Atomistry » Zinc » PDB 5n34-5nek » 5n60
Atomistry »
  Zinc »
    PDB 5n34-5nek »
      5n60 »

Zinc in PDB 5n60: Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I)

Enzymatic activity of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I)

All present enzymatic activity of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I):
2.7.7.6;

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I) (pdb code 5n60). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I), PDB code: 5n60:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5n60

Go back to Zinc Binding Sites List in 5n60
Zinc binding site 1 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:0.0
occ:1.00
SG A:CYS65 1.8 0.0 1.0
NE2 A:HIS75 2.0 0.0 1.0
SG A:CYS62 2.1 0.0 1.0
SG A:CYS72 2.3 0.0 1.0
CD2 A:HIS75 2.8 0.0 1.0
CE1 A:HIS75 3.0 0.0 1.0
CB A:CYS62 3.2 0.0 1.0
CB A:CYS65 3.4 0.0 1.0
CB A:CYS72 3.6 0.0 1.0
N A:CYS65 3.9 0.0 1.0
CG A:HIS75 3.9 0.0 1.0
CD A:PRO73 3.9 0.0 1.0
ND1 A:HIS75 4.0 0.0 1.0
CA A:CYS65 4.3 0.0 1.0
CA A:CYS72 4.3 0.0 1.0
N A:GLY74 4.4 0.0 1.0
CA A:GLY55 4.5 0.0 1.0
N A:PRO73 4.5 0.0 1.0
C A:CYS72 4.6 0.0 1.0
CA A:CYS62 4.7 0.0 1.0
CB A:THR64 4.7 0.0 1.0
CG A:PRO73 4.7 0.0 1.0
CA A:GLY74 4.7 0.0 1.0
C A:THR64 4.9 0.0 1.0
C A:GLY74 4.9 0.0 1.0
N A:GLY66 5.0 0.0 1.0
C A:CYS65 5.0 0.0 1.0

Zinc binding site 2 out of 8 in 5n60

Go back to Zinc Binding Sites List in 5n60
Zinc binding site 2 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:0.0
occ:1.00
SG A:CYS105 2.1 0.0 1.0
SG A:CYS236 2.3 0.0 1.0
SG A:CYS233 2.4 0.0 1.0
SG A:CYS102 2.4 0.0 1.0
CB A:CYS105 3.1 0.0 1.0
CB A:CYS102 3.3 0.0 1.0
CB A:CYS233 3.3 0.0 1.0
CB A:CYS236 3.4 0.0 1.0
N A:CYS105 3.6 0.0 1.0
N A:CYS236 3.8 0.0 1.0
CA A:CYS105 3.9 0.0 1.0
CA A:CYS236 4.2 0.0 1.0
C A:CYS105 4.6 0.0 1.0
N A:HIS106 4.7 0.0 1.0
CB A:ASN235 4.7 0.0 1.0
C A:ASN235 4.7 0.0 1.0
CA A:CYS102 4.8 0.0 1.0
CA A:CYS233 4.8 0.0 1.0
C A:PHE104 4.8 0.0 1.0
C A:CYS236 4.9 0.0 1.0
CB A:PHE104 4.9 0.0 1.0
N A:GLY237 5.0 0.0 1.0

Zinc binding site 3 out of 8 in 5n60

Go back to Zinc Binding Sites List in 5n60
Zinc binding site 3 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:0.0
occ:1.00
SG B:CYS1104 2.2 0.0 1.0
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
CB B:CYS1104 3.0 0.0 1.0
CB B:CYS1107 3.1 0.0 1.0
CB B:CYS1128 3.3 0.0 1.0
CB B:CYS1131 3.3 0.0 1.0
N B:CYS1107 3.6 0.0 1.0
CA B:CYS1107 4.0 0.0 1.0
N B:CYS1131 4.0 0.0 1.0
CA B:CYS1131 4.2 0.0 1.0
CB B:ARG1130 4.3 0.0 1.0
CA B:CYS1104 4.5 0.0 1.0
CB B:GLU1106 4.5 0.0 1.0
OG1 B:THR1112 4.5 0.0 1.0
C B:GLU1106 4.6 0.0 1.0
CA B:CYS1128 4.7 0.0 1.0
CD B:ARG1130 4.7 0.0 1.0
C B:ARG1130 4.8 0.0 1.0
C B:CYS1107 4.8 0.0 1.0
N B:ARG1130 4.9 0.0 1.0
CA B:ARG1130 4.9 0.0 1.0
CG B:ARG1130 4.9 0.0 1.0
CA B:GLU1106 4.9 0.0 1.0
C B:CYS1104 4.9 0.0 1.0
O B:CYS1104 4.9 0.0 1.0
N B:GLU1106 5.0 0.0 1.0

Zinc binding site 4 out of 8 in 5n60

Go back to Zinc Binding Sites List in 5n60
Zinc binding site 4 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1001

b:0.0
occ:1.00
SG I:CYS10 2.2 0.0 1.0
SG I:CYS13 2.2 0.0 1.0
SG I:CYS33 2.3 0.0 1.0
SG I:CYS30 2.4 0.0 1.0
CB I:CYS10 3.1 0.0 1.0
CB I:CYS30 3.4 0.0 1.0
CB I:CYS13 3.4 0.0 1.0
N I:CYS13 3.5 0.0 1.0
CB I:CYS33 3.7 0.0 1.0
CA I:CYS13 3.9 0.0 1.0
N I:CYS33 4.0 0.0 1.0
C I:CYS13 4.3 0.0 1.0
CB I:ASP12 4.4 0.0 1.0
CA I:CYS33 4.4 0.0 1.0
CB I:ALA35 4.4 0.0 1.0
O I:CYS13 4.5 0.0 1.0
CB I:GLN32 4.5 0.0 1.0
CA I:CYS10 4.5 0.0 1.0
C I:ASP12 4.6 0.0 1.0
N I:ASP12 4.8 0.0 1.0
CA I:ASP12 4.8 0.0 1.0
CA I:CYS30 4.8 0.0 1.0
N I:ASP15 4.9 0.0 1.0
C I:CYS10 5.0 0.0 1.0

Zinc binding site 5 out of 8 in 5n60

Go back to Zinc Binding Sites List in 5n60
Zinc binding site 5 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1002

b:0.0
occ:0.75
SG I:CYS114 2.2 0.0 1.0
SG I:CYS117 2.2 0.0 1.0
SG I:CYS89 2.2 0.0 1.0
SG I:CYS86 2.5 0.0 1.0
CB I:CYS117 3.1 0.0 1.0
CB I:CYS86 3.1 0.0 1.0
CB I:CYS89 3.1 0.0 1.0
CB I:CYS114 3.2 0.0 1.0
N I:CYS89 3.7 0.0 1.0
CA I:CYS89 3.9 0.0 1.0
N I:CYS117 3.9 0.0 1.0
CA I:CYS117 4.0 0.0 1.0
CB I:ASN91 4.1 0.0 1.0
OG I:SER116 4.6 0.0 1.0
N I:GLY90 4.6 0.0 1.0
C I:CYS89 4.6 0.0 1.0
CA I:CYS114 4.6 0.0 1.0
CA I:CYS86 4.6 0.0 1.0
N I:ASN91 4.6 0.0 1.0
C I:CYS117 4.7 0.0 1.0
CB I:GLN88 4.8 0.0 1.0
C I:GLN88 4.9 0.0 1.0
N I:GLY118 4.9 0.0 1.0
CB I:TYR119 5.0 0.0 1.0

Zinc binding site 6 out of 8 in 5n60

Go back to Zinc Binding Sites List in 5n60
Zinc binding site 6 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1001

b:0.0
occ:1.00
CA J:CYS46 1.7 0.0 1.0
N J:CYS46 1.8 0.0 1.0
SG J:CYS7 2.2 0.0 1.0
SG J:CYS46 2.3 0.0 1.0
CB J:CYS46 2.3 0.0 1.0
SG J:CYS45 2.3 0.0 1.0
C J:CYS45 2.3 0.0 1.0
SG J:CYS10 2.4 0.0 1.0
O J:CYS45 2.8 0.0 1.0
CB J:CYS7 3.1 0.0 1.0
C J:CYS46 3.2 0.0 1.0
CB J:CYS45 3.4 0.0 1.0
CA J:CYS45 3.4 0.0 1.0
O J:CYS46 3.8 0.0 1.0
CG J:MET49 4.0 0.0 1.0
N J:ARG47 4.1 0.0 1.0
CB J:CYS10 4.1 0.0 1.0
NH1 J:ARG48 4.4 0.0 1.0
CA J:CYS7 4.4 0.0 1.0
N J:CYS45 4.4 0.0 1.0
O J:ARG43 4.5 0.0 1.0
CB J:MET49 4.9 0.0 1.0
N J:CYS10 4.9 0.0 1.0
C J:TYR44 4.9 0.0 1.0
O J:TYR44 4.9 0.0 1.0

Zinc binding site 7 out of 8 in 5n60

Go back to Zinc Binding Sites List in 5n60
Zinc binding site 7 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1001

b:0.0
occ:1.00
SG L:CYS34 2.2 0.0 1.0
SG L:CYS48 2.2 0.0 1.0
SG L:CYS51 2.3 0.0 1.0
SG L:CYS31 2.5 0.0 1.0
CB L:CYS51 2.7 0.0 1.0
CB L:CYS48 2.9 0.0 1.0
CB L:CYS34 3.3 0.0 1.0
N L:CYS51 3.3 0.0 1.0
CB L:CYS31 3.4 0.0 1.0
CA L:CYS51 3.6 0.0 1.0
N L:CYS34 4.0 0.0 1.0
CA L:CYS34 4.2 0.0 1.0
CA L:CYS48 4.4 0.0 1.0
CB L:ASP50 4.4 0.0 1.0
C L:ASP50 4.5 0.0 1.0
OG L:SER36 4.5 0.0 1.0
C L:CYS51 4.7 0.0 1.0
N L:GLY52 4.7 0.0 1.0
CA L:ASP50 4.8 0.0 1.0
CA L:CYS31 4.8 0.0 1.0
N L:ASP50 4.8 0.0 1.0
C L:CYS34 4.9 0.0 1.0
N L:SER35 4.9 0.0 1.0
C L:CYS48 4.9 0.0 1.0
CB L:HIS53 5.0 0.0 1.0

Zinc binding site 8 out of 8 in 5n60

Go back to Zinc Binding Sites List in 5n60
Zinc binding site 8 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation I) 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 4.2 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 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy