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Zinc in PDB 1k83: Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin

Enzymatic activity of Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin

All present enzymatic activity of Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin, PDB code: 1k83 was solved by D.A.Bushnell, P.Cramer, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.80
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 122.510, 222.480, 374.230, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 28

Other elements in 1k83:

The structure of Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin (pdb code 1k83). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin, PDB code: 1k83:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1k83

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Zinc binding site 1 out of 8 in the Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3006

b:64.1
occ:1.00
 SG A:CYS110 2.3 57.0 1.0
SG A:CYS148 2.5 79.2 1.0
SG A:CYS167 2.5 73.9 1.0
SG A:CYS107 2.7 61.1 1.0
CB A:CYS167 3.0 73.6 1.0
CB A:CYS148 3.0 79.7 1.0
CB A:CYS107 3.1 61.0 1.0
O A:CYS167 3.6 75.7 1.0
CB A:CYS110 3.7 59.9 1.0
N A:CYS110 4.0 62.1 1.0
CA A:CYS167 4.2 74.5 1.0
C A:CYS167 4.2 73.9 1.0
CA A:CYS110 4.5 60.1 1.0
CA A:CYS148 4.5 80.9 1.0
CA A:CYS107 4.6 59.9 1.0
CB A:HIS109 4.7 68.7 1.0
CB A:LYS112 4.9 56.4 1.0
O A:CYS148 5.0 81.7 1.0

Zinc binding site 2 out of 8 in 1k83

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Zinc binding site 2 out of 8 in the Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3008

b:82.0
occ:1.00
 SG A:CYS70 2.5 0.8 1.0
NE2 A:HIS80 2.5 82.3 1.0
SG A:CYS67 2.7 0.6 1.0
SG A:CYS77 2.7 90.9 1.0
CD2 A:HIS80 3.1 82.6 1.0
CB A:CYS77 3.3 92.2 1.0
CB A:CYS67 3.4 0.4 1.0
O A:CYS67 3.6 0.9 1.0
CE1 A:HIS80 3.7 83.1 1.0
CA A:CYS77 4.0 92.0 1.0
O A:GLN71 4.1 0.1 1.0
CB A:CYS70 4.2 0.1 1.0
CG A:HIS80 4.4 82.3 1.0
C A:CYS67 4.5 0.2 1.0
CA A:CYS67 4.5 0.8 1.0
O A:CYS70 4.6 0.3 1.0
ND1 A:HIS80 4.6 82.4 1.0
C A:CYS77 4.6 90.4 1.0
CD A:PRO78 4.7 89.2 1.0
N A:PRO78 4.8 89.0 1.0
C A:CYS70 4.9 0.5 1.0
CA A:GLY59 4.9 0.9 1.0

Zinc binding site 3 out of 8 in 1k83

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Zinc binding site 3 out of 8 in the Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3007

b:65.0
occ:1.00
 SG B:CYS1182 2.6 98.5 1.0
SG B:CYS1166 2.6 66.7 1.0
SG B:CYS1163 2.6 61.3 1.0
SG B:CYS1185 2.7 91.9 1.0
CB B:CYS1163 2.9 62.4 1.0
CB B:CYS1185 3.2 94.9 1.0
CB B:CYS1166 3.6 66.0 1.0
CB B:CYS1182 3.9 1.0 1.0
N B:CYS1166 4.0 65.2 1.0
OG1 B:THR1170 4.2 70.9 1.0
O B:CYS1166 4.2 68.7 1.0
CA B:CYS1166 4.3 65.9 1.0
CA B:CYS1163 4.4 63.0 1.0
O B:CYS1182 4.5 0.5 1.0
CA B:CYS1185 4.6 95.7 1.0
C B:CYS1166 4.7 66.4 1.0
CB B:ILE1165 4.8 67.6 1.0
O B:LYS1183 4.8 0.6 1.0
ND2 B:ASN1187 4.8 98.6 1.0
N B:CYS1185 4.9 96.5 1.0

Zinc binding site 4 out of 8 in 1k83

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Zinc binding site 4 out of 8 in the Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3002

b:49.2
occ:1.00
 SG C:CYS86 2.3 47.1 1.0
SG C:CYS92 2.3 54.1 1.0
SG C:CYS88 2.4 54.8 1.0
SG C:CYS95 2.6 54.5 1.0
CB C:CYS88 3.1 53.6 1.0
CB C:CYS86 3.2 47.4 1.0
N C:CYS92 3.2 55.2 1.0
CB C:CYS92 3.3 52.6 1.0
CB C:CYS95 3.5 52.7 1.0
CA C:CYS92 3.8 54.0 1.0
N C:CYS95 4.0 53.8 1.0
C C:HIS91 4.1 56.7 1.0
O C:CYS92 4.2 53.5 1.0
N C:CYS88 4.2 51.8 1.0
CA C:CYS88 4.2 54.1 1.0
C C:CYS92 4.3 53.5 1.0
CA C:HIS91 4.3 57.8 1.0
CA C:CYS95 4.4 53.9 1.0
CA C:CYS86 4.5 48.7 1.0
CB C:LYS94 4.5 52.6 1.0
C C:CYS86 4.7 49.2 1.0
C C:LYS94 4.7 53.7 1.0
N C:LYS94 4.8 52.7 1.0
O C:ASP90 4.9 60.2 1.0
N C:HIS91 4.9 58.5 1.0
CA C:LYS94 4.9 52.9 1.0
C C:CYS88 4.9 55.5 1.0
O C:CYS86 5.0 48.8 1.0

Zinc binding site 5 out of 8 in 1k83

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Zinc binding site 5 out of 8 in the Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3003

b:45.4
occ:1.00
 SG I:CYS10 2.2 51.2 1.0
SG I:CYS29 2.4 44.1 1.0
SG I:CYS7 2.4 50.0 1.0
SG I:CYS32 2.4 55.0 1.0
CB I:CYS29 3.2 44.4 1.0
CB I:CYS32 3.2 50.8 1.0
CB I:CYS7 3.3 50.4 1.0
N I:CYS32 3.5 53.0 1.0
CB I:CYS10 3.9 49.7 1.0
CA I:CYS32 3.9 50.5 1.0
N I:CYS10 4.1 50.3 1.0
CB I:TYR34 4.3 41.3 1.0
CB I:THR31 4.3 54.5 1.0
C I:CYS32 4.5 49.1 1.0
CA I:CYS10 4.5 49.5 1.0
C I:THR31 4.6 54.2 1.0
CA I:CYS29 4.7 45.0 1.0
CG2 I:THR31 4.7 55.2 1.0
CA I:CYS7 4.7 50.8 1.0
N I:TYR34 4.8 41.4 1.0
N I:THR31 4.8 50.8 1.0
CA I:THR31 4.9 52.9 1.0
N I:SER33 5.0 47.4 1.0
O I:CYS32 5.0 48.4 1.0

Zinc binding site 6 out of 8 in 1k83

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Zinc binding site 6 out of 8 in the Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3004

b:62.4
occ:1.00
 SG I:CYS106 2.4 46.5 1.0
SG I:CYS78 2.6 67.7 1.0
SG I:CYS75 2.6 78.0 1.0
SG I:CYS103 2.6 43.9 1.0
CB I:CYS103 3.0 40.8 1.0
CB I:CYS75 3.0 71.6 1.0
N I:CYS78 3.6 70.3 1.0
CB I:HIS108 3.8 53.7 1.0
CB I:CYS78 3.8 69.6 1.0
CB I:CYS106 3.9 51.7 1.0
CB I:LYS77 4.0 71.6 1.0
CA I:CYS78 4.3 69.2 1.0
OG I:SER80 4.3 74.0 1.0
CA I:CYS75 4.4 70.4 1.0
CA I:CYS103 4.5 39.9 1.0
N I:CYS106 4.6 52.0 1.0
C I:LYS77 4.6 71.2 1.0
CA I:LYS77 4.6 71.2 1.0
N I:LYS77 4.6 71.2 1.0
N I:HIS108 4.6 51.8 1.0
CG I:HIS108 4.7 54.7 1.0
O I:CYS75 4.7 70.6 1.0
C I:CYS75 4.7 69.9 1.0
CA I:CYS106 4.8 51.6 1.0
N I:HIS79 4.8 69.3 1.0
C I:CYS78 4.8 69.0 1.0
CA I:HIS108 4.8 53.0 1.0
CD2 I:HIS108 4.8 54.9 1.0

