Atomistry » Zinc » PDB 1w5m-1wfx » 1wcm
Atomistry »
  Zinc »
    PDB 1w5m-1wfx »
      1wcm »

Zinc in PDB 1wcm: Complete 12-Subunit Rna Polymerase II at 3.8 Ang

Enzymatic activity of Complete 12-Subunit Rna Polymerase II at 3.8 Ang

All present enzymatic activity of Complete 12-Subunit Rna Polymerase II at 3.8 Ang:
2.7.7.6;

Protein crystallography data

The structure of Complete 12-Subunit Rna Polymerase II at 3.8 Ang, PDB code: 1wcm was solved by K.-J.Armache, S.Mitterweger, A.Meinhart, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50 / 3.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.718, 395.135, 284.300, 90.00, 90.00, 90.00
R / Rfree (%) 25.69 / 28.54

Other elements in 1wcm:

The structure of Complete 12-Subunit Rna Polymerase II at 3.8 Ang also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang (pdb code 1wcm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang, PDB code: 1wcm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1wcm

Go back to Zinc Binding Sites List in 1wcm
Zinc binding site 1 out of 8 in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complete 12-Subunit Rna Polymerase II at 3.8 Ang within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:86.9
occ:1.00
 SG A:CYS110 2.5 0.3 1.0
SG A:CYS167 2.6 0.1 1.0
SG A:CYS148 2.8 0.2 1.0
O A:MET108 3.5 0.4 1.0
O A:CYS167 3.6 1.0 1.0
CB A:CYS148 3.7 0.9 1.0
CB A:CYS110 3.7 0.0 1.0
N A:CYS110 4.1 0.9 1.0
O A:CYS107 4.2 0.5 1.0
CB A:CYS107 4.3 0.0 1.0
CB A:CYS167 4.3 0.1 1.0
CA A:CYS110 4.4 0.3 1.0
O A:GLY166 4.5 0.8 1.0
N A:GLY111 4.6 0.6 1.0
C A:CYS107 4.6 0.9 1.0
C A:CYS167 4.6 0.9 1.0
C A:MET108 4.7 0.6 1.0
C A:CYS110 4.7 0.0 1.0
SG A:CYS107 4.9 0.8 1.0

Zinc binding site 2 out of 8 in 1wcm

Go back to Zinc Binding Sites List in 1wcm
Zinc binding site 2 out of 8 in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complete 12-Subunit Rna Polymerase II at 3.8 Ang within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:44.9
occ:1.00
 SG A:CYS77 2.1 0.9 1.0
NE2 A:HIS80 2.1 61.0 1.0
CB A:CYS67 2.6 0.7 1.0
SG A:CYS70 2.7 0.7 1.0
O A:CYS67 2.7 0.1 1.0
SG A:CYS67 2.8 0.6 1.0
CD2 A:HIS80 2.8 60.5 1.0
CB A:CYS70 3.1 0.2 1.0
CE1 A:HIS80 3.2 60.9 1.0
C A:CYS67 3.5 0.0 1.0
CB A:CYS77 3.6 97.8 1.0
CA A:CYS67 3.6 0.9 1.0
O A:CYS77 3.9 85.7 1.0
CG A:HIS80 4.0 61.8 1.0
ND1 A:HIS80 4.2 60.6 1.0
CA A:CYS77 4.4 90.9 1.0
CA A:CYS70 4.5 0.3 1.0
C A:CYS77 4.6 85.5 1.0
O A:PRO78 4.7 82.8 1.0
NE2 A:GLN68 4.7 0.1 1.0
N A:CYS67 4.8 0.9 1.0
C A:CYS70 4.8 0.1 1.0
N A:GLN68 4.8 0.0 1.0
O A:GLN71 5.0 0.0 1.0
O A:CYS70 5.0 0.7 1.0

Zinc binding site 3 out of 8 in 1wcm

Go back to Zinc Binding Sites List in 1wcm
Zinc binding site 3 out of 8 in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complete 12-Subunit Rna Polymerase II at 3.8 Ang within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:44.9
occ:1.00
 SG B:CYS1166 2.2 69.2 1.0
SG B:CYS1182 2.3 82.3 1.0
SG B:CYS1185 2.4 79.8 1.0
CB B:CYS1185 2.6 79.8 1.0
SG B:CYS1163 2.6 71.8 1.0
CB B:CYS1163 2.9 67.5 1.0
O B:CYS1182 3.8 88.8 1.0
CB B:CYS1182 3.8 86.3 1.0
CA B:CYS1185 3.9 83.4 1.0
CB B:CYS1166 4.0 68.7 1.0
O B:CYS1166 4.1 68.6 1.0
N B:CYS1185 4.1 85.5 1.0
N B:CYS1166 4.2 69.0 1.0
C B:CYS1185 4.3 83.8 1.0
CA B:CYS1163 4.4 65.5 1.0
OG1 B:THR1170 4.6 62.2 1.0
CA B:CYS1166 4.6 68.3 1.0
N B:ASP1186 4.7 84.2 1.0
C B:CYS1182 4.7 89.1 1.0
CG2 B:ILE1165 4.8 75.2 1.0
CB B:THR1170 4.8 61.2 1.0
C B:CYS1166 4.9 68.7 1.0
CB B:ILE1165 4.9 73.5 1.0
CA B:CYS1182 4.9 88.0 1.0
O B:CYS1185 4.9 85.0 1.0

Zinc binding site 4 out of 8 in 1wcm

Go back to Zinc Binding Sites List in 1wcm
Zinc binding site 4 out of 8 in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complete 12-Subunit Rna Polymerase II at 3.8 Ang within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:39.5
occ:1.00
 SG C:CYS88 2.2 49.3 1.0
SG C:CYS95 2.3 63.0 1.0
SG C:CYS86 2.4 41.5 1.0
SG C:CYS92 2.5 73.0 1.0
CB C:CYS86 2.9 47.1 1.0
N C:CYS92 3.0 69.1 1.0
CB C:CYS95 3.2 63.7 1.0
CB C:CYS92 3.6 72.3 1.0
C C:HIS91 3.6 68.9 1.0
CA C:HIS91 3.6 70.7 1.0
CA C:CYS92 3.7 71.5 1.0
O C:CYS92 3.8 72.2 1.0
CB C:CYS88 3.8 51.4 1.0
N C:CYS95 4.1 64.2 1.0
C C:CYS92 4.1 72.4 1.0
CA C:CYS95 4.2 63.3 1.0
CA C:CYS86 4.2 50.6 1.0
N C:HIS91 4.3 74.5 1.0
O C:CYS86 4.3 51.5 1.0
C C:CYS86 4.5 50.3 1.0
N C:CYS88 4.5 49.4 1.0
O C:HIS91 4.5 66.9 1.0
C C:LYS94 4.5 65.6 1.0
CA C:CYS88 4.7 51.9 1.0
CB C:HIS91 4.8 68.5 1.0
O C:CYS88 4.8 55.0 1.0
CB C:LYS94 4.8 70.6 1.0
N C:LYS94 4.9 70.0 1.0
CA C:LYS94 5.0 67.9 1.0
C C:CYS95 5.0 62.1 1.0

Zinc binding site 5 out of 8 in 1wcm

Go back to Zinc Binding Sites List in 1wcm
Zinc binding site 5 out of 8 in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Complete 12-Subunit Rna Polymerase II at 3.8 Ang within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:90.7
occ:1.00
 SG I:CYS10 2.3 89.4 1.0
SG I:CYS32 2.4 86.2 1.0
SG I:CYS7 2.4 0.4 1.0
SG I:CYS29 2.7 88.5 1.0
CB I:CYS29 2.9 94.2 1.0
CB I:CYS32 3.5 91.2 1.0
CB I:CYS10 3.8 99.7 1.0
CB I:CYS7 3.8 0.5 1.0
O I:ARG8 4.1 0.6 1.0
N I:CYS32 4.2 96.7 1.0
CB I:TYR34 4.3 73.8 1.0
N I:CYS10 4.3 0.7 1.0
CA I:CYS29 4.4 96.0 1.0
CA I:CYS10 4.4 0.1 1.0
CA I:CYS32 4.4 93.7 1.0
OD2 I:ASP9 4.5 0.7 1.0
C I:CYS10 4.6 0.2 1.0
N I:ASN11 4.6 0.6 1.0
N I:TYR34 5.0 77.6 1.0
N I:ASN12 5.0 0.3 1.0

