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Zinc in PDB 3h0g: Rna Polymerase II From Schizosaccharomyces Pombe

Enzymatic activity of Rna Polymerase II From Schizosaccharomyces Pombe

All present enzymatic activity of Rna Polymerase II From Schizosaccharomyces Pombe:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II From Schizosaccharomyces Pombe, PDB code: 3h0g was solved by H.Spahr, G.Calero, D.A.Bushnell, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.70 / 3.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 163.034, 202.684, 391.258, 90.00, 90.00, 90.00
R / Rfree (%) 29.7 / 32.1

Other elements in 3h0g:

The structure of Rna Polymerase II From Schizosaccharomyces Pombe also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Rna Polymerase II From Schizosaccharomyces Pombe (pdb code 3h0g). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Rna Polymerase II From Schizosaccharomyces Pombe, PDB code: 3h0g:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 3h0g

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Zinc binding site 1 out of 16 in the Rna Polymerase II From Schizosaccharomyces Pombe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase II From Schizosaccharomyces Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:0.8
occ:1.00
CB A:CYS175 2.6 0.1 1.0
SG A:CYS109 2.8 0.7 1.0
SG A:CYS150 2.9 0.1 1.0
SG A:CYS112 2.9 0.3 1.0
SG A:CYS175 3.2 0.8 1.0
CB A:CYS112 3.6 0.5 1.0
N A:GLY176 3.9 0.6 1.0
O A:GLY174 3.9 0.0 1.0
CA A:CYS175 4.0 0.6 1.0
N A:ALA177 4.1 0.3 1.0
CB A:CYS109 4.3 0.2 1.0
CB A:CYS150 4.3 0.1 1.0
C A:GLY174 4.5 0.7 1.0
C A:CYS175 4.5 0.6 1.0
N A:CYS175 4.6 0.2 1.0
CA A:ALA177 4.6 0.8 1.0
C A:GLY176 4.7 0.4 1.0
N A:CYS112 4.7 0.5 1.0
CA A:CYS112 4.8 0.8 1.0
O A:TRP110 4.8 0.7 1.0
CA A:GLY176 4.9 0.8 1.0
O A:ALA177 5.0 0.2 1.0

Zinc binding site 2 out of 16 in 3h0g

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Zinc binding site 2 out of 16 in the Rna Polymerase II From Schizosaccharomyces Pombe


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase II From Schizosaccharomyces Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:0.8
occ:1.00
SG A:CYS79 2.5 0.6 1.0
NE2 A:HIS82 2.8 0.1 1.0
SG A:CYS69 2.8 0.6 1.0
CD2 A:HIS82 3.0 0.9 1.0
CA A:GLY61 3.6 0.9 1.0
O A:LEU60 3.8 1.0 1.0
SG A:CYS72 3.8 0.0 1.0
O A:PRO80 3.9 1.0 1.0
O A:CYS69 4.0 0.1 1.0
CE1 A:HIS82 4.0 0.4 1.0
CB A:CYS79 4.1 0.9 1.0
CB A:CYS72 4.1 0.1 1.0
CG A:HIS82 4.2 0.9 1.0
CG2 A:THR71 4.3 0.7 1.0
C A:GLY61 4.3 0.6 1.0
CB A:CYS69 4.4 0.3 1.0
O A:GLY61 4.4 0.5 1.0
N A:GLY61 4.5 0.8 1.0
C A:LEU60 4.5 0.9 1.0
N A:CYS72 4.5 0.1 1.0
CB A:THR71 4.6 0.5 1.0
ND1 A:HIS82 4.7 0.3 1.0
CA A:CYS79 4.7 0.7 1.0
O A:GLN70 4.7 0.6 1.0
CA A:CYS72 4.8 0.7 1.0
C A:CYS79 4.8 0.2 1.0
N A:GLY73 4.9 0.6 1.0
C A:CYS72 4.9 0.9 1.0
C A:CYS69 5.0 0.5 1.0
C A:THR71 5.0 0.7 1.0

