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Zinc in PDB 3s1m: Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 1)

Enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 1)

All present enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 1):
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 1), PDB code: 3s1m 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) 47.72 / 3.13
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 156.920, 220.711, 191.769, 90.00, 97.48, 90.00
R / Rfree (%) 18.3 / 23.3

Other elements in 3s1m:

The structure of Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 1) 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 5-Nt Rna (Variant 1) (pdb code 3s1m). 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 5-Nt Rna (Variant 1), PDB code: 3s1m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3s1m

Go back to Zinc Binding Sites List in 3s1m
Zinc binding site 1 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 1)


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 5-Nt Rna (Variant 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.0
occ:1.00
 SG A:CYS167 2.4 0.7 1.0
SG A:CYS107 2.4 0.6 1.0
SG A:CYS148 2.4 0.0 1.0
SG A:CYS110 2.4 0.6 1.0
CB A:CYS148 3.3 0.8 1.0
CB A:CYS107 3.3 0.8 1.0
CB A:CYS110 3.7 0.7 1.0
CB A:CYS167 3.7 0.4 1.0
O A:MET108 3.8 0.0 1.0
N A:CYS167 3.9 0.7 1.0
CA A:CYS167 4.2 1.0 1.0
N A:CYS110 4.5 0.8 1.0
C A:CYS167 4.6 0.7 1.0
CA A:CYS110 4.6 0.7 1.0
CA A:CYS107 4.7 0.0 1.0
O A:CYS167 4.7 0.0 1.0
CA A:CYS148 4.7 0.6 1.0
C A:CYS107 4.8 0.3 1.0
C A:GLY166 5.0 0.7 1.0
C A:MET108 5.0 0.5 1.0
N A:MET108 5.0 0.2 1.0

Zinc binding site 2 out of 8 in 3s1m

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Zinc binding site 2 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 1)


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 5-Nt Rna (Variant 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.6
occ:1.00
 NE2 A:HIS80 2.1 0.7 1.0
SG A:CYS77 2.3 0.7 1.0
SG A:CYS67 2.4 0.2 1.0
SG A:CYS70 2.5 0.5 1.0
CD2 A:HIS80 2.7 0.1 1.0
CE1 A:HIS80 3.3 0.7 1.0
CB A:CYS67 3.3 0.4 1.0
CB A:CYS77 3.8 0.5 1.0
CB A:CYS70 3.9 0.5 1.0
O A:CYS67 3.9 0.2 1.0
CG A:HIS80 4.0 0.9 1.0
ND1 A:HIS80 4.2 0.1 1.0
NE2 A:GLN68 4.4 0.1 1.0
CA A:CYS67 4.5 0.3 1.0
O A:GLN71 4.6 0.2 1.0
C A:CYS67 4.6 0.1 1.0
O A:LEU58 4.6 0.3 1.0
CA A:CYS77 4.7 1.0 1.0

Zinc binding site 3 out of 8 in 3s1m

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Zinc binding site 3 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 1)


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 5-Nt Rna (Variant 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.7
occ:1.00
 SG B:CYS1166 2.4 0.8 1.0
SG B:CYS1182 2.4 0.3 1.0
SG B:CYS1185 2.4 0.5 1.0
SG B:CYS1163 2.4 0.6 1.0
CB B:CYS1163 3.0 0.9 1.0
CB B:CYS1185 3.2 0.5 1.0
CB B:CYS1166 3.3 0.1 1.0
N B:CYS1166 3.6 0.8 1.0
CB B:CYS1182 3.8 0.8 1.0
CA B:CYS1166 4.0 0.3 1.0
CA B:CYS1163 4.5 0.0 1.0
OG1 B:THR1170 4.6 0.7 1.0
CA B:CYS1185 4.6 0.1 1.0
CB B:THR1170 4.7 0.3 1.0
CB B:ILE1165 4.7 0.9 1.0
C B:ILE1165 4.8 0.1 1.0
C B:CYS1166 4.9 0.8 1.0
N B:GLY1167 4.9 0.7 1.0
CG2 B:THR1170 5.0 0.4 1.0
N B:CYS1185 5.0 0.2 1.0

Zinc binding site 4 out of 8 in 3s1m

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Zinc binding site 4 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 1)


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 5-Nt Rna (Variant 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:92.5
occ:1.00
 SG C:CYS92 2.3 0.5 1.0
SG C:CYS86 2.3 89.8 1.0
SG C:CYS95 2.3 93.0 1.0
SG C:CYS88 2.3 81.7 1.0
CB C:CYS86 3.1 84.4 1.0
CB C:CYS88 3.3 79.7 1.0
CB C:CYS95 3.3 89.2 1.0
CB C:CYS92 3.4 96.8 1.0
N C:CYS92 3.5 94.8 1.0
CA C:CYS92 3.9 96.0 1.0
N C:CYS95 4.0 90.7 1.0
C C:HIS91 4.0 97.7 1.0
CA C:CYS95 4.3 89.1 1.0
CA C:HIS91 4.3 92.0 1.0
N C:CYS88 4.3 79.1 1.0
CA C:CYS88 4.4 80.0 1.0
CA C:CYS86 4.5 83.8 1.0
C C:CYS92 4.5 99.8 1.0
O C:ASP90 4.7 98.4 1.0
CB C:LYS94 4.7 94.7 1.0
O C:HIS91 4.7 97.8 1.0
C C:LYS94 4.7 96.1 1.0
C C:CYS86 4.8 84.1 1.0
O C:CYS92 4.8 98.9 1.0
N C:LYS94 4.9 93.7 1.0

Zinc binding site 5 out of 8 in 3s1m

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Zinc binding site 5 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 1)


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 5-Nt Rna (Variant 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:1.0
occ:1.00
 SG I:CYS10 2.3 0.3 1.0
SG I:CYS29 2.3 0.3 1.0
SG I:CYS32 2.4 0.1 1.0
SG I:CYS7 2.4 0.5 1.0
CB I:CYS10 2.9 0.5 1.0
CB I:CYS7 3.1 0.6 1.0
CB I:CYS29 3.4 0.9 1.0
CB I:CYS32 3.4 0.6 1.0
N I:CYS10 3.8 0.1 1.0
N I:CYS32 3.9 0.1 1.0
CA I:CYS10 3.9 0.6 1.0
CA I:CYS32 4.1 0.2 1.0
CB I:TYR34 4.2 0.8 1.0
CB I:THR31 4.3 0.3 1.0
C I:THR31 4.5 0.9 1.0
CA I:CYS7 4.6 0.8 1.0
C I:CYS32 4.7 0.4 1.0
CA I:CYS29 4.8 0.9 1.0
OG1 I:THR31 4.8 0.5 1.0
CA I:THR31 4.9 0.6 1.0
N I:TYR34 4.9 0.4 1.0
N I:THR31 4.9 0.9 1.0

Zinc binding site 6 out of 8 in 3s1m

Go back to Zinc Binding Sites List in 3s1m
Zinc binding site 6 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 1)


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 5-Nt Rna (Variant 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:83.9
occ:1.00
 SG I:CYS106 2.2 93.6 1.0
SG I:CYS78 2.3 87.1 1.0
SG I:CYS103 2.3 91.5 1.0
SG I:CYS75 2.4 89.5 1.0
CB I:CYS103 3.1 85.7 1.0
CB I:CYS75 3.2 85.2 1.0
CB I:CYS106 3.3 91.2 1.0
CB I:CYS78 3.6 84.7 1.0
N I:CYS78 3.7 85.2 1.0
N I:CYS106 3.8 90.9 1.0
O I:CYS78 4.1 90.7 1.0
CA I:CYS106 4.1 90.9 1.0
CA I:CYS78 4.1 84.9 1.0
CB I:HIS108 4.3 89.3 1.0
C I:CYS78 4.3 90.8 1.0
CB I:SER80 4.5 90.1 1.0
CA I:CYS103 4.6 83.3 1.0
CA I:CYS75 4.6 85.1 1.0
CB I:LYS77 4.6 87.6 1.0
CB I:SER105 4.7 96.3 1.0
C I:CYS106 4.7 96.0 1.0
C I:SER105 4.8 96.0 1.0
C I:LYS77 4.8 89.7 1.0
N I:SER80 4.8 87.2 1.0

Zinc binding site 7 out of 8 in 3s1m

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Zinc binding site 7 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 1)


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 5-Nt Rna (Variant 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:85.0
occ:1.00
 SG J:CYS7 2.3 73.3 1.0
SG J:CYS45 2.3 77.5 1.0
SG J:CYS10 2.3 77.5 1.0
SG J:CYS46 2.4 81.8 1.0
CB J:CYS7 3.2 70.5 1.0
N J:CYS46 3.2 76.9 1.0
CB J:CYS10 3.3 71.6 1.0
CA J:CYS46 3.6 76.9 1.0
CB J:CYS46 3.6 78.2 1.0
C J:CYS45 3.7 79.4 1.0
N J:CYS10 3.7 66.2 1.0
CB J:CYS45 3.8 73.0 1.0
CD J:ARG43 3.8 93.9 1.0
CG J:ARG43 3.9 86.4 1.0
CA J:CYS10 4.0 68.8 1.0
NE J:ARG43 4.0 0.1 1.0
CA J:CYS45 4.3 73.9 1.0
O J:CYS45 4.4 79.2 1.0
CA J:CYS7 4.6 70.1 1.0
N J:GLY11 4.7 70.3 1.0
C J:CYS10 4.7 72.2 1.0
CB J:LYS12 4.7 79.9 1.0
CB J:SER9 4.8 62.8 1.0
C J:SER9 4.8 66.9 1.0
N J:LYS12 4.9 76.6 1.0
N J:CYS45 4.9 75.8 1.0
O J:CYS7 5.0 72.5 1.0
C J:CYS7 5.0 72.0 1.0

Zinc binding site 8 out of 8 in 3s1m

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Zinc binding site 8 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 1)


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 5-Nt Rna (Variant 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.5
occ:1.00
 CB L:CYS51 2.3 0.7 1.0
SG L:CYS51 2.3 0.5 1.0
SG L:CYS34 2.3 0.1 1.0
SG L:CYS48 2.4 0.5 1.0
SG L:CYS31 2.4 0.6 1.0
CB L:CYS31 3.2 0.5 1.0
CB L:CYS48 3.3 0.9 1.0
CB L:CYS34 3.5 0.9 1.0
CA L:CYS51 3.8 0.3 1.0
N L:CYS34 3.8 0.4 1.0
CA L:CYS34 4.1 0.8 1.0
O L:ASP50 4.4 0.8 1.0
N L:CYS51 4.5 0.3 1.0
C L:CYS51 4.6 0.2 1.0
CA L:CYS31 4.7 0.1 1.0
N L:GLY52 4.7 0.3 1.0
CA L:CYS48 4.8 0.6 1.0
C L:ASP50 4.8 0.2 1.0
C L:CYS34 4.8 0.3 1.0
C L:GLU33 5.0 0.3 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 15:17:50 2024

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