1.0
CB L:CYS34 3.3 0.0 1.0
N L:CYS51 3.3 0.0 1.0
CB L:CYS31 3.4 0.0 1.0
CA L:CYS51 3.6 0.0 1.0
N L:CYS34 4.0 0.0 1.0
CA L:CYS34 4.2 0.0 1.0
CA L:CYS48 4.4 0.0 1.0
CB L:ASP50 4.4 0.0 1.0
C L:ASP50 4.5 0.0 1.0
OG L:SER36 4.5 0.0 1.0
C L:CYS51 4.7 0.0 1.0
N L:GLY52 4.7 0.0 1.0
CA L:ASP50 4.8 0.0 1.0
CA L:CYS31 4.8 0.0 1.0
N L:ASP50 4.8 0.0 1.0
C L:CYS34 4.9 0.0 1.0
N L:SER35 4.9 0.0 1.0
C L:CYS48 4.9 0.0 1.0
CB L:HIS53 5.0 0.0 1.0

Zinc binding site 8 out of 8 in 5n5y

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Zinc binding site 8 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) 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 4.2 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 22:35:37 2024

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