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Zinc in PDB 3s1n: Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 2)

Enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 2)

All present enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 2):
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 2), PDB code: 3s1n 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) 47.80 / 3.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.303, 221.128, 191.935, 90.00, 97.52, 90.00
R / Rfree (%) 19.1 / 23.2

Other elements in 3s1n:

The structure of Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 2) 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 2) (pdb code 3s1n). 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 2), PDB code: 3s1n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3s1n

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


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.0
occ:1.00
 SG A:CYS107 2.3 0.6 1.0
SG A:CYS167 2.3 1.0 1.0
SG A:CYS110 2.4 0.1 1.0
SG A:CYS148 2.4 0.2 1.0
CB A:CYS107 3.3 0.8 1.0
CB A:CYS148 3.3 0.6 1.0
CB A:CYS110 3.5 0.7 1.0
CB A:CYS167 3.8 0.5 1.0
N A:CYS167 4.0 0.2 1.0
N A:CYS110 4.2 0.9 1.0
CA A:CYS167 4.3 0.0 1.0
CA A:CYS110 4.4 0.6 1.0
C A:CYS167 4.6 0.5 1.0
O A:CYS167 4.6 0.5 1.0
CA A:CYS107 4.7 0.7 1.0
CA A:CYS148 4.8 0.3 1.0
O A:MET108 4.9 0.4 1.0

Zinc binding site 2 out of 8 in 3s1n

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


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.0
occ:1.00
 NE2 A:HIS80 2.1 0.3 1.0
SG A:CYS77 2.4 0.7 1.0
SG A:CYS67 2.4 1.0 1.0
SG A:CYS70 2.5 0.2 1.0
CD2 A:HIS80 2.8 0.9 1.0
CE1 A:HIS80 3.3 0.3 1.0
CB A:CYS70 3.5 0.3 1.0
CB A:CYS77 3.8 0.0 1.0
CB A:CYS67 3.8 0.2 1.0
CG A:HIS80 4.0 0.9 1.0
ND1 A:HIS80 4.3 0.9 1.0
O A:GLN71 4.3 0.8 1.0
O A:CYS67 4.4 0.6 1.0
O A:LEU58 4.5 0.6 1.0
NE2 A:GLN68 4.6 0.6 1.0
CG A:GLN68 4.7 0.6 1.0
CD A:GLN68 4.7 1.0 1.0
CA A:CYS77 4.7 0.3 1.0
CA A:CYS70 4.8 0.3 1.0
C A:CYS67 4.8 0.7 1.0
CD A:PRO78 4.9 0.7 1.0
CA A:CYS67 4.9 0.8 1.0
CA A:GLY59 5.0 0.5 1.0
C A:CYS70 5.0 0.7 1.0

Zinc binding site 3 out of 8 in 3s1n

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Zinc binding site 3 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.6
occ:1.00
 SG B:CYS1166 2.3 0.3 1.0
SG B:CYS1163 2.4 0.4 1.0
SG B:CYS1185 2.4 0.6 1.0
SG B:CYS1182 2.4 0.6 1.0
CB B:CYS1185 3.0 0.7 1.0
CB B:CYS1163 3.2 0.0 1.0
CB B:CYS1182 3.4 0.6 1.0
CB B:CYS1166 3.6 0.5 1.0
N B:CYS1166 3.8 0.1 1.0
CA B:CYS1166 4.3 0.4 1.0
CA B:CYS1185 4.5 0.0 1.0
CA B:CYS1163 4.6 0.1 1.0
CB B:ILE1165 4.7 0.6 1.0
CB B:ASN1187 4.7 0.9 1.0
CA B:CYS1182 4.8 0.2 1.0
O B:CYS1182 4.8 0.2 1.0
C B:ILE1165 4.9 0.3 1.0
ND2 B:ASN1187 5.0 0.9 1.0

Zinc binding site 4 out of 8 in 3s1n

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Zinc binding site 4 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:66.9
occ:1.00
 SG C:CYS86 2.3 62.8 1.0
SG C:CYS92 2.3 70.9 1.0
SG C:CYS95 2.4 65.6 1.0
SG C:CYS88 2.4 59.1 1.0
CB C:CYS86 3.1 57.8 1.0
CB C:CYS95 3.3 61.8 1.0
CB C:CYS88 3.4 57.0 1.0
CB C:CYS92 3.5 67.1 1.0
N C:CYS92 3.5 66.0 1.0
N C:CYS95 3.9 63.3 1.0
CA C:CYS92 4.0 66.5 1.0
C C:HIS91 4.1 69.6 1.0
CA C:CYS95 4.2 61.9 1.0
CA C:HIS91 4.4 65.9 1.0
N C:CYS88 4.4 57.5 1.0
CA C:CYS86 4.4 57.6 1.0
C C:CYS92 4.5 70.5 1.0
CA C:CYS88 4.5 57.5 1.0
CB C:LYS94 4.5 66.9 1.0
C C:LYS94 4.6 68.3 1.0
O C:CYS92 4.7 69.2 1.0
C C:CYS86 4.8 60.0 1.0
N C:LYS94 4.8 66.1 1.0
O C:HIS91 4.8 69.0 1.0
O C:ASP90 4.9 71.5 1.0
CA C:LYS94 4.9 65.1 1.0

Zinc binding site 5 out of 8 in 3s1n

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


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:94.2
occ:1.00
 SG I:CYS10 2.3 0.9 1.0
SG I:CYS29 2.3 0.7 1.0
SG I:CYS7 2.4 95.9 1.0
SG I:CYS32 2.4 0.7 1.0
CB I:CYS10 2.9 94.3 1.0
CB I:CYS7 3.2 90.4 1.0
CB I:CYS29 3.3 96.6 1.0
CB I:CYS32 3.5 0.3 1.0
N I:CYS10 3.8 95.0 1.0
N I:CYS32 3.9 0.6 1.0
CA I:CYS10 3.9 93.8 1.0
CA I:CYS32 4.2 0.1 1.0
CB I:THR31 4.3 0.6 1.0
CB I:TYR34 4.3 93.8 1.0
CA I:CYS7 4.7 90.0 1.0
C I:THR31 4.7 0.8 1.0
CA I:CYS29 4.8 96.1 1.0
C I:CYS32 4.8 0.3 1.0
OG1 I:THR31 4.9 0.8 1.0
CA I:THR31 5.0 0.0 1.0

Zinc binding site 6 out of 8 in 3s1n

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Zinc binding site 6 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:63.3
occ:1.00
 SG I:CYS78 2.3 72.9 1.0
SG I:CYS103 2.3 65.1 1.0
SG I:CYS106 2.3 65.4 1.0
SG I:CYS75 2.4 67.2 1.0
CB I:CYS103 3.0 60.0 1.0
CB I:CYS75 3.2 62.8 1.0
CB I:CYS106 3.3 63.2 1.0
CB I:CYS78 3.5 70.4 1.0
O I:CYS78 3.7 76.9 1.0
N I:CYS78 3.7 70.2 1.0
N I:CYS106 3.9 63.4 1.0
CA I:CYS78 4.1 70.3 1.0
CA I:CYS106 4.1 63.4 1.0
C I:CYS78 4.2 75.8 1.0
CB I:HIS108 4.5 65.4 1.0
CA I:CYS103 4.5 58.5 1.0
CB I:SER80 4.5 71.0 1.0
CA I:CYS75 4.7 62.7 1.0
CB I:LYS77 4.7 70.6 1.0
CB I:SER105 4.7 68.2 1.0
C I:SER105 4.8 68.1 1.0
C I:CYS106 4.8 69.8 1.0
C I:LYS77 4.8 74.1 1.0
N I:SER80 4.9 68.6 1.0
C I:CYS103 5.0 61.7 1.0

Zinc binding site 7 out of 8 in 3s1n

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Zinc binding site 7 out of 8 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna (Variant 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:57.5
occ:1.00
 SG J:CYS10 2.3 56.7 1.0
SG J:CYS45 2.3 54.0 1.0
SG J:CYS7 2.4 51.6 1.0
SG J:CYS46 2.4 60.9 1.0
N J:CYS46 3.3 54.2 1.0
CB J:CYS7 3.3 48.9 1.0
CB J:CYS10 3.3 51.9 1.0
CB J:CYS45 3.6 49.1 1.0
CA J:CYS46 3.7 54.9 1.0
CB J:CYS46 3.7 56.7 1.0
C J:CYS45 3.7 55.7 1.0
N J:CYS10 3.8 49.5 1.0
NE J:ARG43 4.0 72.8 1.0
CA J:CYS10 4.1 50.6 1.0
CA J:CYS45 4.2 49.1 1.0
CG J:ARG43 4.2 56.0 1.0
O J:CYS45 4.4 54.9 1.0
CD J:ARG43 4.5 61.7 1.0
CA J:CYS7 4.7 48.8 1.0
N J:GLY11 4.8 52.2 1.0
CB J:LYS12 4.8 58.5 1.0
CB J:SER9 4.8 48.6 1.0
N J:CYS45 4.9 49.6 1.0
C J:CYS10 4.9 55.4 1.0
C J:SER9 4.9 52.2 1.0
CZ J:ARG43 4.9 89.2 1.0
N J:LYS12 5.0 55.5 1.0

Zinc binding site 8 out of 8 in 3s1n

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


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.3
occ:1.00
 SG L:CYS51 2.3 0.3 1.0
SG L:CYS48 2.3 0.1 1.0
SG L:CYS34 2.3 0.6 1.0
SG L:CYS31 2.5 1.0 1.0
CB L:CYS51 2.8 0.4 1.0
CB L:CYS48 3.2 0.0 1.0
CB L:CYS34 3.2 0.3 1.0
CB L:CYS31 3.4 97.8 1.0
N L:CYS34 3.7 0.0 1.0
N L:CYS51 3.7 0.7 1.0
CA L:CYS51 3.8 0.9 1.0
CA L:CYS34 4.0 0.7 1.0
C L:CYS51 4.5 0.8 1.0
N L:GLY52 4.6 0.7 1.0
C L:ASP50 4.6 0.1 1.0
CA L:CYS48 4.6 0.4 1.0
C L:CYS34 4.8 0.5 1.0
CA L:CYS31 4.8 96.0 1.0
C L:GLU33 4.9 0.2 1.0
CB L:ASP50 4.9 0.9 1.0
N L:HIS53 5.0 0.2 1.0
CB 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 15:17:52 2024

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