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Zinc in PDB 3s14: Rna Polymerase II Initiation Complex with A 6-Nt Rna

Enzymatic activity of Rna Polymerase II Initiation Complex with A 6-Nt Rna

All present enzymatic activity of Rna Polymerase II Initiation Complex with A 6-Nt Rna:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Initiation Complex with A 6-Nt Rna, PDB code: 3s14 was solved by X.Liu, D.A.Bushnell, D.A.Silva, X.Huang, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.46 / 2.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 159.335, 221.345, 192.368, 90.00, 98.00, 90.00
R / Rfree (%) 18.9 / 22.7

Other elements in 3s14:

The structure of Rna Polymerase II Initiation Complex with A 6-Nt Rna also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Initiation Complex with A 6-Nt Rna (pdb code 3s14). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Rna Polymerase II Initiation Complex with A 6-Nt Rna, PDB code: 3s14:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3s14

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Zinc binding site 1 out of 8 in the Rna Polymerase II Initiation Complex with A 6-Nt Rna


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 Initiation Complex with A 6-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.1
occ:1.00
 CB A:CYS110 1.9 0.3 1.0
SG A:CYS148 2.4 0.5 1.0
SG A:CYS107 2.4 0.5 1.0
SG A:CYS167 2.4 0.3 1.0
SG A:CYS110 2.5 0.8 1.0
CB A:CYS107 3.3 0.5 1.0
CA A:CYS110 3.4 0.7 1.0
CB A:CYS148 3.5 0.4 1.0
CB A:CYS167 3.7 0.3 1.0
N A:CYS167 3.9 0.6 1.0
N A:CYS110 3.9 0.2 1.0
CA A:CYS167 4.2 0.5 1.0
C A:CYS110 4.4 0.5 1.0
C A:CYS167 4.6 0.7 1.0
CA A:CYS107 4.7 0.8 1.0
O A:CYS167 4.8 0.2 1.0
CA A:CYS148 4.8 0.1 1.0
N A:GLY111 4.8 0.8 1.0
O A:MET108 4.9 1.0 1.0
C A:GLY166 4.9 0.4 1.0
C A:CYS107 5.0 1.0 1.0

Zinc binding site 2 out of 8 in 3s14

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Zinc binding site 2 out of 8 in the Rna Polymerase II Initiation Complex with A 6-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase II Initiation Complex with A 6-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.3
occ:1.00
 NE2 A:HIS80 2.1 0.4 1.0
SG A:CYS67 2.4 0.3 1.0
SG A:CYS77 2.4 0.0 1.0
SG A:CYS70 2.5 0.6 1.0
CD2 A:HIS80 3.0 0.1 1.0
CE1 A:HIS80 3.2 0.7 1.0
CB A:CYS77 3.6 0.2 1.0
CB A:CYS67 3.6 0.4 1.0
CB A:CYS70 3.9 0.1 1.0
CG A:HIS80 4.2 0.3 1.0
NE2 A:GLN68 4.2 67.7 1.0
ND1 A:HIS80 4.3 0.4 1.0
O A:CYS67 4.4 0.3 1.0
O A:GLN71 4.4 0.8 1.0
CD A:GLN68 4.5 93.8 1.0
CA A:CYS77 4.5 0.7 1.0
CG A:GLN68 4.8 0.9 1.0
C A:CYS67 4.8 0.0 1.0
CA A:CYS67 4.8 0.6 1.0
OE1 A:GLN68 4.9 82.6 1.0
CD A:PRO78 4.9 0.7 1.0

Zinc binding site 3 out of 8 in 3s14

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Zinc binding site 3 out of 8 in the Rna Polymerase II Initiation Complex with A 6-Nt Rna


