Zinc in PDB 7z31: Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore).

Enzymatic activity of Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore).

All present enzymatic activity of Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore).:
2.7.7.6;

Other elements in 7z31:

The structure of Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore). also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore). (pdb code 7z31). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore)., PDB code: 7z31:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7z31

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Zinc binding site 1 out of 6 in the Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1501

b:111.2
occ:1.00
 NE2 A:HIS80 2.0 61.9 1.0
SG A:CYS70 2.2 73.6 1.0
SG A:CYS67 2.3 81.7 1.0
SG A:CYS77 2.3 58.9 1.0
CD2 A:HIS80 2.4 56.7 1.0
CB A:CYS67 3.0 74.9 1.0
CB A:CYS70 3.2 72.7 1.0
CE1 A:HIS80 3.3 56.6 1.0
N A:CYS70 3.3 72.7 1.0
CG A:HIS80 3.7 54.2 1.0
CA A:CYS70 3.8 73.3 1.0
CB A:CYS77 3.9 57.1 1.0
CB A:THR69 4.0 68.3 1.0
ND1 A:HIS80 4.0 56.6 1.0
C A:THR69 4.2 70.0 1.0
CA A:CYS67 4.5 74.9 1.0
CA A:THR69 4.5 72.0 1.0
CA A:CYS77 4.6 57.1 1.0
N A:THR69 4.6 74.2 1.0
C A:CYS70 4.7 73.5 1.0
CG2 A:THR69 4.7 70.0 1.0
N A:HIS71 4.8 77.9 1.0
OG1 A:THR69 4.8 66.5 1.0
CB A:HIS80 4.9 54.8 1.0
N A:HIS78 5.0 54.6 1.0
N A:GLY79 5.0 52.3 1.0

Zinc binding site 2 out of 6 in 7z31

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Zinc binding site 2 out of 6 in the Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1502

b:116.2
occ:1.00
 SG A:CYS110 2.3 79.1 1.0
SG A:CYS157 2.4 90.2 1.0
SG A:CYS107 2.4 85.6 1.0
SG A:CYS154 2.4 80.8 1.0
O A:CYS157 2.6 76.9 1.0
CB A:CYS154 3.0 79.5 1.0
N A:CYS157 3.2 78.9 1.0
C A:CYS157 3.3 79.8 1.0
CB A:CYS110 3.5 73.5 1.0
CB A:CYS157 3.5 81.5 1.0
CA A:CYS157 3.5 79.8 1.0
CB A:CYS107 3.7 74.5 1.0
N A:CYS110 3.9 76.0 1.0
ND1 A:HIS156 4.2 81.0 1.0
CB A:HIS156 4.2 79.9 1.0
C A:HIS156 4.3 81.6 1.0
CA A:CYS110 4.3 75.1 1.0
CA A:CYS154 4.4 79.0 1.0
N A:GLY158 4.5 80.7 1.0
CB A:ASN109 4.6 77.4 1.0
CA A:HIS156 4.7 79.8 1.0
CG A:HIS156 4.7 81.9 1.0
C A:CYS154 4.7 76.7 1.0
O A:CYS154 4.7 75.6 1.0
N A:HIS156 4.8 79.8 1.0
C A:ASN109 5.0 77.6 1.0

Zinc binding site 3 out of 6 in 7z31

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Zinc binding site 3 out of 6 in the Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2000

b:118.0
occ:1.00
 SG B:CYS1095 2.3 49.2 1.0
SG B:CYS1098 2.3 50.7 1.0
SG B:CYS1107 2.3 59.2 1.0
SG B:CYS1110 2.3 67.7 1.0
N B:CYS1098 3.3 46.1 1.0
CB B:CYS1110 3.3 60.7 1.0
CB B:CYS1095 3.3 43.9 1.0
CB B:CYS1098 3.5 44.5 1.0
CB B:CYS1107 3.7 59.1 1.0
CB B:LYS1097 3.8 44.1 1.0
CA B:CYS1098 4.0 41.5 1.0
N B:CYS1110 4.1 61.7 1.0
O B:CYS1098 4.3 53.7 1.0
C B:LYS1097 4.3 46.8 1.0
CA B:CYS1110 4.3 62.1 1.0
CA B:LYS1097 4.4 42.1 1.0
CG B:LYS1097 4.4 48.0 1.0
N B:LYS1097 4.4 46.8 1.0
C B:CYS1098 4.6 47.2 1.0
CA B:CYS1095 4.7 42.6 1.0
CA B:CYS1107 4.9 58.3 1.0

