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Zinc in PDB 1i50: Rna Polymerase II Crystal Form II at 2.8 A Resolution

Enzymatic activity of Rna Polymerase II Crystal Form II at 2.8 A Resolution

All present enzymatic activity of Rna Polymerase II Crystal Form II at 2.8 A Resolution:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Crystal Form II at 2.8 A Resolution, PDB code: 1i50 was solved by P.Cramer, D.A.Bushnell, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.80
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 122.700, 223.000, 376.100, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 28.2

Other elements in 1i50:

The structure of Rna Polymerase II Crystal Form II at 2.8 A Resolution also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Crystal Form II at 2.8 A Resolution (pdb code 1i50). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Rna Polymerase II Crystal Form II at 2.8 A Resolution, PDB code: 1i50:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1i50

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Zinc binding site 1 out of 8 in the Rna Polymerase II Crystal Form II at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase II Crystal Form II at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3006

b:80.5
occ:1.00
 SG A:CYS110 2.2 63.6 1.0
SG A:CYS167 2.4 84.8 1.0
SG A:CYS107 2.5 70.5 1.0
SG A:CYS148 2.6 74.1 1.0
CB A:CYS167 2.8 84.6 1.0
CB A:CYS107 3.2 67.2 1.0
CB A:CYS148 3.2 81.2 1.0
O A:CYS167 3.3 94.1 1.0
CB A:CYS110 3.8 67.1 1.0
CA A:CYS167 4.0 88.2 1.0
C A:CYS167 4.1 90.0 1.0
N A:CYS110 4.2 71.6 1.0
CA A:CYS110 4.6 68.7 1.0
CA A:CYS107 4.6 65.6 1.0
CB A:HIS109 4.6 78.3 1.0
CA A:CYS148 4.7 84.5 1.0
CB A:LYS112 4.7 63.8 1.0
N A:CYS167 4.7 89.5 1.0
C A:HIS109 4.9 73.3 1.0

Zinc binding site 2 out of 8 in 1i50

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Zinc binding site 2 out of 8 in the Rna Polymerase II Crystal Form II at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase II Crystal Form II at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3008

b:0.9
occ:1.00
 SG A:CYS70 2.0 0.7 1.0
SG A:CYS77 2.0 1.0 1.0
NE2 A:HIS80 2.4 89.2 1.0
SG A:CYS67 2.6 0.2 1.0
CD2 A:HIS80 2.9 88.9 1.0
CB A:CYS67 3.3 0.7 1.0
O A:CYS67 3.3 0.6 1.0
CB A:CYS77 3.4 0.1 1.0
CB A:CYS70 3.6 0.5 1.0
CE1 A:HIS80 3.6 90.4 1.0
C A:CYS67 4.2 0.6 1.0
CG A:HIS80 4.2 88.2 1.0
CA A:CYS77 4.3 0.2 1.0
O A:GLN71 4.4 0.7 1.0
CA A:CYS67 4.4 0.8 1.0
ND1 A:HIS80 4.5 88.8 1.0
CA A:CYS70 4.8 0.1 1.0
C A:CYS70 4.9 0.8 1.0
CD A:PRO78 4.9 0.6 1.0
C A:CYS77 4.9 0.4 1.0

Zinc binding site 3 out of 8 in 1i50

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Zinc binding site 3 out of 8 in the Rna Polymerase II Crystal Form II at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase II Crystal Form II at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3007

b:70.2
occ:1.00
 SG B:CYS1182 2.4 91.0 1.0
SG B:CYS1166 2.5 62.0 1.0
SG B:CYS1163 2.6 61.8 1.0
SG B:CYS1185 2.7 87.2 1.0
CB B:CYS1185 3.0 92.4 1.0
CB B:CYS1163 3.1 60.2 1.0
CB B:CYS1166 3.6 61.2 1.0
CB B:CYS1182 3.7 0.2 1.0
N B:CYS1166 4.0 61.5 1.0
O B:CYS1182 4.2 0.1 1.0
OG1 B:THR1170 4.3 67.9 1.0
CA B:CYS1166 4.4 63.0 1.0
ND2 B:ASN1187 4.4 0.8 1.0
CA B:CYS1185 4.5 94.4 1.0
O B:CYS1166 4.5 67.1 1.0
CA B:CYS1163 4.6 61.9 1.0
CB B:ILE1165 4.7 67.6 1.0
N B:CYS1185 4.8 94.5 1.0
O B:LYS1183 4.8 99.3 1.0
C B:CYS1182 4.9 0.5 1.0
CA B:CYS1182 4.9 0.6 1.0
C B:CYS1166 4.9 64.5 1.0

