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Zinc in PDB 5w66: Rna Polymerase I Initial Transcribing Complex State 3

Enzymatic activity of Rna Polymerase I Initial Transcribing Complex State 3

All present enzymatic activity of Rna Polymerase I Initial Transcribing Complex State 3:
2.7.7.6;

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase I Initial Transcribing Complex State 3 (pdb code 5w66). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Rna Polymerase I Initial Transcribing Complex State 3, PDB code: 5w66:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5w66

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Zinc binding site 1 out of 6 in the Rna Polymerase I Initial Transcribing Complex State 3


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 Initial Transcribing Complex State 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1701

b:0.0
occ:1.00
 SG A:CYS105 1.8 0.0 1.0
CB A:CYS102 2.0 0.0 1.0
SG A:CYS233 2.1 0.0 1.0
SG A:CYS102 2.2 0.0 1.0
SG A:CYS236 2.2 0.0 1.0
CB A:CYS236 3.3 0.0 1.0
CB A:CYS233 3.4 0.0 1.0
CA A:CYS102 3.5 0.0 1.0
CB A:CYS105 3.5 0.0 1.0
O A:HIS107 3.7 0.0 1.0
N A:CYS236 4.0 0.0 1.0
N A:HIS107 4.1 0.0 1.0
N A:CYS102 4.2 0.0 1.0
C A:HIS107 4.2 0.0 1.0
CA A:CYS236 4.2 0.0 1.0
CB A:HIS107 4.4 0.0 1.0
C A:CYS102 4.4 0.0 1.0
N A:HIS106 4.4 0.0 1.0
CA A:HIS107 4.5 0.0 1.0
CA A:CYS105 4.6 0.0 1.0
CG A:ARG109 4.6 0.0 1.0
N A:CYS105 4.6 0.0 1.0
CA A:CYS233 4.6 0.0 1.0
O A:PHE108 4.7 0.0 1.0
CA A:ARG109 4.7 0.0 1.0
C A:PHE108 4.8 0.0 1.0
N A:ARG109 4.9 0.0 1.0
C A:CYS105 4.9 0.0 1.0
O A:CYS102 4.9 0.0 1.0
C A:CYS236 5.0 0.0 1.0
ND2 A:ASN235 5.0 0.0 1.0
CB A:ASN235 5.0 0.0 1.0

Zinc binding site 2 out of 6 in 5w66

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Zinc binding site 2 out of 6 in the Rna Polymerase I Initial Transcribing Complex State 3


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 Initial Transcribing Complex State 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1702

b:0.0
occ:1.00
 CD2 A:HIS75 1.8 0.0 1.0
SG A:CYS72 1.9 0.0 1.0
NE2 A:HIS75 1.9 0.0 1.0
SG A:CYS62 2.1 0.0 1.0
SG A:CYS65 2.3 0.0 1.0
CB A:CYS62 3.0 0.0 1.0
CG A:HIS75 3.1 0.0 1.0
CE1 A:HIS75 3.1 0.0 1.0
CA A:GLY74 3.4 0.0 1.0
CB A:CYS65 3.4 0.0 1.0
N A:GLY74 3.5 0.0 1.0
ND1 A:HIS75 3.6 0.0 1.0
C A:GLY74 3.7 0.0 1.0
CB A:CYS72 3.7 0.0 1.0
CA A:GLY55 3.8 0.0 1.0
N A:HIS75 3.9 0.0 1.0
N A:CYS65 4.0 0.0 1.0
O A:GLY74 4.2 0.0 1.0
CB A:HIS75 4.2 0.0 1.0
CA A:CYS65 4.3 0.0 1.0
CA A:CYS62 4.4 0.0 1.0
N A:GLY55 4.4 0.0 1.0
CA A:CYS72 4.6 0.0 1.0
CB A:THR64 4.6 0.0 1.0
C A:GLY55 4.6 0.0 1.0
C A:CYS72 4.6 0.0 1.0
CA A:HIS75 4.7 0.0 1.0
CD A:PRO73 4.7 0.0 1.0
C A:THR64 4.7 0.0 1.0
N A:PRO73 4.8 0.0 1.0
C A:PRO73 4.8 0.0 1.0
N A:ALA56 4.8 0.0 1.0
O A:ALA53 4.8 0.0 1.0
N A:THR64 5.0 0.0 1.0

