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Zinc in PDB 6tps: Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic

Enzymatic activity of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic

All present enzymatic activity of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic:
2.7.7.6;

Other elements in 6tps:

The structure of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic (pdb code 6tps). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic, PDB code: 6tps:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6tps

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Zinc binding site 1 out of 7 in the Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1701

b:0.9
occ:1.00
 SG A:CYS65 2.4 62.7 1.0
SG A:CYS72 2.4 61.6 1.0
SG A:CYS62 2.4 63.2 1.0
CB A:CYS62 2.6 63.2 1.0
NE2 A:HIS75 2.8 61.6 1.0
CD2 A:HIS75 3.2 61.6 1.0
OG1 A:THR64 3.4 62.4 1.0
CB A:CYS65 3.9 62.7 1.0
N A:CYS65 3.9 62.7 1.0
CE1 A:HIS75 4.0 61.6 1.0
CA A:CYS62 4.1 63.2 1.0
CB A:CYS72 4.1 61.6 1.0
C A:CYS62 4.4 63.2 1.0
CA A:CYS65 4.5 62.7 1.0
O A:CYS62 4.5 63.2 1.0
CG A:HIS75 4.5 61.6 1.0
N A:GLY66 4.7 61.6 1.0
CB A:THR64 4.7 62.4 1.0
N A:THR64 4.8 62.4 1.0
CA A:CYS72 4.9 61.6 1.0
ND1 A:HIS75 4.9 61.6 1.0
N A:CYS62 4.9 63.2 1.0
N A:GLY74 4.9 61.6 1.0
C A:THR64 5.0 62.4 1.0
C A:CYS65 5.0 62.7 1.0

Zinc binding site 2 out of 7 in 6tps

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Zinc binding site 2 out of 7 in the Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1702

b:0.0
occ:1.00
 SG A:CYS105 3.6 88.2 1.0
O A:CYS105 3.6 88.2 1.0
CD2 A:HIS107 4.3 76.0 1.0
NE2 A:HIS107 4.3 76.0 1.0
C A:CYS105 4.6 88.2 1.0
SG A:CYS236 4.6 95.4 1.0
CA A:CYS105 4.7 88.2 1.0
CB A:CYS105 4.8 88.2 1.0

Zinc binding site 3 out of 7 in 6tps

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Zinc binding site 3 out of 7 in the Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.3
occ:1.00
 SG B:CYS1107 2.4 60.2 1.0
SG B:CYS1104 2.5 60.5 1.0
SG B:CYS1131 2.5 72.4 1.0
SG B:CYS1128 2.5 64.5 1.0
CB B:CYS1104 2.8 60.5 1.0
CB B:CYS1107 3.4 60.2 1.0
CB B:CYS1128 3.5 64.5 1.0
CB B:CYS1131 3.7 72.4 1.0
N B:CYS1107 3.8 60.2 1.0
N B:CYS1131 4.0 72.4 1.0
CA B:CYS1107 4.2 60.2 1.0
CA B:CYS1104 4.3 60.5 1.0
CA B:CYS1131 4.4 72.4 1.0
CB B:ARG1130 4.6 65.4 1.0
OG1 B:THR1112 4.8 51.3 1.0
N B:GLY1108 4.9 54.4 1.0
C B:ARG1130 4.9 65.4 1.0
C B:CYS1107 4.9 60.2 1.0
CA B:CYS1128 4.9 64.5 1.0
C B:GLU1106 5.0 60.7 1.0
N B:ARG1130 5.0 65.4 1.0
CB B:GLU1106 5.0 60.7 1.0

Zinc binding site 4 out of 7 in 6tps

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Zinc binding site 4 out of 7 in the Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.9
occ:1.00
 SG I:CYS30 2.5 98.3 1.0
SG I:CYS10 2.5 99.1 1.0
SG I:CYS33 2.6 0.5 1.0
SG I:CYS13 2.6 0.4 1.0
CB I:CYS10 2.7 99.1 1.0
CB I:CYS30 2.7 98.3 1.0
CB I:CYS33 3.8 0.5 1.0
CB I:CYS13 4.1 0.4 1.0
CA I:CYS10 4.2 99.1 1.0
CA I:CYS30 4.2 98.3 1.0
N I:CYS33 4.2 0.5 1.0
N I:CYS13 4.2 0.4 1.0
CA I:CYS33 4.5 0.5 1.0
O I:ASP15 4.6 90.1 1.0
CA I:CYS13 4.7 0.4 1.0
CD2 I:LEU17 4.8 96.6 1.0
CB I:ASP15 4.9 90.1 1.0
N I:ASP15 4.9 90.1 1.0
C I:CYS13 4.9 0.4 1.0
N I:CYS10 4.9 99.1 1.0
N I:LYS34 4.9 96.2 1.0
C I:CYS33 5.0 0.5 1.0
N I:CYS30 5.0 98.3 1.0
C I:CYS10 5.0 99.1 1.0

