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Zinc in PDB 1wcm: Complete 12-Subunit Rna Polymerase II at 3.8 Ang

Enzymatic activity of Complete 12-Subunit Rna Polymerase II at 3.8 Ang

All present enzymatic activity of Complete 12-Subunit Rna Polymerase II at 3.8 Ang:
2.7.7.6;

Protein crystallography data

The structure of Complete 12-Subunit Rna Polymerase II at 3.8 Ang, PDB code: 1wcm was solved by K.-J.Armache, S.Mitterweger, A.Meinhart, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50 / 3.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.718, 395.135, 284.300, 90.00, 90.00, 90.00
R / Rfree (%) 25.69 / 28.54

Other elements in 1wcm:

The structure of Complete 12-Subunit Rna Polymerase II at 3.8 Ang also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang (pdb code 1wcm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang, PDB code: 1wcm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1wcm

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Zinc binding site 1 out of 8 in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complete 12-Subunit Rna Polymerase II at 3.8 Ang within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:86.9
occ:1.00
 SG A:CYS110 2.5 0.3 1.0
SG A:CYS167 2.6 0.1 1.0
SG A:CYS148 2.8 0.2 1.0
O A:MET108 3.5 0.4 1.0
O A:CYS167 3.6 1.0 1.0
CB A:CYS148 3.7 0.9 1.0
CB A:CYS110 3.7 0.0 1.0
N A:CYS110 4.1 0.9 1.0
O A:CYS107 4.2 0.5 1.0
CB A:CYS107 4.3 0.0 1.0
CB A:CYS167 4.3 0.1 1.0
CA A:CYS110 4.4 0.3 1.0
O A:GLY166 4.5 0.8 1.0
N A:GLY111 4.6 0.6 1.0
C A:CYS107 4.6 0.9 1.0
C A:CYS167 4.6 0.9 1.0
C A:MET108 4.7 0.6 1.0
C A:CYS110 4.7 0.0 1.0
SG A:CYS107 4.9 0.8 1.0

Zinc binding site 2 out of 8 in 1wcm

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Zinc binding site 2 out of 8 in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complete 12-Subunit Rna Polymerase II at 3.8 Ang within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:44.9
occ:1.00
 SG A:CYS77 2.1 0.9 1.0
NE2 A:HIS80 2.1 61.0 1.0
CB A:CYS67 2.6 0.7 1.0
SG A:CYS70 2.7 0.7 1.0
O A:CYS67 2.7 0.1 1.0
SG A:CYS67 2.8 0.6 1.0
CD2 A:HIS80 2.8 60.5 1.0
CB A:CYS70 3.1 0.2 1.0
CE1 A:HIS80 3.2 60.9 1.0
C A:CYS67 3.5 0.0 1.0
CB A:CYS77 3.6 97.8 1.0
CA A:CYS67 3.6 0.9 1.0
O A:CYS77 3.9 85.7 1.0
CG A:HIS80 4.0 61.8 1.0
ND1 A:HIS80 4.2 60.6 1.0
CA A:CYS77 4.4 90.9 1.0
CA A:CYS70 4.5 0.3 1.0
C A:CYS77 4.6 85.5 1.0
O A:PRO78 4.7 82.8 1.0
NE2 A:GLN68 4.7 0.1 1.0
N A:CYS67 4.8 0.9 1.0
C A:CYS70 4.8 0.1 1.0
N A:GLN68 4.8 0.0 1.0
O A:GLN71 5.0 0.0 1.0
O A:CYS70 5.0 0.7 1.0

Zinc binding site 3 out of 8 in 1wcm

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Zinc binding site 3 out of 8 in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complete 12-Subunit Rna Polymerase II at 3.8 Ang within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:44.9
occ:1.00
 SG B:CYS1166 2.2 69.2 1.0
SG B:CYS1182 2.3 82.3 1.0
SG B:CYS1185 2.4 79.8 1.0
CB B:CYS1185 2.6 79.8 1.0
SG B:CYS1163 2.6 71.8 1.0
CB B:CYS1163 2.9 67.5 1.0
O B:CYS1182 3.8 88.8 1.0
CB B:CYS1182 3.8 86.3 1.0
CA B:CYS1185 3.9 83.4 1.0
CB B:CYS1166 4.0 68.7 1.0
O B:CYS1166 4.1 68.6 1.0
N B:CYS1185 4.1 85.5 1.0
N B:CYS1166 4.2 69.0 1.0
C B:CYS1185 4.3 83.8 1.0
CA B:CYS1163 4.4 65.5 1.0
OG1 B:THR1170 4.6 62.2 1.0
CA B:CYS1166 4.6 68.3 1.0
N B:ASP1186 4.7 84.2 1.0
C B:CYS1182 4.7 89.1 1.0
CG2 B:ILE1165 4.8 75.2 1.0
CB B:THR1170 4.8 61.2 1.0
C B:CYS1166 4.9 68.7 1.0
CB B:ILE1165 4.9 73.5 1.0
CA B:CYS1182 4.9 88.0 1.0
O B:CYS1185 4.9 85.0 1.0

Zinc binding site 4 out of 8 in 1wcm

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Zinc binding site 4 out of 8 in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complete 12-Subunit Rna Polymerase II at 3.8 Ang within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:39.5
occ:1.00
 SG C:CYS88 2.2 49.3 1.0
SG C:CYS95 2.3 63.0 1.0
SG C:CYS86 2.4 41.5 1.0
SG C:CYS92 2.5 73.0 1.0
CB C:CYS86 2.9 47.1 1.0
N C:CYS92 3.0 69.1 1.0
CB C:CYS95 3.2 63.7 1.0
CB C:CYS92 3.6 72.3 1.0
C C:HIS91 3.6 68.9 1.0
CA C:HIS91 3.6 70.7 1.0
CA C:CYS92 3.7 71.5 1.0
O C:CYS92 3.8 72.2 1.0
CB C:CYS88 3.8 51.4 1.0
N C:CYS95 4.1 64.2 1.0
C C:CYS92 4.1 72.4 1.0
CA C:CYS95 4.2 63.3 1.0
CA C:CYS86 4.2 50.6 1.0
N C:HIS91 4.3 74.5 1.0
O C:CYS86 4.3 51.5 1.0
C C:CYS86 4.5 50.3 1.0
N C:CYS88 4.5 49.4 1.0
O C:HIS91 4.5 66.9 1.0
C C:LYS94 4.5 65.6 1.0
CA C:CYS88 4.7 51.9 1.0
CB C:HIS91 4.8 68.5 1.0
O C:CYS88 4.8 55.0 1.0
CB C:LYS94 4.8 70.6 1.0
N C:LYS94 4.9 70.0 1.0
CA C:LYS94 5.0 67.9 1.0
C C:CYS95 5.0 62.1 1.0

Zinc binding site 5 out of 8 in 1wcm

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Zinc binding site 5 out of 8 in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Complete 12-Subunit Rna Polymerase II at 3.8 Ang within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:90.7
occ:1.00
 SG I:CYS10 2.3 89.4 1.0
SG I:CYS32 2.4 86.2 1.0
SG I:CYS7 2.4 0.4 1.0
SG I:CYS29 2.7 88.5 1.0
CB I:CYS29 2.9 94.2 1.0
CB I:CYS32 3.5 91.2 1.0
CB I:CYS10 3.8 99.7 1.0
CB I:CYS7 3.8 0.5 1.0
O I:ARG8 4.1 0.6 1.0
N I:CYS32 4.2 96.7 1.0
CB I:TYR34 4.3 73.8 1.0
N I:CYS10 4.3 0.7 1.0
CA I:CYS29 4.4 96.0 1.0
CA I:CYS10 4.4 0.1 1.0
CA I:CYS32 4.4 93.7 1.0
OD2 I:ASP9 4.5 0.7 1.0
C I:CYS10 4.6 0.2 1.0
N I:ASN11 4.6 0.6 1.0
N I:TYR34 5.0 77.6 1.0
N I:ASN12 5.0 0.3 1.0

Zinc binding site 6 out of 8 in 1wcm

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Zinc binding site 6 out of 8 in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Complete 12-Subunit Rna Polymerase II at 3.8 Ang within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.4
occ:1.00
 SG I:CYS106 2.3 0.7 1.0
SG I:CYS78 2.4 0.6 1.0
SG I:CYS103 2.6 0.5 1.0
CB I:CYS103 3.0 0.1 1.0
CB I:CYS75 3.1 0.3 1.0
SG I:CYS75 3.3 0.5 1.0
CB I:CYS106 3.4 0.3 1.0
CB I:CYS78 3.7 0.1 1.0
CA I:CYS103 4.3 0.7 1.0
CA I:CYS106 4.5 0.2 1.0
CA I:CYS75 4.5 0.3 1.0
O I:SER105 4.6 0.2 1.0
CB I:HIS108 4.6 0.1 1.0
N I:CYS106 4.7 0.3 1.0
C I:SER105 4.7 1.0 1.0
N I:HIS108 4.8 0.6 1.0
N I:SER107 4.9 0.3 1.0
CA I:CYS78 5.0 0.1 1.0

Zinc binding site 7 out of 8 in 1wcm

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Zinc binding site 7 out of 8 in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Complete 12-Subunit Rna Polymerase II at 3.8 Ang within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:65.2
occ:1.00
 SG J:CYS46 2.2 65.8 1.0
N J:CYS46 2.3 68.8 1.0
SG J:CYS10 2.4 61.0 1.0
CB J:CYS46 2.5 65.5 1.0
SG J:CYS45 2.5 78.5 1.0
CB J:CYS10 2.5 58.1 1.0
SG J:CYS7 2.6 51.5 1.0
CA J:CYS46 2.6 68.5 1.0
C J:CYS45 3.0 70.0 1.0
CB J:CYS45 3.1 74.2 1.0
CB J:CYS7 3.4 47.3 1.0
N J:CYS10 3.6 56.5 1.0
CA J:CYS10 3.6 57.8 1.0
CA J:CYS45 3.7 71.9 1.0
O J:CYS45 3.8 69.3 1.0
OG J:SER9 4.0 51.5 1.0
C J:CYS46 4.1 70.2 1.0
N J:GLY11 4.4 57.5 1.0
C J:CYS10 4.5 57.4 1.0
N J:CYS45 4.6 71.5 1.0
CB J:SER9 4.7 51.7 1.0
NE J:ARG43 4.7 73.5 1.0
N J:ARG47 4.7 73.7 1.0
CG J:ARG43 4.8 74.6 1.0
O J:ARG43 4.8 77.0 1.0
C J:SER9 4.8 54.1 1.0
CA J:CYS7 4.9 47.1 1.0
O J:CYS46 4.9 69.7 1.0

Zinc binding site 8 out of 8 in 1wcm

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Zinc binding site 8 out of 8 in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Complete 12-Subunit Rna Polymerase II at 3.8 Ang within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.3
occ:1.00
 SG L:CYS48 2.4 0.8 1.0
SG L:CYS31 2.4 0.2 1.0
SG L:CYS34 2.6 0.7 1.0
SG L:CYS51 2.7 0.2 1.0
CB L:CYS48 3.0 0.4 1.0
CB L:CYS31 3.2 0.8 1.0
O L:CYS51 3.6 0.4 1.0
CA L:CYS31 4.0 0.1 1.0
CB L:CYS51 4.1 0.3 1.0
CB L:CYS34 4.3 0.1 1.0
CA L:CYS48 4.4 0.4 1.0
C L:CYS51 4.5 0.2 1.0
OG L:SER36 4.7 0.3 1.0
CA L:CYS51 4.9 0.2 1.0
N L:CYS34 4.9 1.0 1.0

Reference:

K.-J.Armache, S.Mitterweger, A.Meinhart, P.Cramer. Structures of Complete Rna Polymerase II and Its Subcomplex,RPB4/7 J.Biol.Chem. V. 280 7131 2005.
ISSN: ISSN 0021-9258
PubMed: 15591044
DOI: 10.1074/JBC.M413038200
Page generated: Wed Oct 16 19:57:37 2024

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