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Zinc in PDB 3hoy: Complete Rna Polymerase II Elongation Complex VI

Enzymatic activity of Complete Rna Polymerase II Elongation Complex VI

All present enzymatic activity of Complete Rna Polymerase II Elongation Complex VI:
2.7.7.6;

Protein crystallography data

The structure of Complete Rna Polymerase II Elongation Complex VI, PDB code: 3hoy was solved by J.F.Sydow, F.Brueckner, A.C.M.Cheung, G.E.Damsma, S.Dengl, E.Lehmann, D.Vassylyev, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.144, 392.690, 282.377, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 25.4

Other elements in 3hoy:

The structure of Complete Rna Polymerase II Elongation Complex VI also contains other interesting chemical elements:

Bromine (Br) 1 atom
Magnesium (Mg) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 3hoy

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Zinc binding site 1 out of 8 in the Complete Rna Polymerase II Elongation Complex VI


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 VI within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:85.3
occ:1.00
 SG A:CYS110 2.4 88.6 1.0
SG A:CYS167 2.4 0.7 1.0
SG A:CYS148 2.7 87.0 1.0
SG A:CYS107 2.8 0.7 1.0
CB A:CYS110 3.1 90.9 1.0
O A:MET108 3.2 95.6 1.0
CB A:CYS107 3.3 98.4 1.0
CB A:CYS148 3.4 90.8 1.0
N A:CYS110 3.6 94.3 1.0
CA A:CYS110 3.8 91.8 1.0
CB A:CYS167 3.8 0.9 1.0
C A:CYS107 4.3 95.0 1.0
N A:GLY111 4.3 89.9 1.0
O A:CYS107 4.3 93.9 1.0
O A:CYS167 4.3 0.1 1.0
CA A:CYS107 4.4 95.5 1.0
C A:MET108 4.4 96.2 1.0
C A:CYS110 4.5 90.9 1.0
ND2 A:ASN169 4.6 0.9 1.0
N A:MET108 4.7 95.0 1.0
C A:HIS109 4.8 97.3 1.0
CA A:CYS167 4.9 0.8 1.0
CA A:CYS148 4.9 92.5 1.0
CB A:HIS109 5.0 0.7 1.0
C A:CYS167 5.0 0.4 1.0

Zinc binding site 2 out of 8 in 3hoy

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Zinc binding site 2 out of 8 in the Complete Rna Polymerase II Elongation Complex VI


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 VI within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:53.5
occ:1.00
 NE2 A:HIS80 2.2 38.9 1.0
SG A:CYS77 2.3 42.7 1.0
SG A:CYS70 2.3 67.5 1.0
SG A:CYS67 2.3 60.3 1.0
CD2 A:HIS80 2.6 40.4 1.0
CB A:CYS70 3.3 73.7 1.0
CE1 A:HIS80 3.4 40.4 1.0
CB A:CYS77 3.5 42.0 1.0
CB A:CYS67 3.8 70.0 1.0
CG A:HIS80 3.9 42.6 1.0
O A:CYS67 4.0 76.0 1.0
OE1 A:GLN68 4.2 59.1 1.0
ND1 A:HIS80 4.3 40.6 1.0
CA A:CYS77 4.4 44.0 1.0
CD A:GLN68 4.5 63.1 1.0
O A:PRO78 4.6 45.5 1.0
CA A:CYS70 4.7 77.2 1.0
NE2 A:GLN68 4.8 60.2 1.0
O A:GLN71 4.8 78.8 1.0
C A:CYS67 4.8 75.4 1.0
CA A:CYS67 4.9 74.6 1.0

Zinc binding site 3 out of 8 in 3hoy

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Zinc binding site 3 out of 8 in the Complete Rna Polymerase II Elongation Complex VI


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 VI within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:73.6
occ:1.00
 SG B:CYS1166 2.2 30.4 1.0
SG B:CYS1182 2.3 48.6 1.0
SG B:CYS1163 2.4 41.1 1.0
SG B:CYS1185 2.5 49.8 1.0
CB B:CYS1185 2.7 53.2 1.0
CB B:CYS1163 3.2 48.8 1.0
CB B:CYS1166 3.9 42.7 1.0
CB B:CYS1182 3.9 52.1 1.0
CA B:CYS1185 4.1 55.8 1.0
O B:CYS1182 4.3 59.1 1.0
N B:CYS1166 4.4 51.3 1.0
O B:CYS1166 4.5 59.0 1.0
N B:CYS1185 4.6 56.0 1.0
CA B:CYS1163 4.7 49.7 1.0
CA B:CYS1166 4.7 50.4 1.0
CB B:THR1170 4.9 46.1 1.0

Zinc binding site 4 out of 8 in 3hoy

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Zinc binding site 4 out of 8 in the Complete Rna Polymerase II Elongation Complex VI


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 VI within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:65.1
occ:1.00
 SG C:CYS86 2.1 39.1 1.0
SG C:CYS88 2.2 30.5 1.0
SG C:CYS92 2.3 45.0 1.0
SG C:CYS95 2.3 49.5 1.0
CB C:CYS86 3.1 40.9 1.0
CB C:CYS95 3.3 55.1 1.0
N C:CYS92 3.3 57.0 1.0
CB C:CYS92 3.6 54.0 1.0
CB C:CYS88 3.7 41.9 1.0
C C:HIS91 3.8 56.5 1.0
CA C:CYS92 3.9 56.9 1.0
N C:CYS95 4.0 57.4 1.0
CA C:HIS91 4.0 55.9 1.0
CA C:CYS95 4.3 56.1 1.0
O C:CYS92 4.3 61.9 1.0
C C:CYS92 4.3 59.6 1.0
N C:CYS88 4.4 42.1 1.0
CB C:LYS94 4.5 57.5 1.0
C C:LYS94 4.5 57.2 1.0
CA C:CYS86 4.5 43.5 1.0
O C:HIS91 4.6 58.1 1.0
CA C:CYS88 4.6 45.3 1.0
N C:LYS94 4.7 57.5 1.0
CA C:LYS94 4.8 56.8 1.0
C C:CYS86 4.8 44.2 1.0
N C:HIS91 4.9 56.0 1.0
CB C:HIS91 5.0 54.4 1.0

Zinc binding site 5 out of 8 in 3hoy

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Zinc binding site 5 out of 8 in the Complete Rna Polymerase II Elongation Complex VI


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 VI within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:75.8
occ:1.00
 SG I:CYS32 2.2 83.8 1.0
SG I:CYS10 2.3 87.1 1.0
SG I:CYS29 2.4 85.9 1.0
CB I:CYS10 2.5 87.2 1.0
SG I:CYS7 2.5 69.4 1.0
CB I:CYS32 2.8 82.4 1.0
CB I:CYS29 3.4 86.0 1.0
N I:CYS32 3.4 84.6 1.0
CA I:CYS32 3.7 82.3 1.0
CB I:CYS7 3.8 79.3 1.0
CA I:CYS10 3.9 86.4 1.0
C I:THR31 4.3 86.5 1.0
C I:CYS10 4.4 84.2 1.0
CB I:THR31 4.4 86.5 1.0
C I:CYS32 4.4 80.8 1.0
N I:CYS10 4.5 89.0 1.0
O I:CYS10 4.6 82.6 1.0
CB I:TYR34 4.7 63.4 1.0
O I:ARG8 4.7 86.0 1.0
N I:THR31 4.7 87.5 1.0
CA I:THR31 4.7 86.8 1.0
OG1 I:THR31 4.8 84.4 1.0
CA I:CYS29 4.8 86.9 1.0
O I:CYS32 4.9 82.4 1.0
CB I:ASN12 4.9 83.3 1.0

Zinc binding site 6 out of 8 in 3hoy

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Zinc binding site 6 out of 8 in the Complete Rna Polymerase II Elongation Complex VI