Zinc binding site 6 out of 8 in 1wcm

Go back to Zinc Binding Sites List in 1wcm
Zinc binding site 6 out of 8 in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Complete 12-Subunit Rna Polymerase II at 3.8 Ang within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.4
occ:1.00
 SG I:CYS106 2.3 0.7 1.0
SG I:CYS78 2.4 0.6 1.0
SG I:CYS103 2.6 0.5 1.0
CB I:CYS103 3.0 0.1 1.0
CB I:CYS75 3.1 0.3 1.0
SG I:CYS75 3.3 0.5 1.0
CB I:CYS106 3.4 0.3 1.0
CB I:CYS78 3.7 0.1 1.0
CA I:CYS103 4.3 0.7 1.0
CA I:CYS106 4.5 0.2 1.0
CA I:CYS75 4.5 0.3 1.0
O I:SER105 4.6 0.2 1.0
CB I:HIS108 4.6 0.1 1.0
N I:CYS106 4.7 0.3 1.0
C I:SER105 4.7 1.0 1.0
N I:HIS108 4.8 0.6 1.0
N I:SER107 4.9 0.3 1.0
CA I:CYS78 5.0 0.1 1.0

Zinc binding site 7 out of 8 in 1wcm

Go back to Zinc Binding Sites List in 1wcm
Zinc binding site 7 out of 8 in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Complete 12-Subunit Rna Polymerase II at 3.8 Ang within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:65.2
occ:1.00
 SG J:CYS46 2.2 65.8 1.0
N J:CYS46 2.3 68.8 1.0
SG J:CYS10 2.4 61.0 1.0
CB J:CYS46 2.5 65.5 1.0
SG J:CYS45 2.5 78.5 1.0
CB J:CYS10 2.5 58.1 1.0
SG J:CYS7 2.6 51.5 1.0
CA J:CYS46 2.6 68.5 1.0
C J:CYS45 3.0 70.0 1.0
CB J:CYS45 3.1 74.2 1.0
CB J:CYS7 3.4 47.3 1.0
N J:CYS10 3.6 56.5 1.0
CA J:CYS10 3.6 57.8 1.0
CA J:CYS45 3.7 71.9 1.0
O J:CYS45 3.8 69.3 1.0
OG J:SER9 4.0 51.5 1.0
C J:CYS46 4.1 70.2 1.0
N J:GLY11 4.4 57.5 1.0
C J:CYS10 4.5 57.4 1.0
N J:CYS45 4.6 71.5 1.0
CB J:SER9 4.7 51.7 1.0
NE J:ARG43 4.7 73.5 1.0
N J:ARG47 4.7 73.7 1.0
CG J:ARG43 4.8 74.6 1.0
O J:ARG43 4.8 77.0 1.0
C J:SER9 4.8 54.1 1.0
CA J:CYS7 4.9 47.1 1.0
O J:CYS46 4.9 69.7 1.0

Zinc binding site 8 out of 8 in 1wcm

Go back to Zinc Binding Sites List in 1wcm
Zinc binding site 8 out of 8 in the Complete 12-Subunit Rna Polymerase II at 3.8 Ang


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Complete 12-Subunit Rna Polymerase II at 3.8 Ang within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.3
occ:1.00
 SG L:CYS48 2.4 0.8 1.0
SG L:CYS31 2.4 0.2 1.0
SG L:CYS34 2.6 0.7 1.0
SG L:CYS51 2.7 0.2 1.0
CB L:CYS48 3.0 0.4 1.0
CB L:CYS31 3.2 0.8 1.0
O L:CYS51 3.6 0.4 1.0
CA L:CYS31 4.0 0.1 1.0
CB L:CYS51 4.1 0.3 1.0
CB L:CYS34 4.3 0.1 1.0
CA L:CYS48 4.4 0.4 1.0
C L:CYS51 4.5 0.2 1.0
OG L:SER36 4.7 0.3 1.0
CA L:CYS51 4.9 0.2 1.0
N L:CYS34 4.9 1.0 1.0

Reference:

K.-J.Armache, S.Mitterweger, A.Meinhart, P.Cramer. Structures of Complete Rna Polymerase II and Its Subcomplex,RPB4/7 J.Biol.Chem. V. 280 7131 2005.
ISSN: ISSN 0021-9258
PubMed: 15591044
DOI: 10.1074/JBC.M413038200
Page generated: Wed Oct 16 19:57:37 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy