Zinc in PDB 8bws: Structure of Yeast Rna Polymerase III Elongation Complex at 3.3 A

Enzymatic activity of Structure of Yeast Rna Polymerase III Elongation Complex at 3.3 A

All present enzymatic activity of Structure of Yeast Rna Polymerase III Elongation Complex at 3.3 A:
2.7.7.6;

Other elements in 8bws:

The structure of Structure of Yeast Rna Polymerase III Elongation Complex at 3.3 A 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 Elongation Complex at 3.3 A (pdb code 8bws). 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 Elongation Complex at 3.3 A, PDB code: 8bws:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8bws

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Zinc binding site 1 out of 6 in the Structure of Yeast Rna Polymerase III Elongation Complex at 3.3 A


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 Elongation Complex at 3.3 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1501

b:88.2
occ:1.00
 NE2 A:HIS80 2.0 56.3 1.0
SG A:CYS70 2.3 71.3 1.0
SG A:CYS77 2.3 62.7 1.0
SG A:CYS67 2.3 71.6 1.0
CB A:CYS67 2.8 71.6 1.0
CD2 A:HIS80 2.9 56.3 1.0
CE1 A:HIS80 2.9 56.3 1.0
CB A:CYS77 3.6 62.7 1.0
CB A:CYS70 3.7 71.3 1.0
N A:CYS70 3.9 71.3 1.0
ND1 A:HIS80 3.9 56.3 1.0
CG A:HIS80 4.0 56.3 1.0
CA A:CYS67 4.2 71.6 1.0
CA A:CYS77 4.3 62.7 1.0
CA A:CYS70 4.4 71.3 1.0
CA A:GLY59 4.5 64.2 1.0
N A:GLY79 4.6 54.4 1.0
O A:CYS67 4.7 71.6 1.0
CB A:THR69 4.7 68.1 1.0
C A:CYS67 4.7 71.6 1.0
C A:CYS77 4.8 62.7 1.0
C A:THR69 4.8 68.1 1.0
N A:GLY59 4.9 64.2 1.0
N A:HIS78 4.9 56.8 1.0
CA A:GLY79 4.9 54.4 1.0
N A:THR69 5.0 68.1 1.0

Zinc binding site 2 out of 6 in 8bws

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Zinc binding site 2 out of 6 in the Structure of Yeast Rna Polymerase III Elongation Complex at 3.3 A


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 Elongation Complex at 3.3 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1502

b:80.2
occ:1.00
 SG A:CYS157 2.0 69.1 1.0
SG A:CYS154 2.1 73.1 1.0
SG A:CYS110 2.1 59.0 1.0
CB A:CYS107 2.2 59.2 1.0
SG A:CYS107 2.3 59.2 1.0
CB A:CYS154 2.8 73.1 1.0
N A:CYS110 3.3 59.0 1.0
CB A:CYS110 3.4 59.0 1.0
CB A:CYS157 3.6 69.1 1.0
CA A:CYS107 3.7 59.2 1.0
CA A:CYS110 3.8 59.0 1.0
N A:ASN109 4.0 63.6 1.0
CA A:CYS154 4.2 73.1 1.0
N A:LYS108 4.2 59.9 1.0
N A:SER111 4.3 55.5 1.0
C A:ASN109 4.3 63.6 1.0
C A:CYS107 4.4 59.2 1.0
CB A:ASN109 4.4 63.6 1.0
C A:CYS110 4.4 59.0 1.0
CA A:ASN109 4.5 63.6 1.0
N A:CYS157 4.5 69.1 1.0
N A:CYS107 4.6 59.2 1.0
CA A:CYS157 4.6 69.1 1.0
OD1 A:ASN161 4.7 68.0 1.0
N A:ALA112 4.8 53.9 1.0
CB A:ALA159 4.8 68.2 1.0

Zinc binding site 3 out of 6 in 8bws

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Zinc binding site 3 out of 6 in the Structure of Yeast Rna Polymerase III Elongation Complex at 3.3 A


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 Elongation Complex at 3.3 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2000

b:118.1
occ:1.00
 SG B:CYS1095 2.2 55.0 1.0
SG B:CYS1110 2.3 74.7 1.0
SG B:CYS1107 2.3 66.1 1.0
SG B:CYS1098 2.3 55.3 1.0
CB B:CYS1095 3.1 55.0 1.0
CB B:CYS1110 3.3 74.7 1.0
N B:CYS1098 3.7 55.3 1.0
CB B:CYS1107 3.7 66.1 1.0
CB B:CYS1098 3.8 55.3 1.0
O B:CYS1098 3.8 55.3 1.0
N B:CYS1110 3.8 74.7 1.0
CA B:CYS1110 4.2 74.7 1.0
CA B:CYS1098 4.2 55.3 1.0
CB B:LYS1097 4.4 53.9 1.0
C B:CYS1098 4.5 55.3 1.0
CA B:CYS1095 4.5 55.0 1.0
C B:LYS1097 4.8 53.9 1.0
CB B:THR1109 4.8 65.4 1.0
N B:LYS1097 4.9 53.9 1.0
C B:THR1109 4.9 65.4 1.0
CA B:LYS1097 4.9 53.9 1.0
NZ B:LYS1097 4.9 53.9 1.0

Zinc binding site 4 out of 6 in 8bws

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Zinc binding site 4 out of 6 in the Structure of Yeast Rna Polymerase III Elongation Complex at 3.3 A


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 Elongation Complex at 3.3 A within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn2002

b:157.1
occ:1.00
 CB I:CYS26 2.2 136.9 1.0
SG I:CYS5 2.3 127.0 1.0
SG I:CYS29 2.3 139.8 1.0
SG I:CYS26 2.6 136.9 1.0
CB I:CYS29 2.8 139.8 1.0
SG I:CYS8 2.9 122.8 1.0
CB I:CYS8 2.9 122.8 1.0
CA I:CYS26 3.5 136.9 1.0
C I:CYS26 3.8 136.9 1.0
CB I:CYS5 3.8 127.0 1.0
O I:ARG27 3.9 135.5 1.0
O I:CYS26 3.9 136.9 1.0
N I:CYS26 4.1 136.9 1.0
CA I:CYS29 4.3 139.8 1.0
CA I:CYS8 4.4 122.8 1.0
N I:CYS29 4.6 139.8 1.0
CB I:ASN10 4.6 116.7 1.0
N I:ARG27 4.6 135.5 1.0
C I:ARG27 4.8 135.5 1.0
CB I:TYR31 4.8 142.2 1.0
N I:ASN10 4.8 116.7 1.0
C I:CYS8 4.9 122.8 1.0

Zinc binding site 5 out of 6 in 8bws

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Zinc binding site 5 out of 6 in the Structure of Yeast Rna Polymerase III Elongation Complex at 3.3 A


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 Elongation Complex at 3.3 A within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2000

b:71.1
occ:1.00
 SG J:CYS7 2.3 42.5 1.0
SG J:CYS45 2.3 48.2 1.0
SG J:CYS46 2.3 47.1 1.0
SG J:CYS10 2.8 47.3 1.0
CB J:CYS10 2.8 47.3 1.0
CB J:CYS7 3.3 42.5 1.0
N J:CYS46 3.3 47.1 1.0
CB J:CYS45 3.5 48.2 1.0
N J:CYS10 3.7 47.3 1.0
CB J:CYS46 3.7 47.1 1.0
CA J:CYS46 3.8 47.1 1.0
CA J:CYS10 3.8 47.3 1.0
C J:CYS45 3.9 48.2 1.0
N J:GLY11 4.2 41.2 1.0
NE J:ARG43 4.3 48.0 1.0
CA J:CYS45 4.3 48.2 1.0
O J:CYS7 4.4 42.5 1.0
N J:LYS12 4.4 38.5 1.0
CB J:LYS12 4.5 38.5 1.0
C J:CYS10 4.6 47.3 1.0
NH2 J:ARG43 4.6 48.0 1.0
CA J:CYS7 4.6 42.5 1.0
O J:CYS45 4.8 48.2 1.0
C J:CYS7 4.8 42.5 1.0
CB J:ARG43 4.8 48.0 1.0
C J:SER9 4.8 39.2 1.0
N J:CYS45 4.9 48.2 1.0
CZ J:ARG43 5.0 48.0 1.0

Zinc binding site 6 out of 6 in 8bws

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Zinc binding site 6 out of 6 in the Structure of Yeast Rna Polymerase III Elongation Complex at 3.3 A


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 Elongation Complex at 3.3 A within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn2001

b:120.1
occ:1.00
 SG L:CYS51 2.3 100.6 1.0
SG L:CYS34 2.3 90.9 1.0
SG L:CYS48 2.3 97.6 1.0
SG L:CYS31 2.3 87.4 1.0
CB L:CYS48 2.8 97.6 1.0
CB L:CYS34 3.1 90.9 1.0
CB L:CYS31 3.1 87.4 1.0
N L:CYS51 3.6 100.6 1.0
N L:CYS34 3.7 90.9 1.0
CB L:CYS51 3.7 100.6 1.0
CA L:CYS34 4.0 90.9 1.0
CA L:CYS51 4.1 100.6 1.0
CB L:HIS53 4.1 86.7 1.0
O L:CYS51 4.2 100.6 1.0
C L:CYS51 4.3 100.6 1.0
CA L:CYS48 4.3 97.6 1.0
N L:ASP50 4.5 101.7 1.0
N L:LYS49 4.5 100.3 1.0
N L:HIS53 4.6 86.7 1.0
CA L:CYS31 4.6 87.4 1.0
CB L:ASP50 4.6 101.7 1.0
C L:ASP50 4.6 101.7 1.0
OG L:SER36 4.7 85.6 1.0
CB L:GLU33 4.7 90.0 1.0
C L:CYS48 4.8 97.6 1.0
C L:GLU33 4.8 90.0 1.0
CA L:ASP50 4.8 101.7 1.0
CA L:HIS53 4.9 86.7 1.0
C L:CYS34 5.0 90.9 1.0
N L:GLU33 5.0 90.0 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 18:27:16 2024

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