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Zinc in PDB 3hov: Complete Rna Polymerase II Elongation Complex II

Enzymatic activity of Complete Rna Polymerase II Elongation Complex II

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

Protein crystallography data

The structure of Complete Rna Polymerase II Elongation Complex II, PDB code: 3hov 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 / 3.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.252, 393.383, 283.091, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 22.6

Other elements in 3hov:

The structure of Complete Rna Polymerase II Elongation Complex II 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 II (pdb code 3hov). 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 II, PDB code: 3hov:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3hov

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


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

b:86.3
occ:1.00
 SG A:CYS110 2.4 0.7 1.0
SG A:CYS167 2.6 0.6 1.0
SG A:CYS148 2.6 0.3 1.0
SG A:CYS107 2.7 0.2 1.0
CB A:CYS110 3.0 0.2 1.0
O A:CYS167 3.3 0.9 1.0
CB A:CYS148 3.3 0.4 1.0
CB A:CYS107 3.4 0.6 1.0
O A:MET108 3.8 0.2 1.0
N A:CYS110 3.8 0.6 1.0
CB A:CYS167 3.9 0.3 1.0
CA A:CYS110 4.0 0.8 1.0
O A:GLY166 4.2 1.0 1.0
ND2 A:ASN169 4.3 0.2 1.0
C A:CYS167 4.3 0.5 1.0
CA A:CYS167 4.6 0.5 1.0
CA A:CYS107 4.7 0.7 1.0
C A:CYS107 4.8 0.0 1.0
O A:CYS107 4.8 0.8 1.0
N A:GLY111 4.8 97.7 1.0
CA A:CYS148 4.8 0.6 1.0
CB A:HIS109 4.8 0.6 1.0
C A:CYS110 4.9 99.1 1.0
C A:GLY166 4.9 0.3 1.0
C A:HIS109 4.9 0.7 1.0
ND1 A:HIS109 5.0 0.9 1.0

Zinc binding site 2 out of 8 in 3hov

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


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

b:51.2
occ:1.00
 NE2 A:HIS80 2.2 54.5 1.0
SG A:CYS77 2.2 49.5 1.0
SG A:CYS70 2.3 75.2 1.0
SG A:CYS67 2.3 78.7 1.0
CD2 A:HIS80 2.4 54.3 1.0
CB A:CYS70 3.3 82.4 1.0
CE1 A:HIS80 3.5 55.4 1.0
CB A:CYS77 3.7 49.6 1.0
CG A:HIS80 3.8 55.0 1.0
CB A:CYS67 3.8 80.9 1.0
O A:CYS67 3.9 87.7 1.0
ND1 A:HIS80 4.2 53.7 1.0
OE1 A:GLN68 4.2 72.0 1.0
O A:PRO78 4.4 52.1 1.0
CD A:GLN68 4.5 75.3 1.0
CA A:CYS77 4.6 49.2 1.0
CA A:CYS70 4.7 87.0 1.0
C A:CYS67 4.8 86.3 1.0
CA A:CYS67 4.8 84.8 1.0
NE2 A:GLN68 4.9 72.8 1.0
C A:CYS70 5.0 88.8 1.0
CB A:HIS80 5.0 55.2 1.0

Zinc binding site 3 out of 8 in 3hov

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


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

b:54.7
occ:1.00
 SG B:CYS1166 2.2 46.4 1.0
SG B:CYS1182 2.2 56.6 1.0
SG B:CYS1185 2.4 61.0 1.0
SG B:CYS1163 2.6 52.7 1.0
CB B:CYS1185 2.8 62.6 1.0
CB B:CYS1163 3.1 53.8 1.0
CB B:CYS1182 3.7 59.1 1.0
CB B:CYS1166 3.9 52.8 1.0
O B:CYS1166 4.2 60.4 1.0
CA B:CYS1185 4.2 64.4 1.0
O B:CYS1182 4.2 65.3 1.0
N B:CYS1166 4.3 55.5 1.0
CB B:THR1170 4.6 50.4 1.0
CA B:CYS1163 4.6 53.9 1.0
N B:CYS1185 4.6 65.2 1.0
CA B:CYS1166 4.7 55.0 1.0
CG2 B:THR1170 4.7 53.7 1.0
OG1 B:THR1170 4.8 51.5 1.0
CB B:ILE1165 4.8 58.4 1.0
C B:CYS1166 4.9 57.2 1.0
CA B:CYS1182 4.9 60.9 1.0
C B:CYS1182 5.0 63.7 1.0

Zinc binding site 4 out of 8 in 3hov

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


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

b:49.5
occ:1.00
 SG C:CYS86 2.2 43.2 1.0
SG C:CYS95 2.3 55.8 1.0
SG C:CYS88 2.4 39.3 1.0
SG C:CYS92 2.5 58.7 1.0
CB C:CYS86 3.0 43.2 1.0
N C:CYS92 3.1 60.9 1.0
CB C:CYS95 3.3 57.7 1.0
CB C:CYS92 3.5 61.5 1.0
C C:HIS91 3.6 60.4 1.0
CA C:CYS92 3.8 62.4 1.0
CA C:HIS91 3.8 59.8 1.0
CB C:CYS88 3.8 45.2 1.0
N C:CYS95 4.0 59.9 1.0
O C:CYS92 4.2 65.5 1.0
C C:CYS92 4.3 64.2 1.0
CA C:CYS95 4.3 58.8 1.0
CA C:CYS86 4.4 44.5 1.0
N C:CYS88 4.5 44.1 1.0
O C:HIS91 4.5 60.8 1.0
CB C:LYS94 4.5 63.8 1.0
C C:LYS94 4.6 61.2 1.0
N C:HIS91 4.7 60.2 1.0
CB C:HIS91 4.7 58.4 1.0
C C:CYS86 4.8 44.3 1.0
CA C:CYS88 4.8 46.7 1.0
N C:LYS94 4.8 63.3 1.0
CA C:LYS94 4.9 62.5 1.0

Zinc binding site 5 out of 8 in 3hov

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


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

b:90.4
occ:1.00
 SG I:CYS10 2.2 87.8 1.0
SG I:CYS32 2.3 82.2 1.0
SG I:CYS7 2.3 82.4 1.0
SG I:CYS29 2.5 87.3 1.0
CB I:CYS29 3.2 87.3 1.0
CB I:CYS32 3.4 81.5 1.0
CB I:CYS7 3.6 90.4 1.0
CB I:CYS10 3.7 89.5 1.0
N I:CYS10 3.8 92.6 1.0
N I:CYS32 4.0 83.8 1.0
CA I:CYS10 4.0 89.9 1.0
O I:ARG8 4.2 94.7 1.0
O I:CYS10 4.2 88.0 1.0
C I:CYS10 4.2 88.1 1.0
CA I:CYS32 4.3 81.7 1.0
CB I:TYR34 4.3 64.6 1.0
CB I:THR31 4.7 86.5 1.0
CA I:CYS29 4.7 87.2 1.0
CB I:ASP9 4.8 94.3 1.0
C I:THR31 4.8 85.8 1.0
C I:CYS32 4.9 80.5 1.0
CA I:CYS7 4.9 92.8 1.0
CB I:ASN12 4.9 83.2 1.0
N I:ASN11 5.0 85.8 1.0

Zinc binding site 6 out of 8 in 3hov

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


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

b:0.5
occ:1.00
 SG I:CYS75 2.5 0.1 1.0
SG I:CYS106 2.5 0.7 1.0
CB I:CYS75 2.8 0.7 1.0
SG I:CYS78 3.0 0.1 1.0
SG I:CYS103 3.1 1.0 1.0
CB I:CYS103 3.3 0.2 1.0
CB I:HIS108 3.5 0.5 1.0
N I:CYS78 3.7 0.5 1.0
CB I:CYS106 4.1 0.8 1.0
CB I:LYS77 4.1 0.9 1.0
CB I:CYS78 4.1 0.9 1.0
N I:LYS77 4.2 0.9 1.0
CA I:CYS75 4.2 0.4 1.0
CG I:HIS108 4.3 0.6 1.0
C I:LYS77 4.4 0.5 1.0
CA I:CYS78 4.4 0.9 1.0
CA I:LYS77 4.4 1.0 1.0
CD2 I:HIS108 4.4 0.2 1.0
N I:HIS108 4.6 0.4 1.0
C I:CYS75 4.6 0.3 1.0
CA I:HIS108 4.6 0.6 1.0
O I:SER105 4.7 0.5 1.0
N I:PRO76 4.8 0.4 1.0
CA I:CYS103 4.8 0.7 1.0
CD I:PRO76 4.8 0.1 1.0
C I:CYS78 4.9 0.3 1.0
N I:HIS79 5.0 0.3 1.0

Zinc binding site 7 out of 8 in 3hov

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


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

b:61.3
occ:1.00
 SG J:CYS7 2.3 63.5 1.0
SG J:CYS46 2.3 70.0 1.0
SG J:CYS45 2.4 56.0 1.0
SG J:CYS10 2.5 68.9 1.0
CB J:CYS7 3.2 59.5 1.0
N J:CYS46 3.4 63.3 1.0
CB J:CYS10 3.5 67.5 1.0
C J:CYS45 3.5 61.3 1.0
CB J:CYS45 3.6 58.5 1.0
CB J:CYS46 3.6 65.0 1.0
CA J:CYS46 3.6 65.1 1.0
N J:CYS10 3.6 65.0 1.0
O J:CYS45 3.8 60.9 1.0
CA J:CYS10 4.0 67.2 1.0
CA J:CYS45 4.2 60.0 1.0
C J:CYS10 4.5 67.8 1.0
CB J:LYS12 4.5 73.1 1.0
N J:GLY11 4.6 69.2 1.0
NE J:ARG43 4.6 63.7 1.0
CA J:CYS7 4.6 56.7 1.0
N J:LYS12 4.7 71.1 1.0
CB J:SER9 4.7 59.5 1.0
C J:SER9 4.8 62.1 1.0
NH2 J:ARG43 4.9 61.8 1.0
O J:CYS7 5.0 57.2 1.0
N J:CYS45 5.0 61.0 1.0

Zinc binding site 8 out of 8 in 3hov

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


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

b:0.2
occ:1.00
 SG L:CYS34 2.3 93.9 1.0
SG L:CYS48 2.6 0.3 1.0
CB L:CYS51 2.6 0.3 1.0
SG L:CYS31 2.8 0.4 1.0
CB L:CYS48 2.9 0.5 1.0
O L:CYS51 3.3 0.7 1.0
N L:CYS51 3.3 0.0 1.0
SG L:CYS51 3.3 0.4 1.0
CA L:CYS51 3.4 0.6 1.0
CB L:CYS31 3.5 0.6 1.0
C L:CYS51 3.8 0.1 1.0
CB L:CYS34 3.8 0.3 1.0
CA L:CYS48 4.3 0.5 1.0
C L:ASP50 4.4 0.2 1.0
OG L:SER36 4.5 0.8 1.0
C L:CYS48 4.5 0.6 1.0
N L:LYS49 4.7 0.4 1.0
O L:CYS34 4.7 0.4 1.0
O L:LYS49 4.9 0.5 1.0
C L:LYS49 4.9 0.1 1.0
CB L:ASP50 4.9 0.4 1.0
N L:ASP50 4.9 0.4 1.0
CA L:CYS34 4.9 0.2 1.0
CA L:ASP50 5.0 0.2 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: Sat Oct 26 06:30:43 2024

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