Zinc binding site 4 out of 8 in 1i50

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Zinc binding site 4 out of 8 in the Rna Polymerase II Crystal Form II at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase II Crystal Form II at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3002

b:67.5
occ:1.00
 SG C:CYS88 2.2 58.2 1.0
SG C:CYS86 2.3 53.6 1.0
SG C:CYS92 2.4 63.5 1.0
SG C:CYS95 2.5 55.1 1.0
CB C:CYS88 3.2 58.6 1.0
CB C:CYS92 3.3 57.6 1.0
CB C:CYS86 3.3 49.1 1.0
N C:CYS92 3.5 58.9 1.0
CB C:CYS95 3.6 52.8 1.0
CA C:CYS92 3.9 57.0 1.0
N C:CYS95 4.1 54.6 1.0
C C:HIS91 4.1 60.3 1.0
N C:CYS88 4.2 54.3 1.0
CA C:CYS88 4.3 56.9 1.0
O C:CYS92 4.3 50.6 1.0
C C:CYS92 4.4 55.0 1.0
CA C:HIS91 4.4 62.2 1.0
CA C:CYS95 4.5 54.0 1.0
CB C:LYS94 4.5 56.4 1.0
CA C:CYS86 4.6 50.4 1.0
O C:ASP90 4.7 64.3 1.0
C C:LYS94 4.7 53.2 1.0
C C:CYS86 4.9 51.0 1.0
N C:LYS94 4.9 53.2 1.0
CA C:LYS94 5.0 53.6 1.0
O C:HIS91 5.0 58.9 1.0
N C:HIS91 5.0 62.5 1.0

Zinc binding site 5 out of 8 in 1i50

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Zinc binding site 5 out of 8 in the Rna Polymerase II Crystal Form II at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase II Crystal Form II at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3003

b:78.3
occ:1.00
 SG I:CYS10 1.9 63.8 1.0
SG I:CYS32 2.1 67.1 1.0
SG I:CYS29 2.2 56.6 1.0
SG I:CYS7 2.4 58.8 1.0
CB I:CYS7 3.0 59.1 1.0
CB I:CYS29 3.0 55.3 1.0
CB I:CYS32 3.5 59.1 1.0
CB I:CYS10 3.6 58.1 1.0
N I:CYS32 3.7 61.5 1.0
N I:CYS10 4.0 57.3 1.0
CA I:CYS32 4.1 59.4 1.0
CB I:THR31 4.2 60.2 1.0
CA I:CYS10 4.3 56.8 1.0
CB I:TYR34 4.4 45.3 1.0
CG2 I:THR31 4.4 59.9 1.0
CA I:CYS7 4.5 57.5 1.0
CA I:CYS29 4.5 54.8 1.0
C I:CYS32 4.7 57.9 1.0
C I:THR31 4.7 61.7 1.0
C I:CYS10 4.8 56.4 1.0
N I:THR31 4.9 58.7 1.0
CA I:THR31 4.9 59.5 1.0
N I:ASN11 5.0 55.0 1.0

Zinc binding site 6 out of 8 in 1i50

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Zinc binding site 6 out of 8 in the Rna Polymerase II Crystal Form II at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase II Crystal Form II at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3004

b:81.5
occ:1.00
 SG I:CYS75 2.2 92.2 1.0
SG I:CYS106 2.4 68.2 1.0
SG I:CYS103 2.8 58.0 1.0
SG I:CYS78 2.8 87.5 1.0
CB I:CYS75 3.0 87.5 1.0
CB I:CYS103 3.0 55.8 1.0
N I:CYS78 3.6 88.2 1.0
CB I:HIS108 3.7 60.7 1.0
CB I:LYS77 4.0 89.2 1.0
CB I:CYS78 4.0 87.7 1.0
CB I:CYS106 4.1 68.7 1.0
OG I:SER80 4.3 97.4 1.0
CA I:CYS78 4.3 87.8 1.0
CA I:CYS75 4.4 86.0 1.0
CG I:HIS108 4.5 58.5 1.0
N I:LYS77 4.5 89.0 1.0
CA I:LYS77 4.5 89.2 1.0
CA I:CYS103 4.5 53.1 1.0
C I:LYS77 4.5 89.4 1.0
CD2 I:HIS108 4.6 58.6 1.0
O I:CYS75 4.7 85.8 1.0
C I:CYS75 4.7 85.8 1.0
N I:HIS108 4.7 63.9 1.0
CA I:HIS108 4.8 62.5 1.0
N I:CYS106 4.8 67.2 1.0
C I:CYS78 4.9 88.3 1.0
N I:HIS79 4.9 90.2 1.0
CA I:CYS106 5.0 67.8 1.0
CG I:LYS77 5.0 90.7 1.0