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 Initiation Complex with A 6-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.6
occ:1.00
 SG B:CYS1163 2.3 0.9 1.0
SG B:CYS1166 2.3 0.5 1.0
SG B:CYS1182 2.4 0.2 1.0
SG B:CYS1185 2.4 0.3 1.0
CB B:CYS1163 3.1 0.7 1.0
CB B:CYS1185 3.2 0.1 1.0
CB B:CYS1166 3.4 0.9 1.0
N B:CYS1166 3.6 0.5 1.0
CB B:CYS1182 3.6 0.1 1.0
CA B:CYS1166 4.0 0.8 1.0
CB B:ILE1165 4.5 0.1 1.0
CA B:CYS1185 4.5 0.8 1.0
CA B:CYS1163 4.5 0.4 1.0
C B:ILE1165 4.7 0.1 1.0
N B:CYS1185 4.8 0.8 1.0
OG1 B:THR1170 4.8 0.5 1.0
CB B:THR1170 4.9 0.5 1.0
N B:GLY1167 4.9 0.6 1.0
C B:CYS1166 4.9 0.5 1.0
CA B:ILE1165 4.9 0.5 1.0
CA B:CYS1182 4.9 0.7 1.0
N B:ILE1165 5.0 0.6 1.0

Zinc binding site 4 out of 8 in 3s14

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Zinc binding site 4 out of 8 in the Rna Polymerase II Initiation Complex with A 6-Nt Rna


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 Initiation Complex with A 6-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:60.0
occ:1.00
 SG C:CYS86 2.3 57.3 1.0
SG C:CYS88 2.4 49.2 1.0
SG C:CYS92 2.4 63.4 1.0
SG C:CYS95 2.4 66.2 1.0
CB C:CYS95 3.3 61.9 1.0
CB C:CYS88 3.3 47.5 1.0
CB C:CYS86 3.3 52.3 1.0
CB C:CYS92 3.4 59.4 1.0
N C:CYS92 3.4 57.9 1.0
CA C:CYS92 3.9 58.4 1.0
N C:CYS95 3.9 62.5 1.0
C C:HIS91 4.0 61.7 1.0
O C:CYS92 4.1 63.9 1.0
CA C:CYS95 4.2 60.9 1.0
C C:CYS92 4.2 63.8 1.0
CA C:HIS91 4.3 57.4 1.0
N C:CYS88 4.4 50.1 1.0
CA C:CYS88 4.4 48.7 1.0
CB C:LYS94 4.5 61.4 1.0
C C:LYS94 4.6 65.6 1.0
CA C:CYS86 4.6 52.3 1.0
O C:HIS91 4.7 60.9 1.0
N C:LYS94 4.7 60.1 1.0
CA C:LYS94 4.9 59.6 1.0
C C:CYS86 4.9 55.1 1.0
O C:ASP90 4.9 64.5 1.0
C C:CYS95 5.0 61.2 1.0

Zinc binding site 5 out of 8 in 3s14

Go back to Zinc Binding Sites List in 3s14
Zinc binding site 5 out of 8 in the Rna Polymerase II Initiation Complex with A 6-Nt Rna


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 Initiation Complex with A 6-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:0.2
occ:1.00
 SG I:CYS10 2.2 0.3 1.0
SG I:CYS7 2.2 91.1 1.0
SG I:CYS29 2.3 99.0 1.0
SG I:CYS32 2.3 0.0 1.0
CB I:CYS10 3.0 93.9 1.0
CB I:CYS7 3.0 85.3 1.0
CB I:CYS29 3.3 95.2 1.0
CB I:CYS32 3.6 0.1 1.0
N I:CYS10 3.9 95.2 1.0
N I:CYS32 4.0 0.2 1.0
CA I:CYS10 4.1 93.2 1.0
CB I:THR31 4.2 0.2 1.0
OG1 I:THR31 4.2 0.9 1.0
CA I:CYS32 4.3 0.4 1.0
CB I:TYR34 4.5 93.8 1.0
C I:THR31 4.5 0.4 1.0
CA I:CYS7 4.5 85.6 1.0
CA I:CYS29 4.8 94.4 1.0
CA I:THR31 4.8 0.0 1.0
N I:THR31 4.8 0.1 1.0
C I:CYS32 4.9 0.4 1.0

Zinc binding site 6 out of 8 in 3s14

Go back to Zinc Binding Sites List in 3s14
Zinc binding site 6 out of 8 in the Rna Polymerase II Initiation Complex with A 6-Nt Rna


