Atomistry » Zinc » PDB 9g24-9gkx » 9g27
Atomistry »
  Zinc »
    PDB 9g24-9gkx »
      9g27 »

Zinc in PDB 9g27: Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Pre-Translocation State

Enzymatic activity of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Pre-Translocation State

All present enzymatic activity of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Pre-Translocation State:
2.7.7.6;

Zinc Binding Sites:

The binding sites of Zinc atom in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Pre-Translocation State (pdb code 9g27). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Pre-Translocation State, PDB code: 9g27:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 9g27

Go back to Zinc Binding Sites List in 9g27
Zinc binding site 1 out of 6 in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Pre-Translocation State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Pre-Translocation State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1701

b:123.6
occ:1.00
 NE2 A:HIS75 2.1 86.4 1.0
SG A:CYS65 2.3 93.3 1.0
SG A:CYS72 2.3 111.5 1.0
SG A:CYS62 2.3 91.5 1.0
CD2 A:HIS75 2.8 83.2 1.0
CB A:CYS62 3.0 91.1 1.0
CE1 A:HIS75 3.2 80.1 1.0
CB A:CYS72 3.7 94.9 1.0
CB A:CYS65 3.9 80.9 1.0
CA A:GLY55 4.0 86.5 1.0
N A:CYS65 4.0 90.6 1.0
CG A:HIS75 4.1 79.1 1.0
ND1 A:HIS75 4.2 76.1 1.0
CB A:THR64 4.3 80.5 1.0
CA A:CYS72 4.4 92.6 1.0
N A:ALA56 4.5 89.7 1.0
N A:GLY55 4.5 88.1 1.0
CA A:CYS62 4.5 90.9 1.0
CA A:CYS65 4.5 86.0 1.0
C A:GLY55 4.6 87.9 1.0
CD A:PRO73 4.7 87.9 1.0
N A:GLY74 4.7 85.3 1.0
C A:CYS72 4.9 94.0 1.0
N A:THR64 4.9 88.6 1.0
C A:THR64 4.9 88.3 1.0
CA A:THR64 5.0 83.6 1.0
N A:PRO73 5.0 91.7 1.0

Zinc binding site 2 out of 6 in 9g27

Go back to Zinc Binding Sites List in 9g27
Zinc binding site 2 out of 6 in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Pre-Translocation State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Pre-Translocation State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1702

b:140.3
occ:1.00
 SG A:CYS105 2.3 119.7 1.0
SG A:CYS102 2.3 115.2 1.0
SG A:CYS233 2.3 99.4 1.0
SG A:CYS236 2.3 128.8 1.0
CB A:CYS105 2.8 112.1 1.0
CB A:CYS102 3.0 105.7 1.0
CB A:CYS233 3.5 96.6 1.0
O A:CYS236 3.5 114.7 1.0
N A:CYS105 3.7 113.4 1.0
CA A:CYS105 3.8 111.6 1.0
N A:CYS236 3.9 114.2 1.0
CB A:CYS236 3.9 109.4 1.0
CA A:CYS236 4.3 109.5 1.0
C A:CYS236 4.4 109.9 1.0
CA A:CYS102 4.5 104.8 1.0
CB A:ASN235 4.6 107.8 1.0
C A:CYS105 4.7 110.2 1.0
C A:ASN235 4.8 112.0 1.0
CA A:CYS233 4.9 96.1 1.0
C A:PHE104 4.9 111.9 1.0
CG A:MET238 4.9 119.8 1.0
N A:HIS106 5.0 109.5 1.0
O A:HIS107 5.0 104.5 1.0
CB A:PHE104 5.0 112.2 1.0

Zinc binding site 3 out of 6 in 9g27

Go back to Zinc Binding Sites List in 9g27
Zinc binding site 3 out of 6 in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Pre-Translocation State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Pre-Translocation State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1701

b:134.2
occ:1.00
 SG B:CYS1131 2.3 132.1 1.0
SG B:CYS1104 2.3 104.8 1.0
SG B:CYS1107 2.3 116.9 1.0
SG B:CYS1128 2.3 98.7 1.0
CB B:CYS1128 3.1 102.4 1.0
CB B:CYS1107 3.1 97.6 1.0
CB B:CYS1131 3.2 111.2 1.0
CB B:CYS1104 3.4 99.7 1.0
N B:CYS1131 3.6 106.4 1.0
CA B:CYS1131 4.0 108.5 1.0
N B:CYS1107 4.1 104.4 1.0
CA B:CYS1107 4.2 102.3 1.0
OE2 B:GLU1106 4.3 113.7 1.0
CG B:GLU1106 4.3 107.0 1.0
CA B:CYS1128 4.5 102.8 1.0
CB B:ARG1130 4.5 98.4 1.0
C B:ARG1130 4.6 105.6 1.0
N B:ARG1130 4.7 103.7 1.0
CA B:CYS1104 4.8 95.3 1.0
CD B:GLU1106 4.8 115.1 1.0
C B:CYS1131 4.9 111.5 1.0
CA B:ARG1130 4.9 102.0 1.0
C B:CYS1128 4.9 110.3 1.0

