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Zinc in PDB 5g5l: Rna Polymerase I-RRN3 Complex at 4.8 A Resolution

Enzymatic activity of Rna Polymerase I-RRN3 Complex at 4.8 A Resolution

All present enzymatic activity of Rna Polymerase I-RRN3 Complex at 4.8 A Resolution:
2.7.7.6;

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase I-RRN3 Complex at 4.8 A Resolution (pdb code 5g5l). 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-RRN3 Complex at 4.8 A Resolution, PDB code: 5g5l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 5g5l

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Zinc binding site 1 out of 7 in the Rna Polymerase I-RRN3 Complex at 4.8 A Resolution


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-RRN3 Complex at 4.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2663

b:0.0
occ:1.00
 NE2 A:HIS75 2.0 0.0 1.0
SG A:CYS62 2.1 0.0 1.0
SG A:CYS72 2.2 0.0 1.0
SG A:CYS65 2.2 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:CYS72 3.6 0.0 1.0
CB A:CYS65 3.6 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
N A:CYS65 4.0 0.0 1.0
CA A:CYS72 4.2 0.0 1.0
N A:GLY74 4.2 0.0 1.0
CA A:GLY55 4.3 0.0 1.0
CA A:CYS65 4.4 0.0 1.0
N A:PRO73 4.5 0.0 1.0
C A:CYS72 4.6 0.0 1.0
CA A:GLY74 4.6 0.0 1.0
CA A:CYS62 4.7 0.0 1.0
CG A:PRO73 4.7 0.0 1.0
CB A:THR64 4.8 0.0 1.0
C A:GLY74 4.8 0.0 1.0
N A:ALA56 4.9 0.0 1.0
C A:THR64 5.0 0.0 1.0

Zinc binding site 2 out of 7 in 5g5l

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Zinc binding site 2 out of 7 in the Rna Polymerase I-RRN3 Complex at 4.8 A Resolution


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-RRN3 Complex at 4.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2664

b:0.0
occ:1.00
 SG A:CYS105 2.2 0.0 1.0
SG A:CYS233 2.3 0.0 1.0
SG A:CYS236 2.3 0.0 1.0
SG A:CYS102 2.4 0.0 1.0
CB A:CYS105 3.2 0.0 1.0
CB A:CYS233 3.2 0.0 1.0
CB A:CYS102 3.3 0.0 1.0
CB A:CYS236 3.5 0.0 1.0
N A:CYS105 3.7 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 4.7 0.0 1.0
CA A:CYS233 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 4.7 0.0 1.0
N A:HIS106 4.8 0.0 1.0
C A:PHE104 4.8 0.0 1.0
C A:CYS236 4.9 0.0 1.0
N A:GLY237 4.9 0.0 1.0
CB A:PHE104 4.9 0.0 1.0

Zinc binding site 3 out of 7 in 5g5l

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Zinc binding site 3 out of 7 in the Rna Polymerase I-RRN3 Complex at 4.8 A Resolution


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-RRN3 Complex at 4.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2204

b:0.0
occ:1.00
 SG B:CYS1131 2.3 0.0 1.0
SG B:CYS1128 2.3 0.0 1.0
SG B:CYS1104 2.3 0.0 1.0
SG B:CYS1107 2.3 0.0 1.0
CB B:CYS1104 3.1 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
N B:CYS1131 3.9 0.0 1.0
CA B:CYS1107 3.9 0.0 1.0
CA B:CYS1131 4.2 0.0 1.0
CB B:ARG1130 4.3 0.0 1.0
CB B:GLU1106 4.5 0.0 1.0
OG1 B:THR1112 4.5 0.0 1.0
CA B:CYS1104 4.5 0.0 1.0
C B:GLU1106 4.6 0.0 1.0
CD B:ARG1130 4.7 0.0 1.0
C B:ARG1130 4.7 0.0 1.0
CA B:CYS1128 4.7 0.0 1.0
C B:CYS1107 4.8 0.0 1.0
CG B:ARG1130 4.9 0.0 1.0
CA B:ARG1130 4.9 0.0 1.0
N B:ARG1130 4.9 0.0 1.0
CA B:GLU1106 4.9 0.0 1.0
N B:GLU1106 5.0 0.0 1.0
C B:CYS1104 5.0 0.0 1.0
O B:CYS1104 5.0 0.0 1.0

Zinc binding site 4 out of 7 in 5g5l

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Zinc binding site 4 out of 7 in the Rna Polymerase I-RRN3 Complex at 4.8 A Resolution


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-RRN3 Complex at 4.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1126

b:0.0
occ:1.00
 SG I:CYS13 2.2 0.0 1.0
SG I:CYS33 2.3 0.0 1.0
SG I:CYS30 2.3 0.0 1.0
SG I:CYS10 2.3 0.0 1.0
CB I:CYS10 3.2 0.0 1.0
CB I:CYS30 3.3 0.0 1.0
CB I:CYS13 3.5 0.0 1.0
CB I:CYS33 3.6 0.0 1.0
N I:CYS13 3.6 0.0 1.0
N I:CYS33 3.9 0.0 1.0
CA I:CYS13 4.0 0.0 1.0
CA I:CYS33 4.3 0.0 1.0
CB I:GLN32 4.4 0.0 1.0
C I:CYS13 4.4 0.0 1.0
CB I:ALA35 4.4 0.0 1.0
CB I:ASP12 4.5 0.0 1.0
O I:CYS13 4.6 0.0 1.0
CA I:CYS10 4.6 0.0 1.0
CA I:CYS30 4.7 0.0 1.0
C I:ASP12 4.8 0.0 1.0
C I:GLN32 4.9 0.0 1.0
C I:CYS33 4.9 0.0 1.0
N I:ASP12 4.9 0.0 1.0
CB I:ASP15 5.0 0.0 1.0
CA I:ASP12 5.0 0.0 1.0
N I:ASP15 5.0 0.0 1.0
N I:ALA35 5.0 0.0 1.0

Zinc binding site 5 out of 7 in 5g5l

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Zinc binding site 5 out of 7 in the Rna Polymerase I-RRN3 Complex at 4.8 A Resolution


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-RRN3 Complex at 4.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1127

b:0.0
occ:0.75
 SG I:CYS114 2.2 0.0 1.0
SG I:CYS86 2.2 0.0 1.0
SG I:CYS117 2.3 0.0 1.0
SG I:CYS89 2.4 0.0 1.0
CB I:CYS86 2.9 0.0 1.0
CB I:CYS114 3.2 0.0 1.0
CB I:CYS89 3.2 0.0 1.0
CB I:CYS117 3.2 0.0 1.0
N I:CYS89 3.6 0.0 1.0
CA I:CYS89 3.9 0.0 1.0
CB I:ASN91 4.1 0.0 1.0
N I:CYS117 4.1 0.0 1.0
CA I:CYS117 4.2 0.0 1.0
CA I:CYS86 4.4 0.0 1.0
N I:GLY90 4.5 0.0 1.0
CA I:CYS114 4.6 0.0 1.0
C I:CYS89 4.6 0.0 1.0
N I:ASN91 4.6 0.0 1.0
CB I:GLN88 4.7 0.0 1.0
C I:GLN88 4.8 0.0 1.0
OG I:SER116 4.8 0.0 1.0
C I:CYS117 4.8 0.0 1.0
CB I:TYR119 4.9 0.0 1.0
C I:CYS86 4.9 0.0 1.0

Zinc binding site 6 out of 7 in 5g5l

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Zinc binding site 6 out of 7 in the Rna Polymerase I-RRN3 Complex at 4.8 A Resolution


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-RRN3 Complex at 4.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1070

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 7 in 5g5l

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Zinc binding site 7 out of 7 in the Rna Polymerase I-RRN3 Complex at 4.8 A Resolution


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-RRN3 Complex at 4.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1070

b:0.0
occ:1.00
 SG L:CYS34 2.3 0.0 1.0
SG L:CYS51 2.3 0.0 1.0
SG L:CYS31 2.3 0.0 1.0
SG L:CYS48 2.3 0.0 1.0
CB L:CYS51 2.6 0.0 1.0
CB L:CYS48 2.9 0.0 1.0
CB L:CYS31 3.3 0.0 1.0
CB L:CYS34 3.3 0.0 1.0
N L:CYS51 3.5 0.0 1.0
CA L:CYS51 3.7 0.0 1.0
N L:CYS34 3.8 0.0 1.0
CA L:CYS34 4.1 0.0 1.0
CA L:CYS48 4.4 0.0 1.0
CB L:ASP50 4.7 0.0 1.0
C L:ASP50 4.7 0.0 1.0
CA L:CYS31 4.7 0.0 1.0
OG L:SER36 4.7 0.0 1.0
C L:CYS51 4.8 0.0 1.0
N L:GLY52 4.8 0.0 1.0
CB L:HIS53 4.8 0.0 1.0
CB L:GLU33 4.8 0.0 1.0
C L:CYS34 4.8 0.0 1.0
N L:SER35 4.9 0.0 1.0
C L:GLU33 4.9 0.0 1.0
N L:HIS53 4.9 0.0 1.0
C L:CYS48 5.0 0.0 1.0

Reference:

C.Engel, J.Plitzko, P.Cramer. Rna Polymerase I-RRN3 Complex at 4.8 A Resolution Nat.Commun. V. 7 12129 2016.
ISSN: ESSN 2041-1723
PubMed: 27418309
DOI: 10.1038/NCOMMS12129
Page generated: Sun Oct 27 16:56:57 2024

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