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 VI within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.7
occ:1.00
 SG I:CYS75 2.5 0.5 1.0
SG I:CYS106 2.6 88.4 1.0
CB I:CYS75 2.8 0.5 1.0
SG I:CYS78 3.0 0.0 1.0
SG I:CYS103 3.0 1.0 1.0
CB I:CYS103 3.6 0.7 1.0
CB I:HIS108 3.8 1.0 1.0
CD I:LYS77 3.8 0.9 1.0
CB I:CYS106 3.8 94.4 1.0
N I:CYS78 4.0 0.5 1.0
CG I:LYS77 4.1 0.3 1.0
CB I:CYS78 4.1 0.3 1.0
CA I:CYS75 4.3 0.5 1.0
CD2 I:HIS108 4.3 0.5 1.0
CG I:HIS108 4.4 0.4 1.0
CA I:CYS78 4.5 0.5 1.0
CD I:PRO76 4.6 0.5 1.0
O I:SER105 4.6 0.5 1.0
N I:LYS77 4.6 0.5 1.0
N I:HIS108 4.7 0.4 1.0
C I:CYS75 4.7 0.3 1.0
N I:PRO76 4.8 0.2 1.0
CA I:HIS108 4.8 0.2 1.0
C I:LYS77 4.9 0.8 1.0
CA I:CYS103 4.9 0.8 1.0
C I:CYS78 5.0 0.1 1.0

Zinc binding site 7 out of 8 in 3hoy

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Zinc binding site 7 out of 8 in the Complete Rna Polymerase II Elongation Complex VI


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 VI within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:64.7
occ:1.00
 SG J:CYS45 2.1 46.7 1.0
SG J:CYS46 2.2 60.8 1.0
SG J:CYS7 2.2 63.2 1.0
SG J:CYS10 2.4 50.8 1.0
N J:CYS46 2.7 57.5 1.0
CA J:CYS46 3.1 59.0 1.0
CB J:CYS45 3.1 51.9 1.0
CB J:CYS46 3.2 58.9 1.0
C J:CYS45 3.3 56.6 1.0
CB J:CYS7 3.4 57.5 1.0
CB J:CYS10 3.4 54.8 1.0
N J:CYS10 3.6 53.9 1.0
CA J:CYS45 3.8 55.2 1.0
O J:CYS45 4.0 57.9 1.0
CA J:CYS10 4.1 55.1 1.0
N J:GLY11 4.5 56.3 1.0
N J:CYS45 4.6 58.1 1.0
CB J:SER9 4.6 48.6 1.0
C J:CYS46 4.6 60.1 1.0
NE J:ARG43 4.6 71.4 1.0
C J:SER9 4.7 50.5 1.0
CA J:CYS7 4.8 54.6 1.0
C J:CYS10 4.8 55.6 1.0
O J:ARG43 5.0 64.5 1.0
C J:CYS7 5.0 53.3 1.0
CA J:SER9 5.0 48.6 1.0

Zinc binding site 8 out of 8 in 3hoy

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Zinc binding site 8 out of 8 in the Complete Rna Polymerase II Elongation Complex VI


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 VI within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.9
occ:1.00
 SG L:CYS34 2.4 99.1 1.0
SG L:CYS48 2.6 0.2 1.0
CB L:CYS48 2.7 0.5 1.0
SG L:CYS31 2.8 0.2 1.0
SG L:CYS51 3.1 0.8 1.0
O L:CYS51 3.2 0.5 1.0
CB L:CYS31 3.5 0.6 1.0
CB L:CYS34 4.1 0.8 1.0
CA L:CYS48 4.2 0.1 1.0
C L:CYS51 4.3 0.6 1.0
CB L:CYS51 4.4 0.1 1.0
N L:CYS51 4.5 0.1 1.0
C L:CYS48 4.5 0.3 1.0
CA L:CYS51 4.6 0.2 1.0
OG L:SER36 4.7 0.5 1.0
N L:LYS49 4.7 0.3 1.0
O L:GLY52 4.8 0.2 1.0
O L:LYS49 4.8 0.6 1.0
O L:HIS53 4.9 0.2 1.0
CA L:CYS31 4.9 0.4 1.0
N L:CYS48 5.0 0.4 1.0

Reference:

J.F.Sydow, F.Brueckner, A.C.M.Cheung, G.E.Damsma, S.Dengl, E.Lehmann, D.Vassylyev, P.Cramer. Structural Basis of Transcription: Mismatch-Specific Fidelity Mechanisms and Paused Rna Polymerase II with Frayed Rna. Mol.Cell V. 34 710 2009.
ISSN: ISSN 1097-2765
PubMed: 19560423
DOI: 10.1016/J.MOLCEL.2009.06.002
Page generated: Wed Dec 16 04:24:37 2020

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