Zinc binding site 4 out of 6 in 9g27

Go back to Zinc Binding Sites List in 9g27
Zinc binding site 4 out of 6 in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Pre-Translocation State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Pre-Translocation State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1701

b:92.0
occ:1.00
 CB I:CYS13 1.7 76.2 1.0
SG I:CYS30 2.3 73.5 1.0
SG I:CYS10 2.3 83.0 1.0
SG I:CYS33 2.3 91.5 1.0
SG I:CYS13 2.3 77.1 1.0
CA I:CYS13 3.2 70.2 1.0
CB I:CYS33 3.2 81.2 1.0
N I:CYS33 3.5 81.4 1.0
CB I:CYS10 3.6 68.2 1.0
N I:CYS13 3.7 70.6 1.0
CB I:CYS30 3.7 77.3 1.0
CB I:ASP15 3.8 57.0 1.0
C I:CYS13 3.9 70.1 1.0
CA I:CYS33 3.9 79.2 1.0
N I:ASP15 4.2 56.0 1.0
N I:GLY14 4.2 68.1 1.0
CB I:GLN32 4.5 77.1 1.0
C I:GLN32 4.6 80.1 1.0
CA I:ASP15 4.6 54.5 1.0
O I:CYS13 4.7 70.0 1.0
N I:GLN32 4.8 78.5 1.0
CA I:GLN32 4.9 79.7 1.0
CA I:CYS10 5.0 65.3 1.0
C I:ASP12 5.0 74.5 1.0
CG I:ASP15 5.0 55.4 1.0

Zinc binding site 5 out of 6 in 9g27

Go back to Zinc Binding Sites List in 9g27
Zinc binding site 5 out of 6 in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Pre-Translocation State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Pre-Translocation State within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1701

b:82.6
occ:1.00
 SG J:CYS10 2.3 53.3 1.0
SG J:CYS46 2.3 60.5 1.0
SG J:CYS45 2.3 53.2 1.0
SG J:CYS7 2.3 44.7 1.0
N J:CYS46 3.1 42.2 1.0
CB J:CYS7 3.2 45.5 1.0
CA J:CYS46 3.4 39.3 1.0
CB J:CYS46 3.4 42.9 1.0
CB J:CYS10 3.4 42.9 1.0
C J:CYS45 3.5 39.2 1.0
CB J:CYS45 3.7 37.4 1.0
N J:CYS10 3.9 47.4 1.0
O J:CYS45 4.0 38.2 1.0
CA J:CYS10 4.2 46.6 1.0
CA J:CYS45 4.2 36.5 1.0
NE J:ARG43 4.3 47.5 1.0
N J:GLY11 4.5 47.5 1.0
NH2 J:ARG43 4.6 46.1 1.0
CA J:CYS7 4.6 42.1 1.0
CB J:LYS12 4.7 45.3 1.0
CB J:SER9 4.8 44.5 1.0
N J:LYS12 4.8 45.4 1.0
C J:CYS46 4.9 39.3 1.0
C J:CYS10 4.9 51.7 1.0
C J:SER9 4.9 48.3 1.0
CZ J:ARG43 5.0 50.1 1.0
N J:SER9 5.0 50.0 1.0
C J:CYS7 5.0 47.1 1.0
CB J:ARG43 5.0 42.2 1.0

Zinc binding site 6 out of 6 in 9g27

Go back to Zinc Binding Sites List in 9g27
Zinc binding site 6 out of 6 in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Pre-Translocation State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, Pre-Translocation State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1701

b:104.5
occ:1.00
 SG L:CYS34 2.3 66.8 1.0
SG L:CYS31 2.3 69.5 1.0
SG L:CYS48 2.3 77.3 1.0
SG L:CYS51 2.3 85.3 1.0
CB L:CYS31 3.0 55.8 1.0
CB L:CYS48 3.0 68.3 1.0
CB L:CYS34 3.4 64.2 1.0
CB L:CYS51 3.8 69.9 1.0
OG L:SER36 3.9 65.7 1.0
N L:CYS34 3.9 65.9 1.0
N L:CYS51 4.0 68.4 1.0
CA L:CYS34 4.2 63.1 1.0
CA L:CYS51 4.4 65.1 1.0
CA L:CYS31 4.5 49.4 1.0
CA L:CYS48 4.5 66.8 1.0
C L:CYS51 4.6 67.8 1.0
CB L:HIS53 4.7 59.4 1.0
O L:CYS51 4.7 67.4 1.0
C L:CYS34 4.8 56.4 1.0
N L:SER35 4.9 55.2 1.0
C L:ASP50 4.9 75.8 1.0
CB L:ASP50 5.0 84.2 1.0

Reference:

A.Santos-Aledo, A.Plaza-Pegueroles, M.Sanz-Murillo, F.M.Ruiz, P.Hou, J.Xu, D.Gil-Carton, D.Wang, C.Fernandez-Tornero. Cryo-Em Uncovers A Sequential Mechanism For Rna Polymerase I Pausing and Stalling at Abasic Dna Lesions. Nat Commun V. 16 5254 2025.
ISSN: ESSN 2041-1723
PubMed: 40480971
DOI: 10.1038/S41467-025-60536-4
Page generated: Fri Aug 22 17:48:56 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy