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Zinc in PDB 1y77: Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp

Enzymatic activity of Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp

All present enzymatic activity of Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp:
2.7.7.6;

Protein crystallography data

The structure of Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp, PDB code: 1y77 was solved by H.Kettenberger, K.-J.Armache, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 4.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.460, 393.070, 283.690, 90.00, 90.00, 90.00
R / Rfree (%) 29.7 / n/a

Zinc Binding Sites:

The binding sites of Zinc atom in the Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp (pdb code 1y77). 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 Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp, PDB code: 1y77:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1y77

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Zinc binding site 1 out of 8 in the Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.0
occ:1.00
SG A:CYS167 2.8 0.5 1.0
SG A:CYS110 3.0 0.6 1.0
O A:MET108 3.1 0.5 1.0
SG A:CYS148 3.4 0.9 1.0
O A:CYS167 3.6 0.0 1.0
CB A:CYS107 3.9 0.6 1.0
O A:CYS107 4.0 0.2 1.0
CB A:CYS110 4.1 0.1 1.0
CB A:CYS148 4.1 0.3 1.0
N A:CYS110 4.1 0.7 1.0
C A:CYS107 4.2 0.4 1.0
C A:MET108 4.3 0.7 1.0
SG A:CYS107 4.3 1.0 1.0
CB A:CYS167 4.4 0.2 1.0
CA A:CYS110 4.6 0.3 1.0
N A:GLY111 4.6 0.3 1.0
CA A:CYS107 4.6 0.9 1.0
C A:CYS167 4.7 0.9 1.0
CB A:HIS109 4.7 0.7 1.0
N A:MET108 4.8 0.3 1.0
C A:CYS110 4.9 0.9 1.0
O A:GLY166 5.0 0.7 1.0

Zinc binding site 2 out of 8 in 1y77

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Zinc binding site 2 out of 8 in the Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:68.7
occ:1.00
SG A:CYS77 2.1 0.4 1.0
NE2 A:HIS80 2.2 85.7 1.0
CB A:CYS67 2.4 0.8 1.0
SG A:CYS67 2.6 0.2 1.0
O A:CYS67 2.7 0.3 1.0
SG A:CYS70 2.8 0.2 1.0
CD2 A:HIS80 2.9 85.1 1.0
CB A:CYS70 3.1 0.2 1.0
CE1 A:HIS80 3.3 85.7 1.0
CA A:CYS67 3.4 0.3 1.0
C A:CYS67 3.4 1.0 1.0
O A:CYS77 3.7 0.8 1.0
CB A:CYS77 3.7 0.6 1.0
CG A:HIS80 4.1 85.8 1.0
ND1 A:HIS80 4.3 85.0 1.0
CA A:CYS77 4.3 0.7 1.0
C A:CYS77 4.4 0.1 1.0
CA A:CYS70 4.5 0.2 1.0
O A:PRO78 4.5 0.5 1.0
N A:CYS67 4.6 0.6 1.0
N A:GLN68 4.7 0.4 1.0
NE2 A:GLN68 4.8 0.6 1.0
C A:CYS70 4.8 0.9 1.0
O A:GLN71 4.9 0.9 1.0
O A:CYS70 5.0 0.8 1.0

Zinc binding site 3 out of 8 in 1y77

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Zinc binding site 3 out of 8 in the Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:67.2
occ:1.00
SG B:CYS1182 2.2 0.4 1.0
SG B:CYS1166 2.2 91.8 1.0
SG B:CYS1185 2.3 0.5 1.0
CB B:CYS1185 2.6 0.3 1.0
SG B:CYS1163 2.9 95.9 1.0
CB B:CYS1163 3.1 91.3 1.0
O B:CYS1182 3.7 0.5 1.0
CB B:CYS1182 3.8 0.0 1.0
CA B:CYS1185 3.8 0.7 1.0
CB B:CYS1166 4.0 91.5 1.0
N B:CYS1185 4.1 0.1 1.0
O B:CYS1166 4.2 92.3 1.0
N B:CYS1166 4.4 92.1 1.0
C B:CYS1185 4.4 0.2 1.0
OG1 B:THR1170 4.4 84.8 1.0
CA B:CYS1163 4.6 88.7 1.0
C B:CYS1182 4.6 0.0 1.0
CB B:THR1170 4.7 84.0 1.0
CA B:CYS1166 4.7 91.5 1.0
N B:ASP1186 4.7 0.8 1.0
CA B:CYS1182 4.8 0.0 1.0
C B:CYS1166 4.9 92.1 1.0
CG2 B:ILE1165 4.9 98.5 1.0
O B:CYS1185 5.0 0.7 1.0

