Atomistry » Zinc » PDB 5n2z-5nea » 5n61
Atomistry »
  Zinc »
    PDB 5n2z-5nea »
      5n61 »

Zinc in PDB 5n61: Rna Polymerase I Initially Transcribing Complex

Enzymatic activity of Rna Polymerase I Initially Transcribing Complex

All present enzymatic activity of Rna Polymerase I Initially Transcribing Complex:
2.7.7.6;

Other elements in 5n61:

The structure of Rna Polymerase I Initially Transcribing Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase I Initially Transcribing Complex (pdb code 5n61). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Rna Polymerase I Initially Transcribing Complex, PDB code: 5n61:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 5n61

Go back to Zinc Binding Sites List in 5n61
Zinc binding site 1 out of 7 in the Rna Polymerase I Initially Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase I Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3001

b:0.0
occ:1.00
 CD2 A:HIS75 1.6 0.0 1.0
NE2 A:HIS75 2.1 0.0 1.0
SG A:CYS72 2.3 0.0 1.0
SG A:CYS62 2.3 0.0 1.0
SG A:CYS65 2.3 0.0 1.0
CA A:GLY55 2.7 0.0 1.0
CG A:HIS75 2.9 0.0 1.0
N A:GLY55 3.3 0.0 1.0
CE1 A:HIS75 3.3 0.0 1.0
CB A:CYS65 3.5 0.0 1.0
ND1 A:HIS75 3.7 0.0 1.0
CB A:CYS62 3.7 0.0 1.0
C A:GLY55 3.7 0.0 1.0
N A:CYS65 3.7 0.0 1.0
C A:LEU54 3.8 0.0 1.0
O A:LEU54 3.8 0.0 1.0
CB A:HIS75 3.9 0.0 1.0
CA A:GLY74 3.9 0.0 1.0
C A:GLY74 3.9 0.0 1.0
N A:HIS75 3.9 0.0 1.0
N A:GLY74 3.9 0.0 1.0
N A:ALA56 4.0 0.0 1.0
CB A:CYS72 4.1 0.0 1.0
CB A:THR64 4.2 0.0 1.0
CA A:CYS65 4.3 0.0 1.0
O A:GLY74 4.5 0.0 1.0
CA A:HIS75 4.6 0.0 1.0
O A:ALA53 4.6 0.0 1.0
O A:GLY55 4.6 0.0 1.0
C A:THR64 4.8 0.0 1.0
CA A:CYS62 4.8 0.0 1.0
CG2 A:THR64 4.8 0.0 1.0
O A:LEU52 4.9 0.0 1.0
CA A:THR64 4.9 0.0 1.0
N A:THR64 4.9 0.0 1.0
CA A:LEU54 5.0 0.0 1.0
CA A:CYS72 5.0 0.0 1.0
C A:CYS72 5.0 0.0 1.0

Zinc binding site 2 out of 7 in 5n61

Go back to Zinc Binding Sites List in 5n61
Zinc binding site 2 out of 7 in the Rna Polymerase I Initially Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase I Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3002

b:0.0
occ:1.00
 CB A:CYS233 1.3 0.0 1.0
SG A:CYS233 2.3 0.0 1.0
SG A:CYS102 2.3 0.0 1.0
SG A:CYS236 2.3 0.0 1.0
SG A:CYS105 2.4 0.0 1.0
CA A:CYS233 2.8 0.0 1.0
CB A:CYS102 3.2 0.0 1.0
N A:CYS233 3.3 0.0 1.0
C A:CYS233 3.7 0.0 1.0
O A:CYS233 3.9 0.0 1.0
N A:MET238 3.9 0.0 1.0
O A:MET238 4.0 0.0 1.0
CA A:CYS102 4.0 0.0 1.0
CB A:CYS105 4.1 0.0 1.0
CB A:CYS236 4.1 0.0 1.0
CB A:MET238 4.1 0.0 1.0
C A:MET238 4.1 0.0 1.0
N A:CYS105 4.2 0.0 1.0
CA A:MET238 4.3 0.0 1.0
CG A:ARG109 4.5 0.0 1.0
N A:GLY237 4.5 0.0 1.0
N A:CYS236 4.6 0.0 1.0
C A:LYS232 4.7 0.0 1.0
N A:ASP234 4.7 0.0 1.0
N A:PHE239 4.8 0.0 1.0
CA A:CYS105 4.8 0.0 1.0
CA A:CYS236 4.8 0.0 1.0
C A:GLY237 4.8 0.0 1.0
CB A:PHE104 4.8 0.0 1.0
C A:CYS102 4.9 0.0 1.0
N A:PHE104 4.9 0.0 1.0
CD2 A:PHE104 5.0 0.0 1.0
N A:LEU103 5.0 0.0 1.0