Zinc binding site 7 out of 8 in 1k83

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Zinc binding site 7 out of 8 in the Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3001

b:46.5
occ:1.00
 SG J:CYS10 2.3 38.4 1.0
SG J:CYS7 2.3 30.7 1.0
SG J:CYS46 2.3 43.8 1.0
SG J:CYS45 2.4 50.4 1.0
N J:CYS46 3.0 40.4 1.0
CB J:CYS45 3.2 40.5 1.0
CB J:CYS7 3.5 33.7 1.0
C J:CYS45 3.5 40.0 1.0
CB J:CYS46 3.5 41.1 1.0
CA J:CYS46 3.5 41.2 1.0
CB J:CYS10 3.6 39.0 1.0
CA J:CYS45 3.9 40.9 1.0
N J:CYS10 3.9 38.3 1.0
NE J:ARG43 4.0 43.9 1.0
O J:CYS45 4.2 40.0 1.0
CA J:CYS10 4.3 40.0 1.0
CB J:SER9 4.5 33.0 1.0
CD J:ARG43 4.5 44.5 1.0
N J:CYS45 4.5 41.3 1.0
CG J:ARG43 4.7 45.1 1.0
C J:SER9 4.8 36.9 1.0
CA J:CYS7 4.8 33.8 1.0
O J:ARG43 4.9 44.0 1.0
CB J:LYS12 4.9 43.5 1.0
CA J:SER9 5.0 34.7 1.0
C J:CYS46 5.0 42.3 1.0

Zinc binding site 8 out of 8 in 1k83

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Zinc binding site 8 out of 8 in the Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Yeast Rna Polymerase II Complexed with the Inhibitor Alpha Amanitin within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn3005

b:86.8
occ:1.00
 SG L:CYS34 2.3 77.0 1.0
CB L:CYS51 2.5 0.3 1.0
O L:CYS51 2.5 0.7 1.0
SG L:CYS48 2.7 0.6 1.0
SG L:CYS31 2.7 82.9 1.0
CB L:CYS48 2.8 1.0 1.0
C L:CYS51 3.3 0.4 1.0
CA L:CYS51 3.3 0.6 1.0
N L:CYS51 3.7 0.2 1.0
SG L:CYS51 3.7 0.6 1.0
CB L:CYS31 3.8 82.2 1.0
CB L:CYS34 3.9 81.4 1.0
CD2 L:HIS53 4.0 0.0 1.0
CA L:CYS48 4.1 0.2 1.0
N L:LYS49 4.2 0.5 1.0
OG L:SER36 4.3 89.5 1.0
C L:CYS48 4.3 0.6 1.0
O L:LYS49 4.3 0.3 1.0
N L:CYS34 4.5 85.2 1.0
N L:HIS53 4.5 0.5 1.0
N L:GLY52 4.6 0.8 1.0
CG L:HIS53 4.6 0.8 1.0
CB L:HIS53 4.7 0.2 1.0
C L:LYS49 4.7 0.4 1.0
N L:CYS48 4.7 0.9 1.0
CA L:CYS34 4.8 83.4 1.0
NE2 L:HIS53 5.0 0.2 1.0

Reference:

D.A.Bushnell, P.Cramer, R.D.Kornberg. Structural Basis of Transcription: Alpha-Amanitin-Rna Polymerase II Cocrystal at 2.8 A Resolution. Proc.Natl.Acad.Sci.Usa V. 99 1218 2002.
ISSN: ISSN 0027-8424
PubMed: 11805306
DOI: 10.1073/PNAS.251664698
Page generated: Sun Oct 13 04:09:50 2024

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