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Zinc in PDB 6eu0: Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic)

Enzymatic activity of Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic)

All present enzymatic activity of Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic):
2.7.7.6;

Other elements in 6eu0:

The structure of Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic) (pdb code 6eu0). 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 III Open Pre-Initiation Complex (Oc-Pic), PDB code: 6eu0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6eu0

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Zinc binding site 1 out of 7 in the Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2000

b:24.6
occ:1.00
 SG A:CYS77 2.5 15.6 1.0
NE2 A:HIS80 2.6 8.6 1.0
CB A:ALA68 2.9 30.0 1.0
CD2 A:HIS80 3.4 8.6 1.0
N A:CYS70 3.5 31.1 1.0
C A:ALA68 3.6 30.0 1.0
O A:CYS70 3.6 31.1 1.0
CB A:CYS77 3.6 15.6 1.0
N A:THR69 3.6 36.3 1.0
CA A:ALA68 3.7 30.0 1.0
CE1 A:HIS80 3.7 8.6 1.0
CB A:CYS70 3.8 31.1 1.0
N A:ALA68 4.0 30.0 1.0
CA A:CYS70 4.1 31.1 1.0
O A:ALA68 4.2 30.0 1.0
C A:CYS70 4.3 31.1 1.0
CA A:CYS77 4.4 15.6 1.0
C A:THR69 4.4 36.3 1.0
CA A:THR69 4.5 36.3 1.0
CG A:HIS80 4.6 8.6 1.0
SG A:CYS70 4.7 31.1 1.0
ND1 A:HIS80 4.7 8.6 1.0
CB A:THR69 4.8 36.3 1.0
SG A:CYS67 4.9 30.4 1.0

Zinc binding site 2 out of 7 in 6eu0

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Zinc binding site 2 out of 7 in the Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:38.3
occ:1.00
 SG A:CYS107 2.5 25.6 1.0
SG A:CYS157 2.5 32.1 1.0
SG A:CYS110 2.5 24.9 1.0
SG A:CYS154 2.7 30.8 1.0
N A:CYS110 3.3 24.9 1.0
CB A:CYS157 3.4 32.1 1.0
CB A:CYS107 3.5 25.6 1.0
CB A:CYS154 3.6 30.8 1.0
CB A:CYS110 3.6 24.9 1.0
CA A:CYS110 3.9 24.9 1.0
N A:ASN109 4.1 28.6 1.0
CB A:ASN109 4.1 28.6 1.0
N A:SER111 4.2 18.1 1.0
C A:ASN109 4.3 28.6 1.0
CA A:ASN109 4.4 28.6 1.0
C A:CYS110 4.4 24.9 1.0
N A:CYS157 4.6 32.1 1.0
CA A:CYS157 4.6 32.1 1.0
N A:LYS108 4.7 29.6 1.0
CA A:CYS107 4.9 25.6 1.0
N A:ALA112 4.9 20.2 1.0

Zinc binding site 3 out of 7 in 6eu0

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Zinc binding site 3 out of 7 in the Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:37.0
occ:1.00
 SG B:CYS1110 2.6 28.4 1.0
CB B:CYS1107 2.6 23.8 1.0
SG B:CYS1107 3.0 23.8 1.0
O B:CYS1098 3.3 15.4 1.0
CG2 B:THR1109 3.6 26.1 1.0
O B:LYS1097 3.7 10.4 1.0
CB B:CYS1095 3.8 14.4 1.0
SG B:CYS1095 4.0 14.4 1.0
CB B:CYS1110 4.0 28.4 1.0
SG B:CYS1098 4.0 15.4 1.0
CA B:CYS1107 4.1 23.8 1.0
N B:CYS1110 4.2 28.4 1.0
C B:CYS1098 4.2 15.4 1.0
C B:CYS1107 4.5 23.8 1.0
N B:LEU1100 4.6 8.1 1.0
CA B:CYS1110 4.6 28.4 1.0
O B:CYS1110 4.7 28.4 1.0
N B:CYS1107 4.7 23.8 1.0
O B:CYS1107 4.8 23.8 1.0
CA B:GLY1099 4.8 11.9 1.0
C B:THR1109 4.9 26.1 1.0
C B:LYS1097 4.9 10.4 1.0
N B:GLY1099 4.9 11.9 1.0
CB B:THR1109 4.9 26.1 1.0
N B:THR1109 5.0 26.1 1.0

Zinc binding site 4 out of 7 in 6eu0

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Zinc binding site 4 out of 7 in the Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:39.8
occ:1.00
 SG I:CYS8 2.6 52.0 1.0
CB I:CYS29 2.6 63.6 1.0
CB I:CYS26 2.6 62.8 1.0
SG I:CYS26 2.7 62.8 1.0
SG I:CYS29 2.7 63.6 1.0
CB I:CYS8 3.7 52.0 1.0
CB I:ASN10 3.9 43.2 1.0
CA I:CYS29 4.1 63.6 1.0
CA I:CYS26 4.1 62.8 1.0
O I:ASN10 4.5 43.2 1.0
CB I:CYS5 4.6 56.5 1.0
N I:ARG27 4.7 62.3 1.0
CA I:ASN10 4.7 43.2 1.0
C I:CYS29 4.7 63.6 1.0
N I:ASN10 4.7 43.2 1.0
C I:ASN10 4.7 43.2 1.0
N I:CYS29 4.8 63.6 1.0
C I:CYS26 4.8 62.8 1.0
CG I:ASN10 4.8 43.2 1.0
ND2 I:ASN10 4.8 43.2 1.0
O I:CYS29 4.9 63.6 1.0
N I:CYS26 4.9 62.8 1.0
O I:TYR31 5.0 67.3 1.0
SG I:CYS5 5.0 56.5 1.0
CA I:CYS8 5.0 52.0 1.0

Zinc binding site 5 out of 7 in 6eu0

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Zinc binding site 5 out of 7 in the Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:9.1
occ:1.00
 N J:CYS46 2.3 10.2 1.0
C J:CYS45 2.4 10.8 1.0
O J:CYS45 2.5 10.8 1.0
CA J:CYS46 2.6 10.2 1.0
SG J:CYS45 2.6 10.8 1.0
SG J:CYS46 2.6 10.2 1.0
SG J:CYS7 2.8 8.9 1.0
CB J:CYS46 3.1 10.2 1.0
CA J:CYS45 3.5 10.8 1.0
CB J:CYS45 3.5 10.8 1.0
CB J:CYS7 3.5 8.9 1.0
CB J:CYS10 3.6 9.1 1.0
OG J:SER9 4.0 8.9 1.0
C J:CYS46 4.0 10.2 1.0
N J:CYS10 4.1 9.1 1.0
N J:CYS45 4.2 10.8 1.0
CA J:CYS10 4.4 9.1 1.0
N J:ARG47 4.7 11.0 1.0
O J:CYS46 4.8 10.2 1.0
SG J:CYS10 4.8 9.1 1.0
O J:ARG43 4.9 10.6 1.0
C J:CYS10 5.0 9.1 1.0
CA J:CYS7 5.0 8.9 1.0

Zinc binding site 6 out of 7 in 6eu0

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Zinc binding site 6 out of 7 in the Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:64.3
occ:1.00
 N L:CYS34 2.4 20.1 1.0
SG L:CYS51 2.5 19.9 1.0
CB L:CYS51 2.6 19.9 1.0
CB L:CYS34 2.9 20.1 1.0
CA L:CYS34 3.0 20.1 1.0
CB L:CYS31 3.4 15.4 1.0
C L:GLU33 3.5 20.1 1.0
N L:SER35 3.5 17.4 1.0
C L:CYS34 3.5 20.1 1.0
SG L:CYS34 3.8 20.1 1.0
CB L:GLU33 3.8 20.1 1.0
N L:GLU33 3.9 20.1 1.0
SG L:CYS31 3.9 15.4 1.0
CA L:GLU33 3.9 20.1 1.0
CA L:CYS51 4.1 19.9 1.0
O L:CYS34 4.5 20.1 1.0
O L:GLU33 4.5 20.1 1.0
N L:CYS51 4.5 19.9 1.0
OG L:SER36 4.6 17.1 1.0
N L:SER36 4.6 17.1 1.0
CG L:GLU33 4.7 20.1 1.0
CA L:SER35 4.7 17.4 1.0
CA L:CYS31 4.8 15.4 1.0
N L:ALA32 4.8 11.3 1.0

Zinc binding site 7 out of 7 in 6eu0

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Zinc binding site 7 out of 7 in the Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase III Open Pre-Initiation Complex (Oc-Pic) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Zn601

b:43.3
occ:1.00
 SG Z:CYS7 2.5 59.0 1.0
SG Z:CYS28 2.5 38.4 1.0
SG Z:CYS25 2.5 42.6 1.0
O Z:LYS26 3.2 37.1 1.0
CB Z:CYS25 3.6 42.6 1.0
SG Z:CYS4 3.7 57.8 1.0
CB Z:CYS7 3.8 59.0 1.0
CB Z:CYS28 4.1 38.4 1.0
N Z:LYS26 4.2 37.1 1.0
C Z:LYS26 4.3 37.1 1.0
N Z:CYS7 4.3 59.0 1.0
N Z:CYS28 4.4 38.4 1.0
N Z:GLY29 4.4 34.8 1.0
CA Z:CYS7 4.7 59.0 1.0
CG2 Z:THR10 4.7 44.8 1.0
CA Z:CYS28 4.7 38.4 1.0
C Z:CYS25 4.8 42.6 1.0
CA Z:CYS25 4.8 42.6 1.0
CB Z:ASN6 4.8 52.0 1.0
CA Z:LYS26 4.9 37.1 1.0
N Z:VAL30 4.9 32.1 1.0

Reference:

G.Abascal-Palacios, E.P.Ramsay, F.Beuron, E.Morris, A.Vannini. Structural Basis of Rna Polymerase III Transcription Initiation. Nature V. 553 301 2018.
ISSN: ESSN 1476-4687
PubMed: 29345637
DOI: 10.1038/NATURE25441
Page generated: Mon Oct 28 20:23:41 2024

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