Atomistry » Zinc » PDB 4uxz-4w6e » 4v1n
Atomistry »
  Zinc »
    PDB 4uxz-4w6e »
      4v1n »

Zinc in PDB 4v1n: Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex

Enzymatic activity of Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex

All present enzymatic activity of Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex:
2.7.7.6; 3.6.4.12;

Other elements in 4v1n:

The structure of Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex (pdb code 4v1n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex, PDB code: 4v1n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 4v1n

Go back to Zinc Binding Sites List in 4v1n
Zinc binding site 1 out of 9 in the Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:0.6
occ:1.00
 SG A:CYS148 2.3 0.1 1.0
SG A:CYS110 2.3 0.3 1.0
SG A:CYS167 2.4 1.0 1.0
SG A:CYS107 2.4 0.3 1.0
CB A:CYS167 2.6 0.9 1.0
CB A:CYS110 3.1 0.1 1.0
CB A:CYS148 3.1 0.7 1.0
CB A:CYS107 3.3 0.8 1.0
N A:CYS110 3.7 0.9 1.0
CA A:CYS110 4.0 0.5 1.0
CA A:CYS167 4.0 0.2 1.0
O A:CYS167 4.2 0.9 1.0
O A:GLY166 4.2 0.6 1.0
C A:CYS167 4.3 1.0 1.0
CA A:CYS148 4.6 0.8 1.0
CA A:CYS107 4.7 0.9 1.0
N A:CYS167 4.8 0.9 1.0
C A:HIS109 4.8 0.8 1.0
C A:CYS110 4.8 0.3 1.0
C A:GLY166 4.9 0.5 1.0
CB A:HIS109 4.9 0.9 1.0
NE2 A:GLN171 4.9 0.5 1.0
CD2 A:HIS109 4.9 0.6 1.0
N A:GLY111 5.0 0.9 1.0

Zinc binding site 2 out of 9 in 4v1n

Go back to Zinc Binding Sites List in 4v1n
Zinc binding site 2 out of 9 in the Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:67.6
occ:1.00
 NE2 A:HIS80 1.9 73.8 1.0
SG A:CYS70 2.2 0.5 1.0
CE1 A:HIS80 2.3 78.1 1.0
SG A:CYS67 2.5 69.7 1.0
SG A:CYS77 2.7 95.2 1.0
CB A:CYS70 3.1 0.3 1.0
CD2 A:HIS80 3.3 74.9 1.0
ND1 A:HIS80 3.6 76.4 1.0
O A:CYS67 3.7 0.2 1.0
CB A:CYS67 3.8 0.6 1.0
CB A:CYS77 3.8 74.2 1.0
CG A:HIS80 4.1 72.9 1.0
NE2 A:GLN68 4.2 84.0 1.0
CD A:GLN68 4.4 0.6 1.0
OE1 A:GLN68 4.4 1.0 1.0
CA A:CYS70 4.5 0.5 1.0
CA A:CYS77 4.6 72.3 1.0
O A:GLN71 4.6 0.5 1.0
C A:CYS67 4.6 0.0 1.0
C A:CYS70 4.7 0.8 1.0
CA A:CYS67 4.8 0.7 1.0
CD A:PRO78 4.8 69.6 1.0
N A:GLN71 4.9 0.5 1.0

Zinc binding site 3 out of 9 in 4v1n

Go back to Zinc Binding Sites List in 4v1n
Zinc binding site 3 out of 9 in the Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:77.4
occ:1.00
 SG B:CYS1166 2.2 81.5 1.0
SG B:CYS1182 2.4 78.4 1.0
SG B:CYS1163 2.4 85.5 1.0
SG B:CYS1185 2.4 75.6 1.0
CB B:CYS1163 2.9 79.3 1.0
CB B:CYS1185 3.4 74.6 1.0
O B:CYS1166 3.5 78.8 1.0
CB B:CYS1166 3.7 76.8 1.0
N B:CYS1166 3.7 75.4 1.0
CB B:CYS1182 3.8 76.0 1.0
CA B:CYS1166 4.1 75.3 1.0
C B:CYS1166 4.2 78.5 1.0
CA B:CYS1163 4.4 77.4 1.0
OG1 B:THR1170 4.5 83.4 1.0
CA B:CYS1185 4.7 78.3 1.0
CB B:THR1170 4.7 85.6 1.0
CG2 B:THR1170 4.8 88.3 1.0
CB B:ILE1165 4.8 75.4 1.0
C B:ILE1165 4.8 77.0 1.0
O B:CYS1182 4.9 86.7 1.0
N B:ILE1165 4.9 74.2 1.0
CD1 B:ILE1165 4.9 68.3 1.0
N B:CYS1185 5.0 81.8 1.0
C B:CYS1163 5.0 80.0 1.0

Zinc binding site 4 out of 9 in 4v1n

Go back to Zinc Binding Sites List in 4v1n
Zinc binding site 4 out of 9 in the Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:88.5
occ:1.00
 SG C:CYS95 2.2 74.6 1.0
SG C:CYS92 2.2 80.7 1.0
SG C:CYS86 2.3 79.0 1.0
SG C:CYS88 2.3 74.0 1.0
CB C:CYS92 3.2 77.7 1.0
CB C:CYS86 3.3 73.5 1.0
CB C:CYS95 3.3 71.8 1.0
N C:CYS92 3.5 79.2 1.0
CB C:CYS88 3.7 71.6 1.0
CA C:CYS92 3.9 78.4 1.0
C C:HIS91 4.0 85.5 1.0
N C:CYS95 4.0 76.1 1.0
CA C:CYS95 4.3 73.8 1.0
CA C:HIS91 4.3 83.0 1.0
N C:CYS88 4.3 71.2 1.0
C C:CYS92 4.4 84.2 1.0
O C:ASP90 4.5 90.1 1.0
CA C:CYS86 4.6 72.8 1.0
O C:HIS91 4.6 86.1 1.0
CA C:CYS88 4.6 72.0 1.0
CB C:LYS94 4.7 78.4 1.0
C C:LYS94 4.7 82.5 1.0
O C:CYS92 4.8 82.2 1.0
N C:PHE87 4.8 69.7 1.0
C C:CYS86 4.9 73.4 1.0
N C:LYS94 4.9 79.4 1.0

Zinc binding site 5 out of 9 in 4v1n

Go back to Zinc Binding Sites List in 4v1n
Zinc binding site 5 out of 9 in the Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:0.1
occ:1.00
 SG I:CYS7 2.2 0.9 1.0
SG I:CYS29 2.3 0.6 1.0
SG I:CYS10 2.3 0.4 1.0
SG I:CYS32 2.3 0.5 1.0
CB I:CYS10 2.6 0.0 1.0
CB I:CYS29 3.2 0.6 1.0
CB I:CYS7 3.3 0.5 1.0
CB I:CYS32 3.4 0.0 1.0
N I:CYS10 3.7 0.7 1.0
CA I:CYS10 3.7 0.2 1.0
N I:CYS32 3.8 0.9 1.0
CA I:CYS32 4.1 0.0 1.0
CB I:TYR34 4.3 0.1 1.0
OG1 I:THR31 4.3 0.1 1.0
C I:THR31 4.7 0.2 1.0
CA I:CYS29 4.7 0.4 1.0
CA I:CYS7 4.7 0.6 1.0
C I:CYS32 4.7 0.3 1.0
O I:ARG8 4.8 0.5 1.0
C I:ASP9 4.8 0.2 1.0
CB I:ASP9 4.8 0.9 1.0
C I:CYS10 4.9 0.2 1.0
CB I:THR31 5.0 0.2 1.0

Zinc binding site 6 out of 9 in 4v1n

Go back to Zinc Binding Sites List in 4v1n
Zinc binding site 6 out of 9 in the Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.5
occ:1.00
 SG I:CYS106 2.3 0.5 1.0
SG I:CYS78 2.3 0.6 1.0
SG I:CYS75 2.4 0.8 1.0
SG I:CYS103 2.4 0.2 1.0
CB I:CYS106 3.1 1.0 1.0
CB I:CYS103 3.2 0.2 1.0
CB I:CYS75 3.2 0.1 1.0
CB I:CYS78 3.5 0.7 1.0
N I:CYS78 3.6 0.8 1.0
N I:CYS106 3.7 0.9 1.0
CA I:CYS106 3.9 0.4 1.0
CA I:CYS78 4.0 0.4 1.0
OG I:SER105 4.1 0.9 1.0
CB I:SER80 4.6 0.6 1.0
C I:CYS78 4.6 0.0 1.0
C I:CYS106 4.6 0.1 1.0
CB I:LYS77 4.6 0.9 1.0
N I:HIS79 4.6 0.5 1.0
CA I:CYS103 4.6 0.4 1.0
CA I:CYS75 4.7 0.8 1.0
N I:SER80 4.7 0.2 1.0
C I:LYS77 4.7 0.0 1.0
N I:SER107 4.7 0.6 1.0
CB I:HIS108 5.0 0.1 1.0
CA I:LYS77 5.0 0.1 1.0
N I:LYS77 5.0 0.6 1.0
C I:SER105 5.0 0.4 1.0

