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Zinc in PDB 5fmf: The P-Lobe of Rna Polymerase II Pre-Initiation Complex

Enzymatic activity of The P-Lobe of Rna Polymerase II Pre-Initiation Complex

All present enzymatic activity of The P-Lobe of Rna Polymerase II Pre-Initiation Complex:
2.7.7.6; 3.6.4.12;

Other elements in 5fmf:

The structure of The P-Lobe of Rna Polymerase II Pre-Initiation Complex also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The P-Lobe of Rna Polymerase II Pre-Initiation Complex (pdb code 5fmf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the The P-Lobe of Rna Polymerase II Pre-Initiation Complex, PDB code: 5fmf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 5fmf

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Zinc binding site 1 out of 9 in the The P-Lobe of Rna Polymerase II Pre-Initiation Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The P-Lobe of Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Zn310

b:1.0
occ:1.00
 SG 2:CYS274 2.2 1.0 1.0
CB 2:CYS299 2.6 1.0 1.0
SG 2:CYS271 2.9 1.0 1.0
CB 2:CYS271 3.1 1.0 1.0
SG 2:CYS302 3.2 1.0 1.0
N 2:CYS302 3.3 1.0 1.0
SG 2:CYS299 3.4 1.0 1.0
CA 2:CYS299 3.5 1.0 1.0
CB 2:CYS274 3.8 1.0 1.0
C 2:CYS299 3.9 1.0 1.0
CB 2:CYS302 3.9 1.0 1.0
CA 2:CYS302 4.0 1.0 1.0
N 2:ALA301 4.1 1.0 1.0
O 2:CYS299 4.2 1.0 1.0
C 2:ALA301 4.3 1.0 1.0
CB 2:ALA301 4.3 1.0 1.0
O 2:GLU276 4.3 1.0 1.0
O 2:LYS278 4.3 1.0 1.0
CA 2:ALA301 4.4 1.0 1.0
CG2 2:VAL279 4.6 1.0 1.0
CA 2:CYS271 4.6 1.0 1.0
N 2:GLY303 4.6 1.0 1.0
N 2:GLU300 4.6 1.0 1.0
ND2 2:ASN304 4.7 1.0 1.0
C 2:CYS302 4.8 1.0 1.0
CA 2:CYS274 4.8 1.0 1.0
O 2:CYS274 4.8 1.0 1.0
N 2:CYS299 4.9 1.0 1.0
C 2:CYS274 4.9 1.0 1.0
N 2:GLU276 4.9 1.0 1.0

Zinc binding site 2 out of 9 in 5fmf

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Zinc binding site 2 out of 9 in the The P-Lobe of Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The P-Lobe of Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:1.0
occ:1.00
 SG A:CYS148 2.3 1.0 1.0
SG A:CYS110 2.3 1.0 1.0
SG A:CYS167 2.4 1.0 1.0
SG A:CYS107 2.4 1.0 1.0
CB A:CYS167 2.6 1.0 1.0
CB A:CYS110 3.1 1.0 1.0
CB A:CYS148 3.1 1.0 1.0
CB A:CYS107 3.3 1.0 1.0
N A:CYS110 3.7 1.0 1.0
CA A:CYS110 4.0 1.0 1.0
CA A:CYS167 4.0 1.0 1.0
O A:CYS167 4.2 1.0 1.0
O A:GLY166 4.2 1.0 1.0
C A:CYS167 4.3 1.0 1.0
CA A:CYS148 4.6 1.0 1.0
CA A:CYS107 4.7 1.0 1.0
N A:CYS167 4.8 1.0 1.0
C A:HIS109 4.8 1.0 1.0
C A:CYS110 4.8 1.0 1.0
C A:GLY166 4.9 1.0 1.0
CB A:HIS109 4.9 1.0 1.0
NE2 A:GLN171 4.9 1.0 1.0
CD2 A:HIS109 4.9 1.0 1.0
N A:GLY111 5.0 1.0 1.0

Zinc binding site 3 out of 9 in 5fmf

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Zinc binding site 3 out of 9 in the The P-Lobe of Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The P-Lobe of Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:1.0
occ:1.00
 NE2 A:HIS80 1.9 1.0 1.0
SG A:CYS70 2.2 1.0 1.0
CE1 A:HIS80 2.3 1.0 1.0
SG A:CYS67 2.5 1.0 1.0
SG A:CYS77 2.7 1.0 1.0
CB A:CYS70 3.1 1.0 1.0
CD2 A:HIS80 3.3 1.0 1.0
ND1 A:HIS80 3.6 1.0 1.0
O A:CYS67 3.7 1.0 1.0
CB A:CYS67 3.8 1.0 1.0
CB A:CYS77 3.8 1.0 1.0
CG A:HIS80 4.1 1.0 1.0
NE2 A:GLN68 4.2 1.0 1.0
CD A:GLN68 4.4 1.0 1.0
OE1 A:GLN68 4.4 1.0 1.0
CA A:CYS70 4.5 1.0 1.0
CA A:CYS77 4.6 1.0 1.0
O A:GLN71 4.6 1.0 1.0
C A:CYS67 4.6 1.0 1.0
C A:CYS70 4.7 1.0 1.0
CA A:CYS67 4.8 1.0 1.0
CD A:PRO78 4.8 1.0 1.0
N A:GLN71 4.9 1.0 1.0

Zinc binding site 4 out of 9 in 5fmf

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Zinc binding site 4 out of 9 in the The P-Lobe of Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The P-Lobe of Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:1.0
occ:1.00
 SG B:CYS1166 2.2 1.0 1.0
SG B:CYS1182 2.4 1.0 1.0
SG B:CYS1163 2.4 1.0 1.0
SG B:CYS1185 2.4 1.0 1.0
CB B:CYS1163 2.9 1.0 1.0
CB B:CYS1185 3.4 1.0 1.0
O B:CYS1166 3.5 1.0 1.0
CB B:CYS1166 3.7 1.0 1.0
N B:CYS1166 3.7 1.0 1.0
CB B:CYS1182 3.8 1.0 1.0
CA B:CYS1166 4.1 1.0 1.0
C B:CYS1166 4.2 1.0 1.0
CA B:CYS1163 4.4 1.0 1.0
OG1 B:THR1170 4.5 1.0 1.0
CA B:CYS1185 4.7 1.0 1.0
CB B:THR1170 4.7 1.0 1.0
CD D:LYS17 4.7 1.0 1.0
CG2 B:THR1170 4.8 1.0 1.0
CB B:ILE1165 4.8 1.0 1.0
C B:ILE1165 4.8 1.0 1.0
O B:CYS1182 4.9 1.0 1.0
N B:ILE1165 4.9 1.0 1.0
CD1 B:ILE1165 4.9 1.0 1.0
N B:CYS1185 5.0 1.0 1.0
C B:CYS1163 5.0 1.0 1.0

Zinc binding site 5 out of 9 in 5fmf

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Zinc binding site 5 out of 9 in the The P-Lobe of Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The P-Lobe of Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:1.0
occ:1.00
 SG C:CYS95 2.2 1.0 1.0
SG C:CYS92 2.2 1.0 1.0
SG C:CYS86 2.3 1.0 1.0
SG C:CYS88 2.3 1.0 1.0
CB C:CYS92 3.2 1.0 1.0
CB C:CYS86 3.3 1.0 1.0
CB C:CYS95 3.3 1.0 1.0
N C:CYS92 3.5 1.0 1.0
CB C:CYS88 3.7 1.0 1.0
CA C:CYS92 3.9 1.0 1.0
C C:HIS91 4.0 1.0 1.0
N C:CYS95 4.0 1.0 1.0
CA C:CYS95 4.3 1.0 1.0
CA C:HIS91 4.3 1.0 1.0
N C:CYS88 4.3 1.0 1.0
C C:CYS92 4.4 1.0 1.0
O C:ASP90 4.5 1.0 1.0
CA C:CYS86 4.6 1.0 1.0
O C:HIS91 4.6 1.0 1.0
CA C:CYS88 4.6 1.0 1.0
CB C:LYS94 4.7 1.0 1.0
C C:LYS94 4.7 1.0 1.0
O C:CYS92 4.8 1.0 1.0
N C:PHE87 4.8 1.0 1.0
C C:CYS86 4.9 1.0 1.0
N C:LYS94 4.9 1.0 1.0

Zinc binding site 6 out of 9 in 5fmf

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Zinc binding site 6 out of 9 in the The P-Lobe of Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The P-Lobe of Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:1.0
occ:1.00
 SG I:CYS7 2.2 1.0 1.0
SG I:CYS29 2.3 1.0 1.0
SG I:CYS10 2.3 1.0 1.0
SG I:CYS32 2.3 1.0 1.0
CB I:CYS10 2.6 1.0 1.0
CB I:CYS29 3.2 1.0 1.0
CB I:CYS7 3.3 1.0 1.0
CB I:CYS32 3.4 1.0 1.0
N I:CYS10 3.7 1.0 1.0
CA I:CYS10 3.7 1.0 1.0
N I:CYS32 3.8 1.0 1.0
CA I:CYS32 4.1 1.0 1.0
CB I:TYR34 4.3 1.0 1.0
OG1 I:THR31 4.3 1.0 1.0
C I:THR31 4.7 1.0 1.0
CA I:CYS29 4.7 1.0 1.0
CA I:CYS7 4.7 1.0 1.0
C I:CYS32 4.7 1.0 1.0
O I:ARG8 4.8 1.0 1.0
C I:ASP9 4.8 1.0 1.0
CB I:ASP9 4.8 1.0 1.0
C I:CYS10 4.9 1.0 1.0
CB I:THR31 5.0 1.0 1.0

