Atomistry » Zinc » PDB 5n34-5nek » 5n5y
Atomistry »
  Zinc »
    PDB 5n34-5nek »
      5n5y »

Zinc in PDB 5n5y: Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)

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

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

Other elements in 5n5y:

The structure of Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

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 III) (pdb code 5n5y). 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 III), PDB code: 5n5y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5n5y

Go back to Zinc Binding Sites List in 5n5y
Zinc binding site 1 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)


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 III) 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 5n5y

Go back to Zinc Binding Sites List in 5n5y
Zinc binding site 2 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)


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 III) 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 5n5y

Go back to Zinc Binding Sites List in 5n5y
Zinc binding site 3 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)


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 III) 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 4.3 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 5n5y

Go back to Zinc Binding Sites List in 5n5y
Zinc binding site 4 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)


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 III) 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 5n5y

Go back to Zinc Binding Sites List in 5n5y
Zinc binding site 5 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)


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 III) 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 5n5y

Go back to Zinc Binding Sites List in 5n5y
Zinc binding site 6 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)


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 III) 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 5n5y

Go back to Zinc Binding Sites List in 5n5y
Zinc binding site 7 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)


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 III) 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 5n5y

Go back to Zinc Binding Sites List in 5n5y
Zinc binding site 8 out of 8 in the Cryo-Em Structure of Rna Polymerase I in Complex with RRN3 and Core Factor (Orientation III)


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 III) 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 22:35:37 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