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Zinc in PDB 6exv: Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin

Enzymatic activity of Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin

All present enzymatic activity of Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin:
2.7.7.6;

Other elements in 6exv:

The structure of Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin (pdb code 6exv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin, PDB code: 6exv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6exv

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Zinc binding site 1 out of 8 in the Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:69.3
occ:1.00
 SG A:CYS81 2.4 40.5 1.0
SG A:CYS74 2.5 45.6 1.0
SG A:CYS71 2.5 46.9 1.0
NE2 A:HIS84 2.9 27.7 1.0
CB A:CYS71 3.0 46.9 1.0
O A:CYS74 3.1 45.6 1.0
CD2 A:HIS84 3.4 27.7 1.0
OG1 A:THR73 3.6 43.8 1.0
N A:CYS74 3.6 45.6 1.0
CB A:CYS81 3.7 40.5 1.0
CB A:CYS74 3.8 45.6 1.0
C A:CYS74 3.9 45.6 1.0
CA A:CYS74 4.0 45.6 1.0
CE1 A:HIS84 4.1 27.7 1.0
CA A:CYS71 4.4 46.9 1.0
CA A:GLY63 4.4 34.1 1.0
C A:THR73 4.6 43.8 1.0
C A:CYS71 4.6 46.9 1.0
CA A:CYS81 4.7 40.5 1.0
N A:GLY63 4.7 34.1 1.0
CG A:HIS84 4.7 27.7 1.0
N A:THR73 4.8 43.8 1.0
CB A:THR73 4.9 43.8 1.0
C A:GLY63 4.9 34.1 1.0
O A:CYS71 4.9 46.9 1.0

Zinc binding site 2 out of 8 in 6exv

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Zinc binding site 2 out of 8 in the Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:0.1
occ:1.00
 SG A:CYS154 2.5 79.6 1.0
CB A:CYS114 2.5 63.4 1.0
SG A:CYS114 2.7 63.4 1.0
SG A:CYS111 2.7 62.2 1.0
CB A:CYS184 3.2 80.7 1.0
CB A:CYS154 3.5 79.6 1.0
CB A:CYS111 3.7 62.2 1.0
O A:CYS114 3.9 63.4 1.0
CA A:CYS114 3.9 63.4 1.0
SG A:CYS184 4.0 80.7 1.0
C A:CYS114 4.3 63.4 1.0
CA A:CYS184 4.5 80.7 1.0
N A:CYS114 4.5 63.4 1.0
N A:CYS184 4.7 80.7 1.0
O A:GLY183 4.8 78.1 1.0
NE2 A:GLN188 4.8 66.9 1.0
CA A:CYS154 4.9 79.6 1.0
C A:GLY183 4.9 78.1 1.0
O A:PHE112 5.0 58.7 1.0

Zinc binding site 3 out of 8 in 6exv

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Zinc binding site 3 out of 8 in the Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:90.0
occ:1.00
 SG B:CYS1122 2.4 44.4 1.0
SG B:CYS1119 2.5 41.5 1.0
SG B:CYS1137 3.0 53.6 1.0
SG B:CYS1140 3.1 62.0 1.0
CB B:CYS1119 3.2 41.5 1.0
CB B:CYS1140 3.4 62.0 1.0
N B:CYS1122 3.9 44.4 1.0
CB B:CYS1122 3.9 44.4 1.0
CB B:CYS1137 4.0 53.6 1.0
CB B:ASN1142 4.3 57.5 1.0
CA B:CYS1122 4.4 44.4 1.0
ND2 B:ASN1142 4.5 57.5 1.0
CB B:LEU1121 4.6 47.8 1.0
CA B:CYS1140 4.7 62.0 1.0
N B:CYS1140 4.7 62.0 1.0
CA B:CYS1119 4.7 41.5 1.0
C B:CYS1122 4.8 44.4 1.0
N B:LEU1121 4.9 47.8 1.0
C B:LEU1121 4.9 47.8 1.0
CG B:ASN1142 5.0 57.5 1.0
O B:CYS1122 5.0 44.4 1.0

Zinc binding site 4 out of 8 in 6exv

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Zinc binding site 4 out of 8 in the Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:0.2
occ:1.00
 N C:CYS94 2.2 72.3 1.0
SG C:CYS94 2.5 72.3 1.0
CB C:CYS94 2.6 72.3 1.0
SG C:CYS90 2.6 89.2 1.0
C C:PHE93 2.6 72.7 1.0
CA C:CYS94 2.9 72.3 1.0
SG C:CYS97 3.2 64.2 1.0
CA C:PHE93 3.2 72.7 1.0
O C:PHE93 3.3 72.7 1.0
C C:CYS94 3.7 72.3 1.0
O C:CYS94 3.7 72.3 1.0
N C:PHE93 4.0 72.7 1.0
O C:GLU91 4.1 88.0 1.0
CB C:CYS90 4.1 89.2 1.0
CB C:PHE93 4.5 72.7 1.0
C C:GLU92 4.6 81.9 1.0
SG C:CYS88 4.6 80.5 1.0
O C:GLU92 4.7 81.9 1.0
CB C:CYS97 4.8 64.2 1.0
N C:PRO95 4.9 69.5 1.0
N C:CYS97 4.9 64.2 1.0
C C:GLU91 4.9 88.0 1.0

Zinc binding site 5 out of 8 in 6exv

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Zinc binding site 5 out of 8 in the Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:76.5
occ:1.00
 O I:ASN22 2.1 65.9 1.0
N I:ASN22 2.2 65.9 1.0
C I:ASN22 2.4 65.9 1.0
CB I:CYS17 2.5 70.9 1.0
CA I:ASN22 2.6 65.9 1.0
N I:CYS17 3.0 70.9 1.0
CB I:ASN22 3.1 65.9 1.0
CA I:CYS17 3.3 70.9 1.0
C I:ASN21 3.4 67.0 1.0
N I:MET23 3.4 68.5 1.0
CA I:ASN21 3.8 67.0 1.0
N I:ASN21 3.9 67.0 1.0
SG I:CYS17 4.0 70.9 1.0
SG I:CYS39 4.1 77.5 1.0
C I:PHE16 4.1 62.3 1.0
SG I:CYS20 4.1 72.2 1.0
C I:MET23 4.1 68.5 1.0
CA I:MET23 4.2 68.5 1.0
O I:MET23 4.2 68.5 1.0
C I:CYS17 4.3 70.9 1.0
CG I:ASN22 4.3 65.9 1.0
O I:ASN21 4.4 67.0 1.0
CA I:PHE16 4.4 62.3 1.0
O I:CYS17 4.5 70.9 1.0
N I:LEU24 4.6 68.7 1.0
OD1 I:ASN22 4.6 65.9 1.0
CD2 I:LEU24 4.6 68.7 1.0
C I:CYS20 4.7 72.2 1.0
CG I:LEU24 4.8 68.7 1.0
CB I:PHE16 4.9 62.3 1.0
CB I:CYS39 4.9 77.5 1.0

Zinc binding site 6 out of 8 in 6exv

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Zinc binding site 6 out of 8 in the Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:76.5
occ:1.00
 SG I:CYS89 2.5 47.0 1.0
SG I:CYS114 2.5 36.0 1.0
SG I:CYS86 2.5 50.2 1.0
SG I:CYS119 2.5 56.3 1.0
CB I:CYS114 3.1 36.0 1.0
CB I:CYS86 3.2 50.2 1.0
CB I:CYS119 3.7 56.3 1.0
CB I:CYS89 3.9 47.0 1.0
CB I:HIS121 3.9 35.9 1.0
N I:CYS89 4.3 47.0 1.0
N I:HIS121 4.5 35.9 1.0
CA I:CYS114 4.6 36.0 1.0
CA I:CYS86 4.7 50.2 1.0
CA I:CYS89 4.7 47.0 1.0
CA I:HIS121 4.8 35.9 1.0
CG I:HIS121 4.9 35.9 1.0
CZ3 I:TRP123 4.9 33.0 1.0
CB I:HIS91 4.9 50.9 1.0
CA I:CYS119 5.0 56.3 1.0

Zinc binding site 7 out of 8 in 6exv

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Zinc binding site 7 out of 8 in the Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:71.6
occ:1.00
 O J:CYS44 2.1 27.1 1.0
SG J:CYS45 2.5 27.6 1.0
C J:CYS44 2.7 27.1 1.0
SG J:CYS10 2.7 28.6 1.0
SG J:CYS44 2.9 27.1 1.0
N J:CYS45 3.2 27.6 1.0
CB J:CYS10 3.2 28.6 1.0
CB J:CYS44 3.4 27.1 1.0
CA J:CYS44 3.6 27.1 1.0
CB J:CYS45 3.6 27.6 1.0
CA J:CYS45 3.7 27.6 1.0
N J:CYS10 3.8 28.6 1.0
CA J:CYS10 4.2 28.6 1.0
CB J:CYS7 4.2 28.0 1.0
SG J:CYS7 4.3 28.0 1.0
N J:CYS44 4.4 27.1 1.0
CB J:THR9 4.5 25.5 1.0
O J:ARG42 4.7 27.0 1.0
C J:THR9 4.9 25.5 1.0
CG J:ARG42 4.9 27.0 1.0
NE J:ARG42 5.0 27.0 1.0

Zinc binding site 8 out of 8 in 6exv

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Zinc binding site 8 out of 8 in the Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.9
occ:1.00
 SG L:CYS22 2.4 42.6 1.0
SG L:CYS19 2.4 39.6 1.0
SG L:CYS39 2.4 58.0 1.0
SG L:CYS36 2.5 56.3 1.0
CB L:CYS19 2.9 39.6 1.0
CB L:CYS36 3.3 56.3 1.0
CB L:CYS39 3.8 58.0 1.0
CB L:CYS22 3.9 42.6 1.0
OG1 L:THR24 4.0 44.8 1.0
N L:CYS22 4.1 42.6 1.0
CA L:CYS19 4.4 39.6 1.0
CA L:CYS22 4.5 42.6 1.0
N L:HIS23 4.5 42.6 1.0
O L:ARG37 4.5 60.9 1.0
CA L:CYS36 4.7 56.3 1.0
N L:ARG37 4.8 60.9 1.0
N L:THR24 4.8 44.8 1.0
C L:CYS22 4.8 42.6 1.0
CB L:TYR41 4.8 45.8 1.0
N L:GLU21 5.0 44.1 1.0

Reference:

X.Liu, L.Farnung, C.Wigge, P.Cramer. Cryo-Em Structure of A Mammalian Rna Polymerase II Elongation Complex Inhibited By Alpha-Amanitin. J. Biol. Chem. V. 293 7189 2018.
ISSN: ESSN 1083-351X
PubMed: 29550768
DOI: 10.1074/JBC.RA118.002545
Page generated: Mon Oct 28 20:29:04 2024

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