Zinc binding site 3 out of 16 in 3h0g

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Zinc binding site 3 out of 16 in the Rna Polymerase II From Schizosaccharomyces Pombe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase II From Schizosaccharomyces Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:0.6
occ:1.00
SG B:CYS1173 2.5 0.6 1.0
SG B:CYS1152 2.6 0.9 1.0
SG B:CYS1155 2.6 0.8 1.0
CB B:CYS1173 3.0 0.3 1.0
CB B:CYS1152 3.2 0.3 1.0
OG B:SER1172 3.5 1.0 1.0
N B:CYS1173 3.9 0.4 1.0
O B:CYS1155 3.9 1.0 1.0
CB B:CYS1170 4.0 0.3 1.0
CA B:CYS1173 4.0 0.8 1.0
CB B:CYS1155 4.2 0.1 1.0
N B:CYS1155 4.3 0.7 1.0
SG B:CYS1170 4.3 0.4 1.0
ND2 B:ASN1175 4.6 0.4 1.0
CA B:CYS1155 4.6 0.3 1.0
C B:CYS1155 4.6 0.6 1.0
CA B:CYS1152 4.7 0.1 1.0
CB B:SER1172 4.8 0.3 1.0

Zinc binding site 4 out of 16 in 3h0g

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Zinc binding site 4 out of 16 in the Rna Polymerase II From Schizosaccharomyces Pombe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase II From Schizosaccharomyces Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:0.9
occ:1.00
SG C:CYS90 3.0 0.8 1.0
CB C:CYS96 3.2 0.3 1.0
CB C:CYS99 3.2 0.4 1.0
O C:CYS96 3.3 0.6 1.0
SG C:CYS99 3.3 0.1 1.0
CB C:CYS92 3.4 0.1 1.0
N C:CYS96 3.5 0.6 1.0
CA C:CYS96 3.7 0.3 1.0
N C:CYS99 3.7 0.2 1.0
C C:CYS96 3.8 0.5 1.0
CA C:CYS99 4.0 0.5 1.0
CB C:CYS90 4.0 0.3 1.0
SG C:CYS92 4.1 0.8 1.0
SG C:CYS96 4.2 0.5 1.0
C C:LYS98 4.3 0.6 1.0
CA C:CYS92 4.5 0.6 1.0
C C:TYR95 4.5 0.9 1.0
CB C:LYS98 4.6 0.1 1.0
N C:LYS98 4.6 0.4 1.0
C C:CYS99 4.6 0.8 1.0
N C:CYS92 4.7 0.8 1.0
C C:CYS92 4.7 0.1 1.0
CA C:LYS98 4.7 0.3 1.0
O C:CYS99 4.9 0.3 1.0
CA C:TYR95 4.9 0.9 1.0
O C:CYS92 5.0 0.2 1.0

Zinc binding site 5 out of 16 in 3h0g

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Zinc binding site 5 out of 16 in the Rna Polymerase II From Schizosaccharomyces Pombe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase II From Schizosaccharomyces Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:0.3
occ:1.00
SG I:CYS32 2.2 0.4 1.0
SG I:CYS10 2.7 0.3 1.0
SG I:CYS29 3.0 0.2 1.0
CB I:CYS29 3.3 0.7 1.0
CB I:CYS32 3.4 0.3 1.0
N I:CYS32 3.4 0.5 1.0
SG I:CYS7 3.4 0.6 1.0
CB I:ASN31 3.9 0.8 1.0
O I:CYS10 3.9 0.7 1.0
CA I:CYS32 4.0 0.5 1.0
CB I:CYS10 4.3 0.5 1.0
CB I:ASN12 4.4 0.2 1.0
C I:ASN31 4.4 0.3 1.0
CA I:ASN31 4.5 0.1 1.0
C I:CYS10 4.6 0.2 1.0
N I:ASN31 4.6 0.8 1.0
ND2 I:ASN31 4.7 0.1 1.0
CA I:CYS29 4.7 0.7 1.0
C I:CYS32 4.7 0.7 1.0
CG I:ASN31 4.8 0.0 1.0
N I:ASP33 4.8 0.6 1.0
CB I:TYR34 4.8 0.1 1.0
CA I:CYS10 4.8 0.2 1.0
N I:CYS10 4.9 0.8 1.0
ND2 I:ASN12 4.9 0.5 1.0

Zinc binding site 6 out of 16 in 3h0g

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Zinc binding site 6 out of 16 in the Rna Polymerase II From Schizosaccharomyces Pombe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase II From Schizosaccharomyces Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.4
occ:1.00
SG I:CYS103 2.6 0.4 1.0
SG I:CYS106 2.8 0.0 1.0
SG I:CYS78 3.1 0.7 1.0
CB I:CYS78 3.1 0.7 1.0
O I:HIS79 3.1 0.5 1.0
SG I:CYS75 3.2 1.0 1.0
CB I:CYS103 3.2 0.3 1.0
CB I:CYS106 3.3 0.6 1.0
N I:HIS79 3.6 0.6 1.0
C I:HIS79 3.9 0.9 1.0
C I:HIS105 4.2 0.2 1.0
O I:HIS105 4.2 0.5 1.0
CB I:CYS75 4.2 0.6 1.0
N I:CYS106 4.2 0.7 1.0
CA I:HIS79 4.4 0.4 1.0
CB I:GLN80 4.4 0.8 1.0
CA I:CYS78 4.4 0.1 1.0
CA I:CYS106 4.4 0.4 1.0
C I:CYS78 4.5 0.2 1.0
CB I:HIS105 4.6 0.2 1.0
CA I:CYS103 4.7 0.3 1.0
N I:HIS105 4.8 0.9 1.0
CA I:HIS105 4.8 0.0 1.0
N I:GLN80 4.8 0.5 1.0
O I:CYS75 4.9 0.5 1.0

Zinc binding site 7 out of 16 in 3h0g

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Zinc binding site 7 out of 16 in the Rna Polymerase II From Schizosaccharomyces Pombe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase II From Schizosaccharomyces Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:87.5
occ:1.00
SG J:CYS44 2.2 0.8 1.0
SG J:CYS7 2.2 0.8 1.0
SG J:CYS45 2.4 0.6 1.0
CB J:CYS45 2.4 0.3 1.0
SG J:CYS10 2.9 96.9 1.0
OG J:SER9 3.0 0.1 1.0
CA J:CYS45 3.0 0.2 1.0
N J:CYS45 3.1 0.9 1.0
CB J:CYS7 3.2 0.7 1.0
N J:CYS10 3.3 0.2 1.0
CB J:CYS10 3.4 0.5 1.0
C J:CYS44 3.5 96.5 1.0
O J:CYS44 3.7 0.9 1.0
CB J:CYS44 3.8 0.8 1.0
CA J:CYS10 3.9 0.6 1.0
CB J:SER9 4.1 0.0 1.0
N J:SER9 4.2 0.0 1.0
C J:SER9 4.3 0.2 1.0
CA J:CYS44 4.4 97.6 1.0
C J:CYS45 4.4 0.4 1.0
CA J:SER9 4.4 0.9 1.0
CA J:CYS7 4.5 0.5 1.0
C J:CYS10 4.7 0.3 1.0
C J:CYS7 4.7 0.2 1.0
NE J:ARG42 4.8 86.2 1.0
N J:PHE8 4.9 87.7 1.0
N J:ARG46 5.0 0.1 1.0

Zinc binding site 8 out of 16 in 3h0g

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Zinc binding site 8 out of 16 in the Rna Polymerase II From Schizosaccharomyces Pombe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rna Polymerase II From Schizosaccharomyces Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.1
occ:1.00
SG L:CYS27 2.2 0.3 1.0
SG L:CYS24 2.8 0.5 1.0
SG L:CYS44 2.9 0.2 1.0
CB L:CYS24 3.0 0.3 1.0
CB L:CYS41 3.2 0.3 1.0
CB L:CYS27 3.3 0.4 1.0
SG L:CYS41 3.6 0.8 1.0
O L:GLY45 3.8 0.1 1.0
CB L:CYS44 4.0 1.0 1.0
N L:CYS27 4.3 0.2 1.0
CA L:CYS27 4.4 0.8 1.0
CA L:CYS24 4.6 0.4 1.0
CA L:CYS41 4.7 0.5 1.0
ND2 L:ASN31 4.7 0.4 1.0
N L:GLY45 4.7 0.9 1.0
N L:GLY28 4.8 0.1 1.0
OD1 L:ASN31 4.8 0.2 1.0
C L:GLY45 4.9 0.9 1.0

