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Zinc in PDB 3h3v: Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site

Enzymatic activity of Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site

All present enzymatic activity of Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site:
2.7.7.6;

Protein crystallography data

The structure of Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site, PDB code: 3h3v was solved by S.Dengl, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 4.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.470, 391.620, 284.120, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.1

Other elements in 3h3v:

The structure of Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site (pdb code 3h3v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site, PDB code: 3h3v:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3h3v

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Zinc binding site 1 out of 8 in the Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1734

b:0.4
occ:1.00
 SG B:CYS110 2.4 0.7 1.0
SG B:CYS167 2.6 0.2 1.0
SG B:CYS148 2.7 0.9 1.0
SG B:CYS107 2.7 0.1 1.0
CB B:CYS110 3.1 0.5 1.0
O B:CYS167 3.2 0.3 1.0
CB B:CYS107 3.2 0.6 1.0
CB B:CYS148 3.4 0.6 1.0
O B:MET108 3.6 0.2 1.0
N B:CYS110 3.9 0.4 1.0
CB B:CYS167 3.9 0.8 1.0
CA B:CYS110 4.0 0.7 1.0
C B:CYS167 4.2 0.1 1.0
O B:GLY166 4.3 0.1 1.0
ND2 B:ASN169 4.5 0.6 1.0
CA B:CYS107 4.5 0.5 1.0
N B:GLY111 4.6 0.0 1.0
CA B:CYS167 4.6 0.9 1.0
O B:CYS148 4.7 0.0 1.0
C B:CYS107 4.7 0.9 1.0
C B:MET108 4.8 0.5 1.0
CB B:HIS109 4.9 0.7 1.0
C B:CYS110 4.9 0.6 1.0
CA B:CYS148 4.9 0.5 1.0
C B:HIS109 4.9 0.7 1.0

Zinc binding site 2 out of 8 in 3h3v

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Zinc binding site 2 out of 8 in the Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1735

b:0.3
occ:1.00
 NE2 B:HIS80 2.3 0.8 1.0
SG B:CYS70 2.3 0.1 1.0
SG B:CYS77 2.3 0.4 1.0
SG B:CYS67 2.6 0.4 1.0
CD2 B:HIS80 2.7 0.4 1.0
CB B:CYS67 3.0 0.9 1.0
CB B:CYS70 3.1 0.5 1.0
CE1 B:HIS80 3.4 0.6 1.0
O B:CYS67 3.6 0.4 1.0
CB B:CYS77 3.6 0.0 1.0
CG B:HIS80 3.9 0.9 1.0
CA B:CYS67 4.1 0.1 1.0
OE1 B:GLN68 4.2 0.3 1.0
ND1 B:HIS80 4.2 0.3 1.0
C B:CYS67 4.3 0.0 1.0
CA B:CYS70 4.4 0.5 1.0
O B:GLN71 4.4 0.3 1.0
C B:CYS70 4.6 0.8 1.0
CA B:CYS77 4.6 0.8 1.0
O B:CYS70 4.7 0.1 1.0
CD B:GLN68 4.8 0.9 1.0
O B:PRO78 4.8 0.8 1.0

Zinc binding site 3 out of 8 in 3h3v

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Zinc binding site 3 out of 8 in the Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1225

b:0.7
occ:1.00
 SG C:CYS1182 2.3 0.2 1.0
SG C:CYS1166 2.3 96.5 1.0
SG C:CYS1185 2.6 0.2 1.0
SG C:CYS1163 2.6 0.2 1.0
CB C:CYS1185 2.6 0.9 1.0
CB C:CYS1163 2.8 0.9 1.0
CB C:CYS1166 4.0 0.8 1.0
O C:CYS1182 4.0 0.7 1.0
CB C:CYS1182 4.1 0.5 1.0
CA C:CYS1185 4.1 0.3 1.0
O C:CYS1166 4.1 0.9 1.0
CA C:CYS1163 4.2 0.8 1.0
N C:CYS1166 4.5 0.1 1.0
OG1 C:THR1170 4.6 96.2 1.0
CA C:CYS1166 4.7 0.5 1.0
N C:CYS1185 4.7 0.1 1.0
C C:CYS1166 4.9 0.1 1.0
C C:CYS1182 5.0 0.3 1.0
CB C:THR1170 5.0 97.5 1.0