Zinc binding site 7 out of 8 in 1i50

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Zinc binding site 7 out of 8 in the Rna Polymerase II Crystal Form II at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase II Crystal Form II at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3001

b:64.0
occ:1.00
 SG J:CYS7 2.1 34.8 1.0
SG J:CYS45 2.2 50.0 1.0
SG J:CYS10 2.3 40.3 1.0
SG J:CYS46 2.4 47.4 1.0
N J:CYS46 3.0 43.3 1.0
CB J:CYS45 3.3 42.2 1.0
CB J:CYS7 3.3 35.8 1.0
CA J:CYS46 3.3 43.9 1.0
C J:CYS45 3.4 38.9 1.0
CB J:CYS46 3.4 42.1 1.0
CB J:CYS10 3.6 39.4 1.0
N J:CYS10 3.8 41.8 1.0
CA J:CYS45 3.9 40.1 1.0
O J:CYS45 4.0 39.5 1.0
NE J:ARG43 4.0 35.7 1.0
CA J:CYS10 4.3 42.7 1.0
CB J:SER9 4.5 40.2 1.0
CD J:ARG43 4.5 35.3 1.0
CG J:ARG43 4.6 38.2 1.0
N J:CYS45 4.6 39.1 1.0
CA J:CYS7 4.7 35.0 1.0
C J:SER9 4.8 40.8 1.0
C J:CYS46 4.9 45.2 1.0
CB J:LYS12 5.0 44.9 1.0
CA J:SER9 5.0 38.9 1.0
O J:ARG43 5.0 39.0 1.0

Zinc binding site 8 out of 8 in 1i50

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Zinc binding site 8 out of 8 in the Rna Polymerase II Crystal Form II at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rna Polymerase II Crystal Form II at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn3005

b:1.0
occ:1.00
 SG L:CYS34 2.1 87.0 1.0
CB L:CYS51 2.2 0.0 1.0
SG L:CYS48 2.4 0.1 1.0
CB L:CYS48 2.6 0.2 1.0
SG L:CYS31 2.6 95.7 1.0
O L:CYS51 3.1 0.5 1.0
SG L:CYS51 3.2 0.6 1.0
CA L:CYS51 3.3 0.6 1.0
CB L:CYS31 3.6 93.0 1.0
CB L:CYS34 3.6 93.3 1.0
C L:CYS51 3.6 0.7 1.0
N L:CYS51 3.8 0.4 1.0
CD2 L:HIS53 3.9 0.0 1.0
CA L:CYS48 4.0 0.8 1.0
OG L:SER36 4.0 0.8 1.0
N L:CYS34 4.3 98.6 1.0
N L:LYS49 4.4 0.4 1.0
C L:CYS48 4.4 0.6 1.0
CA L:CYS34 4.6 96.9 1.0
CG L:HIS53 4.7 0.3 1.0
NE2 L:HIS53 4.7 0.5 1.0
O L:LYS49 4.7 0.1 1.0
N L:CYS48 4.7 0.8 1.0
CB L:HIS53 4.9 0.3 1.0
N L:GLY52 5.0 0.0 1.0
C L:LYS49 5.0 0.7 1.0

Reference:

P.Cramer, D.A.Bushnell, R.D.Kornberg. Structural Basis of Transcription: Rna Polymerase II at 2.8 Angstrom Resolution. Science V. 292 1863 2001.
ISSN: ISSN 0036-8075
PubMed: 11313498
DOI: 10.1126/SCIENCE.1059493
Page generated: Sun Oct 13 02:49:59 2024

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