Zinc binding site 7 out of 9 in 5fmf

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Zinc binding site 7 out of 9 in the The P-Lobe of Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The P-Lobe of Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:1.0
occ:1.00
 SG I:CYS106 2.3 1.0 1.0
SG I:CYS78 2.3 1.0 1.0
SG I:CYS75 2.4 1.0 1.0
SG I:CYS103 2.4 1.0 1.0
CB I:CYS106 3.1 1.0 1.0
CB I:CYS75 3.2 1.0 1.0
CB I:CYS103 3.2 1.0 1.0
CB I:CYS78 3.5 1.0 1.0
N I:CYS78 3.6 1.0 1.0
N I:CYS106 3.8 1.0 1.0
CA I:CYS106 3.9 1.0 1.0
CA I:CYS78 4.0 1.0 1.0
OG I:SER105 4.1 1.0 1.0
CB I:SER80 4.6 1.0 1.0
C I:CYS78 4.6 1.0 1.0
C I:CYS106 4.6 1.0 1.0
CB I:LYS77 4.6 1.0 1.0
N I:HIS79 4.6 1.0 1.0
CA I:CYS103 4.6 1.0 1.0
CA I:CYS75 4.7 1.0 1.0
N I:SER80 4.7 1.0 1.0
C I:LYS77 4.7 1.0 1.0
N I:SER107 4.7 1.0 1.0
CB I:HIS108 5.0 1.0 1.0
CA I:LYS77 5.0 1.0 1.0
N I:LYS77 5.0 1.0 1.0
C I:SER105 5.0 1.0 1.0

Zinc binding site 8 out of 9 in 5fmf

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Zinc binding site 8 out of 9 in the The P-Lobe of Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The P-Lobe of Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:1.0
occ:1.00
 SG J:CYS7 2.2 1.0 1.0
SG J:CYS46 2.3 1.0 1.0
SG J:CYS45 2.4 1.0 1.0
SG J:CYS10 2.5 1.0 1.0
CB J:CYS7 3.2 1.0 1.0
N J:CYS46 3.3 1.0 1.0
CB J:CYS45 3.5 1.0 1.0
CB J:CYS10 3.5 1.0 1.0
CB J:CYS46 3.6 1.0 1.0
N J:CYS10 3.6 1.0 1.0
CA J:CYS46 3.6 1.0 1.0
C J:CYS45 3.7 1.0 1.0
CA J:CYS10 4.0 1.0 1.0
CA J:CYS45 4.2 1.0 1.0
O J:CYS45 4.2 1.0 1.0
NE J:ARG43 4.3 1.0 1.0
NH2 J:ARG43 4.5 1.0 1.0
C J:SER9 4.6 1.0 1.0
N J:GLY11 4.6 1.0 1.0
CA J:CYS7 4.6 1.0 1.0
CB J:SER9 4.6 1.0 1.0
C J:CYS10 4.7 1.0 1.0
CA J:SER9 4.9 1.0 1.0
C J:CYS7 4.9 1.0 1.0
N J:LYS12 4.9 1.0 1.0
N J:CYS45 4.9 1.0 1.0
N J:SER9 4.9 1.0 1.0
CZ J:ARG43 4.9 1.0 1.0
CB J:LYS12 5.0 1.0 1.0
CB J:ARG43 5.0 1.0 1.0

Zinc binding site 9 out of 9 in 5fmf

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Zinc binding site 9 out of 9 in the The P-Lobe of Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The P-Lobe of Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:1.0
occ:1.00
 SG L:CYS48 2.3 1.0 1.0
SG L:CYS34 2.3 1.0 1.0
SG L:CYS51 2.4 1.0 1.0
SG L:CYS31 2.5 1.0 1.0
CB L:CYS48 3.1 1.0 1.0
CB L:CYS51 3.4 1.0 1.0
CB L:CYS31 3.6 1.0 1.0
CB L:CYS34 3.6 1.0 1.0
OG L:SER36 4.0 1.0 1.0
N L:CYS51 4.3 1.0 1.0
CA L:CYS51 4.3 1.0 1.0
N L:CYS34 4.5 1.0 1.0
CA L:CYS48 4.5 1.0 1.0
CA L:CYS34 4.6 1.0 1.0
O L:CYS51 4.6 1.0 1.0
C L:CYS51 4.7 1.0 1.0
CG L:GLU33 4.9 1.0 1.0
C L:CYS48 4.9 1.0 1.0

Reference:

K.Murakami, K.Tsai, N.Kalisman, D.A.Bushnell, F.J.Asturias, R.D.Kornberg. Structure of An Rna Polymerase II Pre-Initiation Complex Proc.Natl.Acad.Sci.Usa V. 112 13543 2015.
ISSN: ISSN 0027-8424
PubMed: 26483468
DOI: 10.1073/PNAS.1518255112
Page generated: Sun Oct 27 16:20:09 2024

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