Zinc binding site 4 out of 8 in 3h3v

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Zinc binding site 4 out of 8 in the Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn319

b:98.4
occ:1.00
 SG D:CYS86 2.3 98.4 1.0
SG D:CYS88 2.4 0.6 1.0
SG D:CYS95 2.4 0.2 1.0
SG D:CYS92 2.6 0.4 1.0
CB D:CYS86 2.9 0.4 1.0
N D:CYS92 3.0 0.4 1.0
CB D:CYS95 3.5 0.7 1.0
CB D:CYS92 3.6 0.8 1.0
O D:CYS92 3.7 0.5 1.0
CA D:CYS92 3.7 0.3 1.0
C D:HIS91 3.7 0.2 1.0
CB D:CYS88 3.8 0.5 1.0
CA D:HIS91 3.9 0.6 1.0
C D:CYS92 4.0 0.3 1.0
N D:CYS95 4.3 0.7 1.0
CA D:CYS86 4.3 0.1 1.0
C D:LYS94 4.4 0.4 1.0
CA D:CYS95 4.5 0.4 1.0
N D:CYS88 4.6 0.9 1.0
C D:CYS86 4.6 0.7 1.0
O D:CYS86 4.7 0.8 1.0
O D:HIS91 4.7 0.3 1.0
O D:LYS94 4.7 0.1 1.0
CA D:CYS88 4.8 0.2 1.0
N D:LYS94 4.8 0.2 1.0
CB D:LYS94 4.8 0.1 1.0
N D:HIS91 4.8 0.3 1.0
CB D:HIS91 4.8 0.7 1.0
CA D:LYS94 4.9 0.0 1.0
O D:SER83 5.0 0.1 1.0

Zinc binding site 5 out of 8 in 3h3v

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Zinc binding site 5 out of 8 in the Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn123

b:0.9
occ:1.00
 SG J:CYS10 2.2 0.6 1.0
SG J:CYS32 2.4 0.7 1.0
SG J:CYS29 2.4 0.2 1.0
SG J:CYS7 2.5 0.0 1.0
CB J:CYS29 3.2 0.4 1.0
CB J:CYS32 3.5 0.4 1.0
O J:CYS10 3.6 0.6 1.0
CB J:CYS10 3.8 0.8 1.0
N J:CYS32 3.9 0.2 1.0
N J:CYS10 4.0 1.0 1.0
O J:ARG8 4.0 0.1 1.0
CB J:CYS7 4.1 0.1 1.0
C J:CYS10 4.2 0.6 1.0
CA J:CYS10 4.2 0.1 1.0
CB J:THR31 4.2 1.0 1.0
CA J:CYS32 4.3 0.3 1.0
OG1 J:THR31 4.4 0.4 1.0
CB J:TYR34 4.5 0.6 1.0
CB J:ASP9 4.6 0.3 1.0
CA J:CYS29 4.7 0.3 1.0
C J:THR31 4.7 0.2 1.0
O J:CYS7 4.8 0.2 1.0
CA J:THR31 4.9 0.2 1.0
N J:THR31 5.0 0.0 1.0

Zinc binding site 6 out of 8 in 3h3v

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Zinc binding site 6 out of 8 in the Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn124

b:0.0
occ:1.00
 SG J:CYS75 2.5 0.4 1.0
SG J:CYS106 2.6 0.6 1.0
CB J:CYS106 2.8 0.4 1.0
SG J:CYS78 3.0 0.0 1.0
SG J:CYS103 3.1 0.1 1.0
CB J:CYS103 3.2 0.1 1.0
CB J:CYS75 3.2 0.7 1.0
CB J:HIS108 3.7 0.8 1.0
N J:CYS78 3.9 0.8 1.0
CB J:LYS77 4.0 0.9 1.0
CB J:CYS78 4.3 0.1 1.0
CA J:CYS106 4.3 0.0 1.0
O J:SER105 4.4 0.9 1.0
CG J:HIS108 4.5 0.8 1.0
CA J:CYS78 4.6 0.8 1.0
N J:HIS108 4.7 0.9 1.0
CA J:LYS77 4.7 0.0 1.0
N J:LYS77 4.7 0.1 1.0
CD2 J:HIS108 4.7 0.2 1.0
CA J:CYS75 4.7 0.3 1.0
C J:LYS77 4.7 0.8 1.0
CG J:LYS77 4.7 0.2 1.0
CA J:CYS103 4.8 0.6 1.0
CA J:HIS108 4.8 0.3 1.0
C J:CYS106 4.9 0.0 1.0
C J:SER105 5.0 0.2 1.0
N J:CYS106 5.0 0.3 1.0

Zinc binding site 7 out of 8 in 3h3v

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Zinc binding site 7 out of 8 in the Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn71

b:0.1
occ:1.00
 SG K:CYS45 2.3 0.2 1.0
SG K:CYS46 2.3 0.5 1.0
SG K:CYS10 2.3 0.8 1.0
SG K:CYS7 2.4 0.3 1.0
CB K:CYS10 2.8 0.8 1.0
CB K:CYS45 3.0 0.5 1.0
N K:CYS46 3.1 0.9 1.0
N K:CYS10 3.4 0.6 1.0
CB K:CYS7 3.4 0.6 1.0
CB K:CYS46 3.5 0.9 1.0
C K:CYS45 3.5 0.8 1.0
CA K:CYS46 3.6 0.3 1.0
CA K:CYS10 3.7 0.7 1.0
CA K:CYS45 3.9 0.6 1.0
O K:CYS45 4.3 0.2 1.0
N K:GLY11 4.3 0.2 1.0
CB K:SER9 4.5 0.2 1.0
NH2 K:ARG43 4.5 0.8 1.0
C K:CYS10 4.5 0.8 1.0
NE K:ARG43 4.5 0.6 1.0
C K:SER9 4.6 0.4 1.0
CZ K:ARG43 4.7 0.8 1.0
N K:CYS45 4.7 0.1 1.0
CA K:CYS7 4.9 0.2 1.0
CG K:ARG43 4.9 0.8 1.0
CA K:SER9 4.9 0.1 1.0

Zinc binding site 8 out of 8 in 3h3v

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Zinc binding site 8 out of 8 in the Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Yeast Rnap II Containing Poly(A)-Signal Sequence in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn71

b:0.5
occ:1.00
 SG M:CYS34 2.3 1.0 1.0
SG M:CYS48 2.6 0.1 1.0
CB M:CYS48 2.6 0.4 1.0
CB M:CYS51 2.7 0.9 1.0
SG M:CYS31 2.9 0.2 1.0
SG M:CYS51 3.4 0.6 1.0
O M:CYS51 3.6 0.2 1.0
CB M:CYS31 3.6 0.5 1.0
CA M:CYS51 3.6 0.3 1.0
N M:CYS51 3.6 0.2 1.0
CB M:CYS34 3.9 0.2 1.0
C M:CYS51 3.9 0.4 1.0
CA M:CYS48 4.0 0.3 1.0
C M:CYS48 4.4 0.4 1.0
N M:LYS49 4.6 0.9 1.0
N M:CYS48 4.7 0.6 1.0
C M:ASP50 4.7 0.6 1.0
N M:CYS34 4.8 0.2 1.0
CA M:CYS34 4.8 0.1 1.0
O M:CYS34 4.8 0.5 1.0
O M:CYS48 5.0 0.7 1.0
CA M:CYS31 5.0 0.8 1.0

Reference:

S.Dengl, P.Cramer. Torpedo Nuclease RAT1 Is Insufficient to Terminate Rna Polymerase II in Vitro J.Biol.Chem. V. 284 21270 2009.
ISSN: ISSN 0021-9258
PubMed: 19535338
DOI: 10.1074/JBC.M109.013847
Page generated: Thu Oct 24 14:12:30 2024

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