Zinc binding site 4 out of 6 in 7z31

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Zinc binding site 4 out of 6 in the Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore). within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn2000

b:104.7
occ:1.00
 SG I:CYS8 2.2 72.3 1.0
SG I:CYS5 2.2 68.5 1.0
SG I:CYS26 2.3 71.0 1.0
SG I:CYS29 2.3 77.3 1.0
CB I:CYS5 2.5 63.5 1.0
CB I:CYS29 3.5 70.4 1.0
N I:CYS8 3.5 63.2 1.0
CB I:CYS8 3.6 66.2 1.0
CB I:CYS26 3.8 64.9 1.0
O I:ARG27 3.9 69.0 1.0
CA I:CYS5 4.0 61.7 1.0
CA I:CYS8 4.0 65.8 1.0
CB I:ASN10 4.2 56.2 1.0
N I:ASN10 4.2 57.7 1.0
C I:CYS8 4.4 64.5 1.0
N I:ASN9 4.4 61.1 1.0
OG I:SER28 4.4 70.9 1.0
CB I:SER7 4.4 68.3 1.0
C I:SER7 4.6 65.6 1.0
C I:CYS5 4.6 62.8 1.0
N I:SER7 4.7 64.6 1.0
CB I:TYR31 4.7 67.5 1.0
CA I:ASN10 4.7 55.1 1.0
CA I:CYS29 4.7 70.8 1.0
N I:CYS5 4.7 62.6 1.0
CA I:SER7 4.8 66.1 1.0
N I:CYS29 4.9 68.8 1.0
O I:CYS5 4.9 67.2 1.0

Zinc binding site 5 out of 6 in 7z31

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Zinc binding site 5 out of 6 in the Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore). within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2000

b:50.2
occ:1.00
 SG J:CYS10 2.2 20.7 1.0
SG J:CYS45 2.2 16.6 1.0
SG J:CYS7 2.3 17.4 1.0
SG J:CYS46 2.3 24.4 1.0
N J:CYS46 2.8 13.4 1.0
CB J:CYS45 3.2 14.2 1.0
CB J:CYS7 3.3 3.5 1.0
CA J:CYS46 3.3 6.8 1.0
CB J:CYS10 3.4 8.6 1.0
CB J:CYS46 3.4 11.9 1.0
C J:CYS45 3.4 12.6 1.0
CA J:CYS45 3.8 10.8 1.0
N J:CYS10 3.8 16.8 1.0
NE J:ARG43 4.1 17.1 1.0
O J:CYS45 4.2 18.5 1.0
CA J:CYS10 4.2 9.7 1.0
CB J:ARG43 4.3 13.8 1.0
N J:CYS45 4.3 7.6 1.0
CD J:ARG43 4.6 17.4 1.0
CB J:SER9 4.7 14.8 1.0
CA J:CYS7 4.8 0.5 1.0
C J:CYS46 4.8 11.6 1.0
O J:ARG43 4.9 21.9 1.0
C J:SER9 4.9 23.5 1.0

Zinc binding site 6 out of 6 in 7z31

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Zinc binding site 6 out of 6 in the Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Yeast Rna Polymerase III-TY1 Integrase Complex at 2.7 A (Focus Subunit C11, No C11 C-Terminal Zn-Ribbon in the Funnel Pore). within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:96.2
occ:1.00
 SG L:CYS34 2.2 47.1 1.0
SG L:CYS31 2.3 51.2 1.0
SG L:CYS51 2.3 53.9 1.0
SG L:CYS48 2.3 53.2 1.0
CB L:CYS31 2.9 32.8 1.0
CB L:CYS48 3.0 46.7 1.0
CB L:CYS34 3.7 44.9 1.0
CB L:CYS51 3.9 52.4 1.0
N L:CYS34 3.9 44.6 1.0
N L:CYS51 4.0 53.4 1.0
CB L:HIS53 4.2 41.4 1.0
CA L:CYS31 4.3 34.3 1.0
CA L:CYS34 4.4 42.7 1.0
CA L:CYS51 4.4 49.3 1.0
CB L:GLU33 4.4 39.8 1.0
CA L:CYS48 4.5 50.9 1.0
C L:CYS51 4.7 54.6 1.0
O L:CYS51 4.8 61.0 1.0
CB L:ASP50 4.8 55.0 1.0
N L:HIS53 4.8 37.6 1.0
C L:GLU33 4.9 42.8 1.0
CG L:GLU33 4.9 42.4 1.0
N L:GLU33 4.9 40.0 1.0
C L:CYS31 5.0 42.5 1.0
OG L:SER36 5.0 49.0 1.0
CA L:GLU33 5.0 38.2 1.0

Reference:

P.Q.Nguyen, S.Huecas, A.Asif-Laidin, A.Plaza-Pegueroles, B.Capuzzi, N.Palmic, C.Conesa, J.Acker, J.Reguera, P.Lesage, C.Fernandez-Tornero. Structural Basis of TY1 Integrase Tethering to Rna Polymerase III For Targeted Retrotransposon Integration. Nat Commun V. 14 1729 2023.
ISSN: ESSN 2041-1723
PubMed: 36977686
DOI: 10.1038/S41467-023-37109-4
Page generated: Wed Oct 30 16:14:06 2024

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