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 Initiation Complex with A 6-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:60.9
occ:1.00
 SG I:CYS106 2.3 77.2 1.0
SG I:CYS103 2.3 63.9 1.0
SG I:CYS78 2.3 62.8 1.0
SG I:CYS75 2.4 66.3 1.0
CB I:CYS106 2.8 71.4 1.0
CB I:CYS103 3.0 58.6 1.0
CB I:CYS75 3.1 62.0 1.0
CB I:CYS78 3.6 60.6 1.0
N I:CYS106 3.8 69.9 1.0
N I:CYS78 3.8 62.4 1.0
CA I:CYS106 3.8 71.0 1.0
O I:CYS78 4.0 69.6 1.0
CA I:CYS78 4.2 61.6 1.0
CB I:HIS108 4.4 59.2 1.0
C I:CYS78 4.4 67.8 1.0
CA I:CYS103 4.5 56.6 1.0
CB I:LYS77 4.6 61.5 1.0
C I:SER105 4.6 71.7 1.0
CA I:CYS75 4.6 62.2 1.0
CB I:SER80 4.6 62.5 1.0
CB I:SER105 4.8 70.9 1.0
C I:LYS77 4.9 66.7 1.0
N I:SER80 4.9 60.9 1.0

Zinc binding site 7 out of 8 in 3s14

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Zinc binding site 7 out of 8 in the Rna Polymerase II Initiation Complex with A 6-Nt Rna


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 Initiation Complex with A 6-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:57.9
occ:1.00
 SG J:CYS46 2.3 58.6 1.0
SG J:CYS10 2.3 57.0 1.0
SG J:CYS45 2.4 53.7 1.0
SG J:CYS7 2.4 46.7 1.0
N J:CYS46 3.2 52.2 1.0
CB J:CYS7 3.3 43.8 1.0
CB J:CYS10 3.3 52.7 1.0
CB J:CYS45 3.5 48.6 1.0
CB J:CYS46 3.6 54.3 1.0
CA J:CYS46 3.6 52.7 1.0
C J:CYS45 3.7 53.0 1.0
N J:CYS10 3.8 51.1 1.0
CA J:CYS10 4.1 51.8 1.0
NE J:ARG43 4.1 55.2 1.0
CA J:CYS45 4.1 48.0 1.0
O J:CYS45 4.4 52.2 1.0
CG J:ARG43 4.4 50.5 1.0
CB J:SER9 4.7 45.1 1.0
CA J:CYS7 4.7 43.7 1.0
CB J:LYS12 4.7 48.8 1.0
NH2 J:ARG43 4.8 59.9 1.0
CD J:ARG43 4.8 34.8 1.0
N J:CYS45 4.8 49.2 1.0
N J:GLY11 4.8 49.4 1.0
C J:SER9 4.8 53.6 1.0
CZ J:ARG43 4.9 70.8 1.0
C J:CYS10 4.9 55.9 1.0

Zinc binding site 8 out of 8 in 3s14

Go back to Zinc Binding Sites List in 3s14
Zinc binding site 8 out of 8 in the Rna Polymerase II Initiation Complex with A 6-Nt Rna


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 Initiation Complex with A 6-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:95.6
occ:1.00
 CB L:CYS51 2.3 0.3 1.0
SG L:CYS48 2.3 98.4 1.0
SG L:CYS34 2.4 0.3 1.0
SG L:CYS31 2.4 95.1 1.0
SG L:CYS51 2.4 0.3 1.0
CB L:CYS48 3.2 94.9 1.0
CB L:CYS31 3.4 91.2 1.0
CB L:CYS34 3.6 100.0 1.0
CA L:CYS51 3.8 0.5 1.0
N L:CYS34 3.9 98.3 1.0
CA L:CYS34 4.3 98.5 1.0
N L:CYS51 4.4 0.6 1.0
O L:ASP50 4.4 0.1 1.0
C L:CYS51 4.5 0.8 1.0
CB L:GLU33 4.6 99.3 1.0
CA L:CYS48 4.6 97.3 1.0
N L:GLY52 4.6 0.3 1.0
C L:ASP50 4.7 0.8 1.0
CB L:SER36 4.7 0.2 1.0
CA L:CYS31 4.8 89.8 1.0
N L:HIS53 4.9 0.7 1.0
C L:GLU33 4.9 0.5 1.0
CB L:HIS53 5.0 0.1 1.0

Reference:

X.Liu, D.A.Bushnell, D.A.Silva, X.Huang, R.D.Kornberg. Initiation Complex Structure and Promoter Proofreading. Science V. 333 633 2011.
ISSN: ISSN 0036-8075
PubMed: 21798951
DOI: 10.1126/SCIENCE.1206629
Page generated: Sat Oct 26 15:12:28 2024

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