Zinc binding site 9 out of 16 in 3h0g

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Zinc binding site 9 out of 16 in the Rna Polymerase II From Schizosaccharomyces Pombe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Rna Polymerase II From Schizosaccharomyces Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn2456

b:0.9
occ:1.00
N M:ALA177 2.3 0.2 1.0
CA M:ALA177 2.6 0.9 1.0
O M:ALA177 2.7 0.5 1.0
C M:ALA177 2.9 0.2 1.0
SG M:CYS109 3.1 0.5 1.0
SG M:CYS150 3.2 0.5 1.0
CB M:CYS175 3.3 0.2 1.0
N M:GLY176 3.5 0.8 1.0
C M:GLY176 3.5 0.1 1.0
SG M:CYS175 3.6 0.8 1.0
SG M:CYS112 3.8 0.1 1.0
O M:TRP110 3.9 0.7 1.0
N M:ALA178 4.0 0.0 1.0
CA M:GLY176 4.1 0.3 1.0
CB M:ALA177 4.1 0.7 1.0
CB M:CYS109 4.2 0.4 1.0
CB M:ALA178 4.3 0.8 1.0
CB M:CYS112 4.4 0.2 1.0
C M:CYS175 4.4 0.3 1.0
O M:GLY176 4.5 0.1 1.0
CA M:CYS175 4.5 0.9 1.0
C M:TRP110 4.5 0.2 1.0
CB M:CYS150 4.6 0.1 1.0
CA M:ALA178 4.8 0.6 1.0
N M:ASN111 4.9 0.5 1.0
N M:CYS112 4.9 0.6 1.0

Zinc binding site 10 out of 16 in 3h0g

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Zinc binding site 10 out of 16 in the Rna Polymerase II From Schizosaccharomyces Pombe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Rna Polymerase II From Schizosaccharomyces Pombe within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn2457

b:0.2
occ:1.00
SG M:CYS79 2.5 0.2 1.0
NE2 M:HIS82 2.8 0.5 1.0
SG M:CYS69 2.9 0.2 1.0
CD2 M:HIS82 2.9 0.7 1.0
CA M:GLY61 3.5 0.4 1.0
O M:LEU60 3.7 0.6 1.0
O M:PRO80 3.8 0.8 1.0
SG M:CYS72 3.9 0.2 1.0
CE1 M:HIS82 3.9 0.5 1.0
O M:CYS69 4.1 0.5 1.0
CB M:CYS79 4.1 0.7 1.0
CG M:HIS82 4.1 0.9 1.0
C M:GLY61 4.2 0.5 1.0
CB M:CYS72 4.3 0.1 1.0
O M:GLY61 4.4 0.4 1.0
CG2 M:THR71 4.4 0.1 1.0
N M:GLY61 4.4 0.2 1.0
C M:LEU60 4.4 0.3 1.0
CB M:CYS69 4.4 0.8 1.0
ND1 M:HIS82 4.6 0.9 1.0
CA M:CYS79 4.6 1.0 1.0
CB M:THR71 4.7 0.6 1.0
N M:CYS72 4.7 0.8 1.0
C M:CYS79 4.7 0.1 1.0
O M:GLN70 4.9 0.5 1.0
CA M:CYS72 4.9 0.3 1.0
C M:PRO80 4.9 0.1 1.0
N M:PRO80 4.9 0.7 1.0
N M:GLY73 5.0 0.1 1.0

Reference:

H.Spahr, G.Calero, D.A.Bushnell, R.D.Kornberg. Schizosacharomyces Pombe Rna Polymerase II at 3.6-A Resolution. Proc.Natl.Acad.Sci.Usa V. 106 9185 2009.
ISSN: ISSN 0027-8424
PubMed: 19458260
DOI: 10.1073/PNAS.0903361106
Page generated: Wed Dec 16 04:22:33 2020

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