Zinc binding site 3 out of 6 in 5w66

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Zinc binding site 3 out of 6 in the Rna Polymerase I Initial Transcribing Complex State 3


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 Initial Transcribing Complex State 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.0
occ:1.00
 CB B:CYS1107 2.1 0.0 1.0
SG B:CYS1104 2.1 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 2.8 0.0 1.0
N B:CYS1107 2.9 0.0 1.0
CA B:CYS1107 2.9 0.0 1.0
CB B:CYS1104 3.3 0.0 1.0
C B:GLU1106 3.5 0.0 1.0
CB B:CYS1128 3.6 0.0 1.0
CB B:ARG1130 3.8 0.0 1.0
O B:GLU1106 4.0 0.0 1.0
CB B:CYS1131 4.0 0.0 1.0
N B:CYS1131 4.0 0.0 1.0
CB B:GLU1106 4.1 0.0 1.0
NE B:ARG1130 4.1 0.0 1.0
CA B:GLU1106 4.2 0.0 1.0
C B:CYS1107 4.3 0.0 1.0
N B:GLU1106 4.4 0.0 1.0
NH2 B:ARG1130 4.5 0.0 1.0
CA B:CYS1104 4.6 0.0 1.0
CA B:ARG1130 4.6 0.0 1.0
CA B:CYS1131 4.6 0.0 1.0
N B:ARG1130 4.6 0.0 1.0
CZ B:ARG1130 4.7 0.0 1.0
C B:ARG1130 4.7 0.0 1.0
O B:CYS1104 4.7 0.0 1.0
N B:GLY1108 4.7 0.0 1.0
CG B:ARG1130 4.8 0.0 1.0
C B:CYS1104 4.8 0.0 1.0
CA B:CYS1128 4.9 0.0 1.0
OG1 B:THR1112 5.0 0.0 1.0
CD B:ARG1130 5.0 0.0 1.0

Zinc binding site 4 out of 6 in 5w66

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Zinc binding site 4 out of 6 in the Rna Polymerase I Initial Transcribing Complex State 3


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 Initial Transcribing Complex State 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.0
occ:1.00
 SG I:CYS13 2.1 0.0 1.0
SG I:CYS30 2.2 0.0 1.0
SG I:CYS33 2.3 0.0 1.0
CB I:CYS33 2.3 0.0 1.0
SG I:CYS10 2.4 0.0 1.0
N I:CYS33 2.4 0.0 1.0
CB I:CYS13 2.7 0.0 1.0
CA I:CYS33 2.9 0.0 1.0
C I:GLN32 3.1 0.0 1.0
CB I:CYS30 3.1 0.0 1.0
CB I:GLN32 3.4 0.0 1.0
N I:CYS13 3.5 0.0 1.0
CA I:GLN32 3.6 0.0 1.0
CB I:CYS10 3.6 0.0 1.0
CA I:CYS13 3.7 0.0 1.0
N I:GLN32 3.9 0.0 1.0
O I:GLN32 3.9 0.0 1.0
C I:CYS33 4.0 0.0 1.0
CG I:GLN32 4.2 0.0 1.0
O I:CYS33 4.4 0.0 1.0
CB I:ASP12 4.5 0.0 1.0
CA I:CYS30 4.5 0.0 1.0
C I:ASP12 4.5 0.0 1.0
C I:CYS13 4.7 0.0 1.0
C I:CYS30 4.8 0.0 1.0
N I:LYS34 4.9 0.0 1.0
CA I:ASP12 5.0 0.0 1.0
N I:SER31 5.0 0.0 1.0

Zinc binding site 5 out of 6 in 5w66

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Zinc binding site 5 out of 6 in the Rna Polymerase I Initial Transcribing Complex State 3


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 Initial Transcribing Complex State 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.0
occ:1.00
 SG J:CYS45 2.2 0.0 1.0
SG J:CYS7 2.2 0.0 1.0
N J:CYS46 2.3 0.0 1.0
SG J:CYS10 2.4 0.0 1.0
C J:CYS45 2.7 0.0 1.0
CA J:CYS46 2.7 0.0 1.0
SG J:CYS46 2.7 0.0 1.0
CB J:CYS7 2.8 0.0 1.0
CB J:CYS45 3.1 0.0 1.0
CB J:CYS46 3.2 0.0 1.0
O J:CYS45 3.2 0.0 1.0
CB J:CYS10 3.2 0.0 1.0
CA J:CYS45 3.4 0.0 1.0
N J:CYS10 4.0 0.0 1.0
C J:CYS46 4.1 0.0 1.0
CA J:CYS10 4.2 0.0 1.0
N J:CYS45 4.3 0.0 1.0
CA J:CYS7 4.3 0.0 1.0
O J:ARG43 4.7 0.0 1.0
NH2 J:ARG43 4.7 0.0 1.0
NE J:ARG43 4.7 0.0 1.0
O J:CYS46 4.8 0.0 1.0
C J:CYS7 4.8 0.0 1.0
O J:CYS7 4.8 0.0 1.0
N J:ARG47 4.9 0.0 1.0
N J:GLY11 4.9 0.0 1.0

Zinc binding site 6 out of 6 in 5w66

Go back to Zinc Binding Sites List in 5w66
Zinc binding site 6 out of 6 in the Rna Polymerase I Initial Transcribing Complex State 3


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 Initial Transcribing Complex State 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.0
occ:1.00
 SG L:CYS51 2.0 0.0 1.0
SG L:CYS34 2.1 0.0 1.0
CB L:CYS34 2.1 0.0 1.0
CB L:CYS51 2.1 0.0 1.0
SG L:CYS48 2.3 0.0 1.0
SG L:CYS31 2.3 0.0 1.0
N L:CYS51 3.1 0.0 1.0
CA L:CYS51 3.2 0.0 1.0
CA L:CYS34 3.3 0.0 1.0
CB L:CYS31 3.3 0.0 1.0
CB L:CYS48 3.3 0.0 1.0
N L:CYS34 3.4 0.0 1.0
C L:ASP50 3.9 0.0 1.0
C L:CYS51 4.2 0.0 1.0
C L:GLU33 4.2 0.0 1.0
N L:GLY52 4.3 0.0 1.0
C L:CYS34 4.3 0.0 1.0
CB L:ASP50 4.5 0.0 1.0
OG L:SER36 4.5 0.0 1.0
O L:ASP50 4.6 0.0 1.0
CA L:ASP50 4.6 0.0 1.0
CA L:CYS48 4.7 0.0 1.0
CA L:CYS31 4.8 0.0 1.0
N L:ASP50 4.8 0.0 1.0
CB L:HIS53 4.8 0.0 1.0
N L:HIS53 4.9 0.0 1.0
N L:SER35 4.9 0.0 1.0
O L:GLU33 4.9 0.0 1.0
O L:CYS48 4.9 0.0 1.0
N L:GLU33 4.9 0.0 1.0
CA L:GLU33 5.0 0.0 1.0

Reference:

Y.Han, C.Yan, T.H.D.Nguyen, A.J.Jackobel, I.Ivanov, B.A.Knutson, Y.He. Structural Mechanism of Atp-Independent Transcription Initiation By Rna Polymerase I. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28623663
DOI: 10.7554/ELIFE.27414
Page generated: Mon Oct 28 13:49:25 2024

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