Zinc binding site 5 out of 7 in 6tps

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Zinc binding site 5 out of 7 in the Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:57.4
occ:1.00
 N J:CYS46 2.3 36.2 1.0
SG J:CYS7 2.4 30.0 1.0
SG J:CYS10 2.4 27.8 1.0
SG J:CYS45 2.5 31.9 1.0
CB J:CYS46 2.5 36.2 1.0
CA J:CYS46 2.6 36.2 1.0
C J:CYS45 2.9 31.9 1.0
CB J:CYS7 3.3 30.0 1.0
SG J:CYS46 3.3 36.2 1.0
CB J:CYS45 3.4 31.9 1.0
O J:CYS45 3.4 31.9 1.0
CB J:CYS10 3.7 27.8 1.0
CA J:CYS45 3.7 31.9 1.0
N J:CYS10 4.0 27.8 1.0
C J:CYS46 4.1 36.2 1.0
NH1 J:ARG43 4.2 39.1 1.0
N J:CYS45 4.4 31.9 1.0
CA J:CYS10 4.5 27.8 1.0
CA J:CYS7 4.7 30.0 1.0
N J:ARG47 4.8 37.2 1.0
N J:GLY11 4.9 28.3 1.0
O J:CYS46 4.9 36.2 1.0
N J:SER9 5.0 28.1 1.0

Zinc binding site 6 out of 7 in 6tps

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Zinc binding site 6 out of 7 in the Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:79.5
occ:1.00
 SG L:CYS34 2.4 50.3 1.0
SG L:CYS31 2.4 49.9 1.0
SG L:CYS48 2.5 59.6 1.0
CB L:CYS48 2.6 59.6 1.0
CB L:CYS51 3.2 58.5 1.0
CB L:CYS31 3.4 49.9 1.0
N L:CYS51 3.7 58.5 1.0
CA L:CYS51 3.9 58.5 1.0
CB L:CYS34 4.0 50.3 1.0
CA L:CYS48 4.1 59.6 1.0
N L:HIS53 4.2 53.6 1.0
N L:GLY52 4.3 57.6 1.0
N L:CYS34 4.3 50.3 1.0
CB L:HIS53 4.3 53.6 1.0
C L:CYS51 4.4 58.5 1.0
C L:ASP50 4.6 59.3 1.0
SG L:CYS51 4.6 58.5 1.0
N L:ASP50 4.7 59.3 1.0
C L:CYS48 4.7 59.6 1.0
CA L:CYS34 4.7 50.3 1.0
N L:CYS48 4.8 59.6 1.0
CA L:CYS31 4.8 49.9 1.0
CA L:HIS53 4.8 53.6 1.0
N L:LYS49 4.9 54.2 1.0
CB L:GLU33 4.9 50.5 1.0
CB L:ASP50 5.0 59.3 1.0
CA L:ASP50 5.0 59.3 1.0

Zinc binding site 7 out of 7 in 6tps

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Zinc binding site 7 out of 7 in the Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Early Intermediate Rna Polymerase I Pre-Initiation Complex - Eipic within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn601

b:92.6
occ:1.00
 SG Q:CYS15 2.4 69.0 1.0
SG Q:CYS29 2.5 65.6 1.0
SG Q:CYS10 2.5 86.6 1.0
CB Q:CYS29 2.6 65.6 1.0
ND1 Q:HIS33 3.1 53.3 1.0
CB Q:HIS33 3.3 53.3 1.0
CB Q:CYS15 3.5 69.0 1.0
CG Q:HIS33 3.6 53.3 1.0
CB Q:CYS10 3.9 86.6 1.0
O Q:HIS33 4.0 53.3 1.0
CA Q:CYS29 4.0 65.6 1.0
N Q:HIS33 4.2 53.3 1.0
CA Q:HIS33 4.2 53.3 1.0
CE1 Q:HIS33 4.2 53.3 1.0
N Q:CYS29 4.5 65.6 1.0
C Q:HIS33 4.6 53.3 1.0
C Q:CYS29 4.8 65.6 1.0
CA Q:CYS15 4.8 69.0 1.0
CD2 Q:HIS33 4.9 53.3 1.0
O Q:ILE9 5.0 76.8 1.0
CG2 Q:THR12 5.0 87.6 1.0

Reference:

M.Pilsl, C.Engel. Structural Basis of Rna Polymerase I Pre-Initiation Complex Formation and Promoter Melting. Nat Commun V. 11 1206 2020.
ISSN: ESSN 2041-1723
PubMed: 32139698
DOI: 10.1038/S41467-020-15052-Y
Page generated: Tue Oct 29 08:09:28 2024

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