Zinc in PDB 9bvt: Rna Pol II - High Mn(+2) Concentration

Enzymatic activity of Rna Pol II - High Mn(+2) Concentration

All present enzymatic activity of Rna Pol II - High Mn(+2) Concentration:
2.7.7.6;

Protein crystallography data

The structure of Rna Pol II - High Mn(+2) Concentration, PDB code: 9bvt was solved by G.Calero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.25 / 3.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 221.19, 393.97, 283.28, 90, 90, 90
R / Rfree (%) 22 / 24.9

Other elements in 9bvt:

The structure of Rna Pol II - High Mn(+2) Concentration also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Pol II - High Mn(+2) Concentration (pdb code 9bvt). 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 Pol II - High Mn(+2) Concentration, PDB code: 9bvt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 9bvt

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Zinc binding site 1 out of 8 in the Rna Pol II - High Mn(+2) Concentration


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:159.6
occ:1.00
 SG A:CYS110 2.3 207.4 1.0
SG A:CYS167 2.3 225.8 1.0
SG A:CYS107 2.3 217.2 1.0
CB A:CYS167 2.9 198.8 1.0
CB A:CYS107 3.0 198.3 1.0
SG A:CYS148 3.4 212.3 1.0
CB A:CYS110 3.5 209.1 1.0
CB A:CYS148 3.7 187.0 1.0
N A:CYS110 3.8 208.2 1.0
CA A:CYS110 4.2 209.9 1.0
CA A:CYS167 4.2 207.1 1.0
C A:CYS167 4.3 211.5 1.0
CA A:CYS107 4.5 195.1 1.0
ND1 A:HIS109 4.5 218.1 1.0
N A:GLY168 4.5 193.8 1.0
CB A:HIS109 4.6 192.4 1.0
N A:GLY111 4.7 182.9 1.0
O A:CYS167 4.8 215.4 1.0
C A:HIS109 4.8 184.0 1.0
C A:CYS110 4.9 190.6 1.0
C A:CYS107 4.9 183.2 1.0
N A:ASN169 4.9 173.8 1.0
CG A:HIS109 5.0 211.1 1.0
O A:CYS107 5.0 178.2 1.0
CA A:CYS148 5.0 203.5 1.0

Zinc binding site 2 out of 8 in 9bvt

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Zinc binding site 2 out of 8 in the Rna Pol II - High Mn(+2) Concentration


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:116.0
occ:1.00
 SG A:CYS70 2.3 115.3 1.0
NE2 A:HIS80 2.3 144.7 1.0
SG A:CYS77 2.3 118.8 1.0
SG A:CYS67 2.3 120.9 1.0
CD2 A:HIS80 2.5 103.3 1.0
CB A:CYS67 3.2 153.2 1.0
OG1 A:THR69 3.2 141.8 1.0
CE1 A:HIS80 3.6 174.6 1.0
CB A:CYS77 3.6 112.7 1.0
O A:CYS70 3.8 153.0 1.0
CB A:CYS70 3.8 162.4 1.0
N A:CYS70 3.8 112.0 1.0
CG A:HIS80 3.9 119.3 1.0
CA A:CYS70 4.2 127.4 1.0
ND1 A:HIS80 4.3 177.0 1.0
CA A:CYS77 4.4 116.0 1.0
C A:CYS70 4.5 134.1 1.0
CB A:THR69 4.6 122.8 1.0
CA A:CYS67 4.7 147.8 1.0
C A:THR69 4.8 127.2 1.0
C A:CYS77 4.9 112.8 1.0
N A:THR69 5.0 126.6 1.0
N A:GLY79 5.0 99.8 1.0

Zinc binding site 3 out of 8 in 9bvt

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Zinc binding site 3 out of 8 in the Rna Pol II - High Mn(+2) Concentration


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:135.3
occ:1.00
 SG B:CYS1185 2.3 84.8 1.0
SG B:CYS1166 2.3 126.7 1.0
SG B:CYS1163 2.3 137.3 1.0
CB B:CYS1163 2.9 124.2 1.0
N B:CYS1166 2.9 106.6 1.0
CB B:CYS1166 3.4 138.6 1.0
CB B:CYS1185 3.5 131.2 1.0
CB B:ILE1165 3.6 126.0 1.0
CA B:CYS1166 3.6 124.3 1.0
SG B:CYS1182 3.7 143.3 1.0
O B:CYS1166 3.9 105.7 1.0
C B:ILE1165 3.9 119.6 1.0
N B:ILE1165 3.9 111.6 1.0
CA B:ILE1165 4.0 121.0 1.0
C B:CYS1166 4.1 123.1 1.0
CD1 B:ILE1165 4.2 84.7 1.0
CA B:CYS1163 4.3 95.3 1.0
CG2 B:ILE1165 4.4 163.3 1.0
CG1 B:ILE1165 4.4 85.0 1.0
ND2 B:ASN1187 4.5 185.8 1.0
CB B:CYS1182 4.6 158.8 1.0
O B:CYS1185 4.7 157.2 1.0
C B:CYS1163 4.7 110.2 1.0
N B:GLY1164 4.8 113.6 1.0
CA B:CYS1185 4.9 148.7 1.0

Zinc binding site 4 out of 8 in 9bvt

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Zinc binding site 4 out of 8 in the Rna Pol II - High Mn(+2) Concentration


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:114.0
occ:1.00
 SG C:CYS88 2.3 102.3 1.0
SG C:CYS92 2.3 136.9 1.0
SG C:CYS95 2.3 119.0 1.0
SG C:CYS86 2.3 118.4 1.0
CB C:CYS95 3.4 128.6 1.0
CB C:CYS86 3.4 132.0 1.0
CB C:CYS88 3.5 135.6 1.0
CB C:CYS92 3.5 133.0 1.0
N C:CYS92 3.6 120.1 1.0
N C:CYS95 4.0 142.0 1.0
C C:HIS91 4.1 137.2 1.0
CA C:CYS92 4.1 103.3 1.0
N C:CYS88 4.2 87.2 1.0
CA C:HIS91 4.2 123.0 1.0
CA C:CYS95 4.3 139.8 1.0
CB C:LYS94 4.4 142.4 1.0
CA C:CYS88 4.5 112.8 1.0
C C:LYS94 4.6 137.4 1.0
O C:ASP90 4.6 153.6 1.0
N C:LYS94 4.7 113.5 1.0
C C:CYS92 4.7 121.5 1.0
CD C:LYS94 4.8 156.4 1.0
CA C:CYS86 4.8 112.4 1.0
CA C:LYS94 4.8 120.4 1.0
CG C:LYS94 4.9 148.0 1.0
N C:PHE87 4.9 118.8 1.0
O C:HIS91 4.9 133.4 1.0

Zinc binding site 5 out of 8 in 9bvt

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Zinc binding site 5 out of 8 in the Rna Pol II - High Mn(+2) Concentration


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:150.9
occ:1.00
 SG I:CYS32 2.3 140.9 1.0
SG I:CYS29 2.3 175.9 1.0
SG I:CYS7 2.3 155.0 1.0
CB I:CYS7 2.8 157.0 1.0
CB I:CYS10 3.0 162.6 1.0
SG I:CYS10 3.2 158.6 1.0
CB I:CYS29 3.5 189.5 1.0
N I:CYS10 3.7 147.0 1.0
CB I:CYS32 3.8 157.3 1.0
CA I:CYS10 4.0 174.1 1.0
N I:CYS32 4.0 143.1 1.0
CB I:TYR34 4.1 143.1 1.0
CA I:CYS7 4.3 147.6 1.0
CA I:CYS32 4.4 165.1 1.0
CB I:THR31 4.7 187.6 1.0
C I:ASP9 4.7 166.5 1.0
C I:CYS10 4.8 156.7 1.0
C I:CYS32 4.8 194.1 1.0
CG I:TYR34 4.9 143.6 1.0
CA I:CYS29 4.9 157.6 1.0
O I:ASN12 4.9 176.8 1.0
CB I:ASP9 4.9 185.6 1.0
N I:TYR34 4.9 156.4 1.0
CB I:ASN12 4.9 177.9 1.0
N I:ASP9 5.0 172.8 1.0
N I:ASN11 5.0 148.1 1.0
C I:CYS7 5.0 143.0 1.0

Zinc binding site 6 out of 8 in 9bvt

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Zinc binding site 6 out of 8 in the Rna Pol II - High Mn(+2) Concentration


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:216.0
occ:1.00
 SG I:CYS106 2.3 207.4 1.0
SG I:CYS78 2.3 236.1 1.0
SG I:CYS75 2.3 246.3 1.0
CB I:CYS78 3.2 227.4 1.0
CB I:CYS106 3.3 186.4 1.0
CB I:CYS75 3.4 205.3 1.0
N I:CYS78 3.5 255.1 1.0
OG I:SER105 3.6 235.9 1.0
CA I:CYS78 3.8 250.8 1.0
CB I:CYS103 3.9 225.1 1.0
SG I:CYS103 4.0 252.1 1.0
N I:CYS106 4.1 241.4 1.0
N I:HIS79 4.2 298.1 1.0
CA I:CYS106 4.3 200.2 1.0
C I:CYS78 4.3 260.6 1.0
OG I:SER80 4.7 238.9 1.0
C I:LYS77 4.7 249.0 1.0
CA I:CYS75 4.8 212.6 1.0
CB I:SER105 4.8 239.5 1.0
N I:SER80 4.8 253.8 1.0
CB I:LYS77 4.8 216.9 1.0
N I:LYS77 4.9 246.2 1.0
C I:SER105 4.9 242.4 1.0
C I:CYS106 4.9 216.1 1.0
CB I:SER80 5.0 238.2 1.0

Zinc binding site 7 out of 8 in 9bvt

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Zinc binding site 7 out of 8 in the Rna Pol II - High Mn(+2) Concentration


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:133.5
occ:1.00
 SG J:CYS46 2.3 125.7 1.0
SG J:CYS10 2.3 131.9 1.0
SG J:CYS45 2.3 134.2 1.0
SG J:CYS7 2.3 126.8 1.0
OG J:SER9 2.8 148.3 1.0
N J:CYS46 3.3 155.2 1.0
CB J:CYS7 3.3 108.4 1.0
CB J:CYS46 3.5 123.8 1.0
CA J:CYS46 3.6 132.1 1.0
C J:CYS45 3.7 141.2 1.0
CB J:CYS45 3.7 155.2 1.0
CB J:CYS10 3.8 127.4 1.0
NH2 J:ARG43 3.9 145.6 1.0
N J:CYS10 3.9 137.7 1.0
NE J:ARG43 3.9 144.0 1.0
O J:CYS45 4.2 125.7 1.0
CB J:SER9 4.2 138.8 1.0
CA J:CYS45 4.3 130.9 1.0
CZ J:ARG43 4.4 150.4 1.0
CA J:CYS10 4.4 138.5 1.0
CA J:CYS7 4.7 123.8 1.0
N J:SER9 4.9 116.3 1.0
C J:SER9 4.9 139.3 1.0
CA J:SER9 4.9 132.2 1.0
CB J:ARG43 4.9 156.8 1.0
N J:CYS45 5.0 123.5 1.0

Zinc binding site 8 out of 8 in 9bvt

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Zinc binding site 8 out of 8 in the Rna Pol II - High Mn(+2) Concentration


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:166.7
occ:1.00
 SG L:CYS34 2.3 168.1 1.0
SG L:CYS51 2.3 229.4 1.0
SG L:CYS31 2.3 229.8 1.0
SG L:CYS48 2.3 147.5 1.0
CB L:CYS51 2.5 216.1 1.0
CB L:CYS31 3.2 188.1 1.0
CB L:CYS34 3.4 167.0 1.0
CB L:CYS48 3.4 155.3 1.0
OG L:SER36 3.7 166.3 1.0
CA L:CYS51 3.8 243.8 1.0
N L:CYS51 3.9 257.0 1.0
CB L:SER36 4.2 181.8 1.0
N L:CYS34 4.3 211.8 1.0
CA L:CYS34 4.4 192.6 1.0
OE1 L:GLU33 4.4 218.4 1.0
N L:SER36 4.4 190.4 1.0
C L:ASP50 4.5 242.5 1.0
N L:SER35 4.6 233.4 1.0
O L:CYS48 4.6 206.5 1.0
CA L:CYS31 4.7 181.2 1.0
N L:GLY52 4.7 188.8 1.0
CA L:CYS48 4.8 146.4 1.0
C L:CYS34 4.8 208.7 1.0
C L:CYS51 4.8 225.7 1.0
O L:ASP50 4.9 235.8 1.0
CA L:SER36 5.0 173.8 1.0
N L:ALA32 5.0 176.8 1.0

Reference:

G.Lin, C.O.Barnes, S.Weiss, B.Dutagaci, C.Qiu, M.Feig, J.Song, A.Lyubimov, A.E.Cohen, C.D.Kaplan, G.Calero. Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser. Proc.Natl.Acad.Sci.Usa V. 121 27121 2024.
ISSN: ESSN 1091-6490
PubMed: 39190355
DOI: 10.1073/PNAS.2318527121
Page generated: Thu Oct 31 14:42:26 2024

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