Zinc binding site 4 out of 8 in 1y77

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Zinc binding site 4 out of 8 in the Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:63.3
occ:1.00
SG C:CYS88 2.2 72.4 1.0
SG C:CYS95 2.3 85.8 1.0
SG C:CYS86 2.4 62.6 1.0
SG C:CYS92 2.5 94.6 1.0
CB C:CYS86 2.9 68.9 1.0
N C:CYS92 3.0 91.4 1.0
CB C:CYS95 3.2 87.0 1.0
CB C:CYS92 3.5 94.5 1.0
C C:HIS91 3.6 90.5 1.0
CA C:CYS92 3.6 94.1 1.0
CA C:HIS91 3.7 91.2 1.0
CB C:CYS88 3.8 74.0 1.0
O C:CYS92 3.8 95.5 1.0
N C:CYS95 4.1 87.3 1.0
C C:CYS92 4.1 95.5 1.0
CA C:CYS95 4.3 86.3 1.0
CA C:CYS86 4.3 72.4 1.0
O C:CYS86 4.3 73.5 1.0
O C:HIS91 4.4 89.4 1.0
C C:CYS86 4.5 72.3 1.0
N C:CYS88 4.5 71.8 1.0
C C:LYS94 4.6 88.7 1.0
CA C:CYS88 4.7 74.8 1.0
N C:HIS91 4.7 93.2 1.0
CB C:HIS91 4.7 90.3 1.0
O C:CYS88 4.7 77.6 1.0
CB C:LYS94 4.8 93.3 1.0
N C:LYS94 4.9 93.2 1.0

Zinc binding site 5 out of 8 in 1y77

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Zinc binding site 5 out of 8 in the Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:0.6
occ:1.00
SG I:CYS32 2.3 0.2 1.0
SG I:CYS10 2.3 0.5 1.0
SG I:CYS7 2.3 0.8 1.0
SG I:CYS29 2.6 0.1 1.0
CB I:CYS29 2.9 0.8 1.0
CB I:CYS32 3.6 0.2 1.0
CB I:CYS7 3.7 0.7 1.0
CB I:CYS10 3.8 0.5 1.0
O I:ARG8 4.0 0.9 1.0
CB I:TYR34 4.2 95.9 1.0
N I:CYS32 4.3 0.9 1.0
N I:CYS10 4.3 0.3 1.0
CA I:CYS29 4.4 0.5 1.0
CA I:CYS10 4.4 0.6 1.0
OD2 I:ASP9 4.5 0.4 1.0
CA I:CYS32 4.5 0.7 1.0
N I:ASN11 4.6 0.7 1.0
C I:CYS10 4.6 0.5 1.0
N I:ASN12 4.9 0.7 1.0
N I:TYR34 4.9 99.0 1.0
CA I:CYS7 5.0 0.3 1.0

Zinc binding site 6 out of 8 in 1y77

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Zinc binding site 6 out of 8 in the Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:0.4
occ:1.00
CB I:CYS75 2.8 0.7 1.0
SG I:CYS106 2.8 0.8 1.0
CB I:CYS78 2.9 0.7 1.0
SG I:CYS78 3.0 0.5 1.0
N I:CYS78 3.4 0.2 1.0
SG I:CYS75 3.4 0.6 1.0
CB I:HIS108 3.5 0.2 1.0
CB I:CYS103 3.6 0.7 1.0
CA I:CYS78 3.8 0.4 1.0
SG I:CYS103 4.0 0.5 1.0
CA I:CYS75 4.2 0.3 1.0
CD I:PRO76 4.2 0.7 1.0
CG I:HIS108 4.3 0.3 1.0
N I:LYS77 4.3 0.2 1.0
CB I:LYS77 4.3 0.8 1.0
C I:LYS77 4.4 1.0 1.0
CB I:CYS106 4.4 0.3 1.0
CD2 I:HIS108 4.5 0.1 1.0
CA I:LYS77 4.6 0.4 1.0
N I:PRO76 4.6 0.9 1.0
CA I:HIS108 4.6 0.2 1.0
N I:HIS108 4.7 0.0 1.0
C I:CYS75 4.7 0.2 1.0
C I:CYS78 4.8 0.6 1.0
CA I:CYS103 4.9 0.4 1.0
N I:HIS79 5.0 0.4 1.0

Zinc binding site 7 out of 8 in 1y77

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Zinc binding site 7 out of 8 in the Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:90.9
occ:1.00
SG J:CYS46 2.2 90.8 1.0
N J:CYS46 2.4 92.9 1.0
SG J:CYS10 2.4 85.8 1.0
SG J:CYS45 2.4 96.5 1.0
SG J:CYS7 2.4 77.3 1.0
CB J:CYS10 2.4 82.2 1.0
CB J:CYS46 2.6 91.5 1.0
CA J:CYS46 2.7 92.8 1.0
C J:CYS45 3.1 93.6 1.0
CB J:CYS45 3.1 95.4 1.0
N J:CYS10 3.3 77.9 1.0
CB J:CYS7 3.4 73.1 1.0
CA J:CYS10 3.5 79.4 1.0
CA J:CYS45 3.7 93.4 1.0
O J:CYS45 3.8 92.7 1.0
OG J:SER9 4.0 65.8 1.0
C J:CYS46 4.2 93.6 1.0
C J:CYS10 4.4 78.5 1.0
N J:GLY11 4.5 78.9 1.0
CB J:SER9 4.6 69.3 1.0
C J:SER9 4.6 74.5 1.0
N J:CYS45 4.6 93.3 1.0
NE J:ARG43 4.7 97.1 1.0
CA J:CYS7 4.8 70.6 1.0
N J:ARG47 4.8 95.2 1.0
O J:ARG43 4.9 95.1 1.0
CG J:ARG43 4.9 95.6 1.0
CA J:SER9 5.0 71.5 1.0

Zinc binding site 8 out of 8 in 1y77

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Zinc binding site 8 out of 8 in the Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Complete Rna Polymerase II Elongation Complex with Substrate Analogue Gmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.3
occ:1.00
SG L:CYS34 2.3 0.2 1.0
SG L:CYS48 2.3 0.1 1.0
SG L:CYS31 2.5 0.5 1.0
CB L:CYS48 2.7 0.6 1.0
CB L:CYS51 2.7 0.4 1.0
O L:CYS51 2.9 0.4 1.0
CB L:CYS31 3.5 0.9 1.0
CA L:CYS51 3.5 0.6 1.0
C L:CYS51 3.6 0.6 1.0
SG L:CYS51 3.7 0.3 1.0
N L:CYS51 3.8 0.6 1.0
CA L:CYS48 4.1 0.6 1.0
CB L:CYS34 4.1 0.3 1.0
CA L:CYS31 4.4 1.0 1.0
C L:CYS48 4.5 0.2 1.0
N L:LYS49 4.6 0.5 1.0
OG L:SER36 4.8 0.4 1.0
O L:LYS49 4.8 0.4 1.0
N L:CYS48 4.9 0.2 1.0
C L:ASP50 4.9 0.9 1.0
N L:GLY52 4.9 0.5 1.0

Reference:

H.Kettenberger, K.-J.Armache, P.Cramer. Complete Rna Polymerase II Elongation Complex Structure and Its Interactions with Ntp and Tfiis Mol.Cell V. 16 955 2004.
ISSN: ISSN 1097-2765
PubMed: 15610738
DOI: 10.1016/J.MOLCEL.2004.11.040
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