Zinc binding site 3 out of 7 in 5n61

Go back to Zinc Binding Sites List in 5n61
Zinc binding site 3 out of 7 in the Rna Polymerase I Initially Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase I Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1302

b:0.0
occ:1.00
 SG B:CYS1128 2.3 0.0 1.0
SG B:CYS1131 2.3 0.0 1.0
SG B:CYS1107 2.3 0.0 1.0
SG B:CYS1104 2.3 0.0 1.0
CB B:CYS1131 2.5 0.0 1.0
CB B:CYS1107 2.8 0.0 1.0
CB B:CYS1128 2.8 0.0 1.0
N B:CYS1131 3.1 0.0 1.0
CB B:CYS1104 3.3 0.0 1.0
CA B:CYS1131 3.4 0.0 1.0
N B:CYS1107 3.5 0.0 1.0
CA B:CYS1107 3.8 0.0 1.0
CA B:CYS1128 4.1 0.0 1.0
O B:CYS1128 4.2 0.0 1.0
C B:ARG1130 4.2 0.0 1.0
C B:CYS1128 4.2 0.0 1.0
CA B:GLY1170 4.4 0.0 1.0
CB B:ARG1130 4.4 0.0 1.0
C B:CYS1131 4.4 0.0 1.0
N B:ARG1130 4.5 0.0 1.0
CA B:ARG1130 4.6 0.0 1.0
CB B:GLU1106 4.7 0.0 1.0
CA B:CYS1104 4.7 0.0 1.0
OG1 B:THR1112 4.7 0.0 1.0
C B:GLU1106 4.7 0.0 1.0
OE1 B:GLU1106 4.8 0.0 1.0
C B:CYS1107 4.9 0.0 1.0

Zinc binding site 4 out of 7 in 5n61

Go back to Zinc Binding Sites List in 5n61
Zinc binding site 4 out of 7 in the Rna Polymerase I Initially Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase I Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3001

b:0.0
occ:1.00
 CB I:CYS30 1.4 0.0 1.0
SG I:CYS33 2.3 0.0 1.0
SG I:CYS10 2.3 0.0 1.0
SG I:CYS30 2.3 0.0 1.0
SG I:CYS13 2.3 0.0 1.0
CB I:CYS10 2.6 0.0 1.0
CA I:CYS30 2.7 0.0 1.0
N I:CYS30 3.3 0.0 1.0
CB I:ALA35 3.3 0.0 1.0
N I:ALA35 3.4 0.0 1.0
O I:ALA35 3.4 0.0 1.0
CA I:ALA35 3.7 0.0 1.0
C I:CYS30 3.9 0.0 1.0
CA I:CYS10 3.9 0.0 1.0
C I:ALA35 4.0 0.0 1.0
CB I:CYS33 4.1 0.0 1.0
CB I:CYS13 4.1 0.0 1.0
N I:LYS34 4.2 0.0 1.0
C I:LYS34 4.4 0.0 1.0
N I:CYS13 4.5 0.0 1.0
N I:CYS33 4.5 0.0 1.0
N I:SER31 4.5 0.0 1.0
CE2 I:TYR37 4.5 0.0 1.0
C I:GLU29 4.6 0.0 1.0
C I:CYS33 4.6 0.0 1.0
O I:CYS30 4.6 0.0 1.0
CA I:CYS33 4.6 0.0 1.0
N I:CYS10 4.7 0.0 1.0
CA I:LYS34 4.8 0.0 1.0
CA I:CYS13 4.8 0.0 1.0
C I:CYS10 4.9 0.0 1.0

Zinc binding site 5 out of 7 in 5n61

Go back to Zinc Binding Sites List in 5n61
Zinc binding site 5 out of 7 in the Rna Polymerase I Initially Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase I Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3001

b:0.0
occ:1.00
 CB J:CYS10 1.3 0.0 1.0
CA J:CYS10 2.0 0.0 1.0
N J:CYS10 2.1 0.0 1.0
SG J:CYS10 2.3 0.0 1.0
SG J:CYS7 2.3 0.0 1.0
SG J:CYS46 2.3 0.0 1.0
SG J:CYS45 2.4 0.0 1.0
CB J:CYS7 2.5 0.0 1.0
C J:CYS10 2.8 0.0 1.0
N J:GLY11 2.9 0.0 1.0
C J:SER9 3.4 0.0 1.0
O J:CYS7 3.6 0.0 1.0
N J:LYS12 3.6 0.0 1.0
CA J:CYS7 3.7 0.0 1.0
C J:CYS7 3.8 0.0 1.0
O J:CYS10 3.9 0.0 1.0
CB J:CYS45 4.0 0.0 1.0
CB J:CYS46 4.0 0.0 1.0
CA J:GLY11 4.1 0.0 1.0
O J:SER9 4.2 0.0 1.0
CB J:LYS12 4.2 0.0 1.0
N J:CYS46 4.2 0.0 1.0
CA J:SER9 4.3 0.0 1.0
C J:GLY11 4.3 0.0 1.0
N J:SER9 4.3 0.0 1.0
CA J:CYS46 4.4 0.0 1.0
N J:CYS7 4.4 0.0 1.0
CA J:LYS12 4.5 0.0 1.0
CB J:SER9 4.6 0.0 1.0
N J:PHE8 4.6 0.0 1.0
C J:CYS45 4.7 0.0 1.0
C J:PHE8 4.7 0.0 1.0
O J:LYS12 4.8 0.0 1.0
O C:SER223 4.8 0.0 1.0

Zinc binding site 6 out of 7 in 5n61

Go back to Zinc Binding Sites List in 5n61
Zinc binding site 6 out of 7 in the Rna Polymerase I Initially Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase I Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn3001

b:0.0
occ:1.00
 SG L:CYS48 2.3 0.0 1.0
SG L:CYS31 2.3 0.0 1.0
SG L:CYS34 2.4 0.0 1.0
CB L:CYS51 2.5 0.0 1.0
CB L:CYS48 2.6 0.0 1.0
SG L:CYS51 2.8 0.0 1.0
N L:CYS51 3.2 0.0 1.0
CB L:CYS31 3.3 0.0 1.0
CA L:CYS51 3.4 0.0 1.0
CB L:CYS34 3.4 0.0 1.0
N L:CYS34 3.7 0.0 1.0
OG L:SER36 4.1 0.0 1.0
N L:GLY52 4.1 0.0 1.0
CA L:CYS48 4.1 0.0 1.0
CA L:CYS34 4.2 0.0 1.0
C L:CYS51 4.2 0.0 1.0
CD2 L:HIS53 4.2 0.0 1.0
C L:ASP50 4.4 0.0 1.0
CB L:ASP50 4.6 0.0 1.0
CB L:GLU33 4.6 0.0 1.0
CA L:CYS31 4.7 0.0 1.0
N L:HIS53 4.7 0.0 1.0
C L:CYS48 4.8 0.0 1.0
C L:GLU33 4.9 0.0 1.0
CA L:ASP50 4.9 0.0 1.0
CB L:HIS53 4.9 0.0 1.0
CG L:HIS53 4.9 0.0 1.0
O L:CYS48 5.0 0.0 1.0
N L:CYS48 5.0 0.0 1.0
C L:CYS34 5.0 0.0 1.0

Zinc binding site 7 out of 7 in 5n61

Go back to Zinc Binding Sites List in 5n61
Zinc binding site 7 out of 7 in the Rna Polymerase I Initially Transcribing Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase I Initially Transcribing Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn1001

b:0.0
occ:1.00
 SG Q:CYS10 2.2 0.0 1.0
SG Q:CYS15 2.7 0.0 1.0
SG Q:CYS29 2.8 0.0 1.0
ND1 Q:HIS33 2.8 0.0 1.0
CB Q:THR12 3.3 0.0 1.0
CE1 Q:HIS33 3.5 0.0 1.0
CB Q:CYS15 3.6 0.0 1.0
CG Q:HIS33 3.6 0.0 1.0
CG2 Q:THR12 3.7 0.0 1.0
CB Q:CYS10 3.8 0.0 1.0
CB Q:CYS29 3.9 0.0 1.0
CB Q:HIS33 4.0 0.0 1.0
O Q:THR12 4.1 0.0 1.0
OG1 Q:THR12 4.1 0.0 1.0
O Q:SER17 4.3 0.0 1.0
CA Q:THR12 4.3 0.0 1.0
NE2 Q:HIS33 4.4 0.0 1.0
N Q:THR12 4.4 0.0 1.0
OD1 Q:ASN14 4.5 0.0 1.0
CD2 Q:HIS33 4.5 0.0 1.0
C Q:THR12 4.6 0.0 1.0
N Q:CYS15 4.7 0.0 1.0
N Q:SER17 4.7 0.0 1.0
CA Q:CYS15 4.8 0.0 1.0
CB Q:SER17 4.8 0.0 1.0
CD2 Q:TYR31 4.9 0.0 1.0
CA Q:CYS10 5.0 0.0 1.0

Reference:

C.Engel, T.Gubbey, S.Neyer, S.Sainsbury, C.Oberthuer, C.Baejen, C.Bernecky, P.Cramer. Structural Basis of Rna Polymerase I Transcription Initiation. Cell V. 169 120 2017.
ISSN: ISSN 1097-4172
PubMed: 28340337
DOI: 10.1016/J.CELL.2017.03.003
Page generated: Sun Oct 27 22:37:27 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