Zinc binding site 7 out of 9 in 4v1n

Go back to Zinc Binding Sites List in 4v1n
Zinc binding site 7 out of 9 in the Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:91.4
occ:1.00
 SG J:CYS7 2.2 87.4 1.0
SG J:CYS46 2.3 89.7 1.0
SG J:CYS45 2.4 88.5 1.0
SG J:CYS10 2.5 91.7 1.0
CB J:CYS7 3.2 83.7 1.0
N J:CYS46 3.3 85.2 1.0
CB J:CYS45 3.5 83.8 1.0
CB J:CYS10 3.5 86.3 1.0
CB J:CYS46 3.6 86.0 1.0
N J:CYS10 3.6 80.4 1.0
CA J:CYS46 3.6 85.1 1.0
C J:CYS45 3.7 88.2 1.0
CA J:CYS10 4.0 82.9 1.0
CA J:CYS45 4.2 84.3 1.0
O J:CYS45 4.2 87.6 1.0
NE J:ARG43 4.3 0.6 1.0
NH2 J:ARG43 4.5 0.5 1.0
C J:SER9 4.6 79.9 1.0
N J:GLY11 4.6 79.2 1.0
CA J:CYS7 4.6 81.8 1.0
CB J:SER9 4.6 76.9 1.0
C J:CYS10 4.7 83.7 1.0
CA J:SER9 4.9 73.3 1.0
C J:CYS7 4.9 81.2 1.0
N J:LYS12 4.9 87.5 1.0
N J:CYS45 4.9 86.6 1.0
N J:SER9 4.9 72.7 1.0
CZ J:ARG43 4.9 1.0 1.0
CB J:LYS12 5.0 92.9 1.0
CB J:ARG43 5.0 93.8 1.0

Zinc binding site 8 out of 9 in 4v1n

Go back to Zinc Binding Sites List in 4v1n
Zinc binding site 8 out of 9 in the Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.5
occ:1.00
 SG L:CYS48 2.3 0.1 1.0
SG L:CYS34 2.3 0.5 1.0
SG L:CYS51 2.4 0.6 1.0
SG L:CYS31 2.5 0.1 1.0
CB L:CYS48 3.1 0.9 1.0
CB L:CYS51 3.4 0.4 1.0
CB L:CYS31 3.6 0.4 1.0
CB L:CYS34 3.6 0.9 1.0
OG L:SER36 4.0 0.3 1.0
N L:CYS51 4.3 0.9 1.0
CA L:CYS51 4.3 0.7 1.0
N L:CYS34 4.5 0.2 1.0
CA L:CYS48 4.5 0.2 1.0
CA L:CYS34 4.6 0.3 1.0
O L:CYS51 4.6 0.0 1.0
C L:CYS51 4.7 0.9 1.0
CG L:GLU33 4.9 0.3 1.0
C L:CYS48 4.9 0.2 1.0

Zinc binding site 9 out of 9 in 4v1n

Go back to Zinc Binding Sites List in 4v1n
Zinc binding site 9 out of 9 in the Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn1216

b:0.9
occ:1.00
 SG M:CYS48 2.3 92.6 1.0
SG M:CYS24 2.3 0.5 1.0
SG M:CYS27 2.3 0.0 1.0
SG M:CYS45 2.3 0.0 1.0
CB M:CYS24 3.0 0.9 1.0
CB M:CYS48 3.2 0.6 1.0
CB M:CYS45 3.2 85.0 1.0
CB M:CYS27 3.5 0.3 1.0
N M:CYS48 3.6 0.8 1.0
CA M:CYS48 3.9 97.4 1.0
NZ A:LYS419 4.1 78.7 1.0
N M:CYS27 4.2 1.0 1.0
CA M:CYS24 4.5 0.8 1.0
CA M:CYS27 4.5 0.4 1.0
CB M:LEU47 4.5 100.0 1.0
CA M:CYS45 4.6 82.5 1.0
N M:GLY49 4.7 78.8 1.0
C M:CYS48 4.7 85.8 1.0
C M:LEU47 4.7 99.0 1.0
CB M:LEU50 4.8 80.7 1.0
CE A:LYS419 4.9 65.9 1.0
CB M:GLU26 4.9 0.0 1.0
C M:CYS45 5.0 87.8 1.0
O M:CYS45 5.0 89.1 1.0
CA M:LEU47 5.0 97.7 1.0
N M:LEU50 5.0 84.9 1.0

Reference:

C.Plaschka, L.Lariviere, L.Wenzeck, M.Hemann, D.Tegunov, E.V.Petrotchenko, C.H.Borchers, W.Baumeister, F.Herzog, E.Villa, P.Cramer. Architecture of the Rna Polymerase II-Mediator Core Transcription Initiation Complex Nature 2015.
ISSN: ISSN 0028-0836
DOI: 10.1038/NATURE14229
Page generated: Sun Oct 27 09:28:36 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy