Atomistry » Zinc » PDB 5m2k-5mct » 5m3f
Atomistry »
  Zinc »
    PDB 5m2k-5mct »
      5m3f »

Zinc in PDB 5m3f: Yeast Rna Polymerase I Elongation Complex at 3.8A

Enzymatic activity of Yeast Rna Polymerase I Elongation Complex at 3.8A

All present enzymatic activity of Yeast Rna Polymerase I Elongation Complex at 3.8A:
2.7.7.6;

Other elements in 5m3f:

The structure of Yeast Rna Polymerase I Elongation Complex at 3.8A also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Yeast Rna Polymerase I Elongation Complex at 3.8A (pdb code 5m3f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Yeast Rna Polymerase I Elongation Complex at 3.8A, PDB code: 5m3f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5m3f

Go back to Zinc Binding Sites List in 5m3f
Zinc binding site 1 out of 6 in the Yeast Rna Polymerase I Elongation Complex at 3.8A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast Rna Polymerase I Elongation Complex at 3.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3001

b:75.2
occ:1.00
 CD2 A:HIS75 2.1 57.5 1.0
NE2 A:HIS75 2.2 58.8 1.0
CB A:CYS65 2.2 61.9 1.0
SG A:CYS65 2.3 55.2 1.0
SG A:CYS72 2.3 61.7 1.0
SG A:CYS62 2.3 59.2 1.0
N A:CYS65 2.7 71.8 1.0
CA A:CYS65 3.0 70.8 1.0
CE1 A:HIS75 3.5 61.6 1.0
CG A:HIS75 3.5 56.6 1.0
C A:THR64 3.9 67.2 1.0
CB A:THR64 3.9 58.7 1.0
CB A:CYS62 4.0 64.9 1.0
ND1 A:HIS75 4.1 58.6 1.0
CB A:CYS72 4.1 53.8 1.0
C A:CYS65 4.2 81.1 1.0
CG2 A:THR64 4.3 58.9 1.0
CA A:GLY55 4.3 68.8 1.0
CA A:THR64 4.3 59.9 1.0
N A:GLY66 4.5 59.5 1.0
O A:LEU54 4.6 63.1 1.0
CB A:HIS75 4.6 51.1 1.0
N A:THR64 4.6 64.3 1.0
N A:GLY74 4.8 56.6 1.0
O A:THR64 4.9 66.7 1.0
CA A:GLY74 4.9 60.3 1.0
N A:HIS75 4.9 55.3 1.0
C A:GLY74 5.0 60.5 1.0
CA A:CYS72 5.0 53.1 1.0

Zinc binding site 2 out of 6 in 5m3f

Go back to Zinc Binding Sites List in 5m3f
Zinc binding site 2 out of 6 in the Yeast Rna Polymerase I Elongation Complex at 3.8A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast Rna Polymerase I Elongation Complex at 3.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3002

b:77.5
occ:1.00
 SG A:CYS105 2.3 72.6 1.0
SG A:CYS236 2.3 79.3 1.0
SG A:CYS233 2.3 73.0 1.0
SG A:CYS102 2.3 75.2 1.0
CB A:CYS105 2.8 74.3 1.0
N A:CYS236 3.3 86.4 1.0
CB A:CYS236 3.4 80.5 1.0
N A:CYS105 3.5 81.3 1.0
CB A:CYS233 3.7 81.4 1.0
CB A:ASN235 3.7 79.7 1.0
CA A:CYS105 3.8 73.5 1.0
CB A:CYS102 3.9 77.8 1.0
CA A:CYS236 4.0 86.5 1.0
C A:ASN235 4.4 84.7 1.0
CA A:ASN235 4.5 82.5 1.0
N A:ASN235 4.6 75.5 1.0
N A:GLY237 4.6 91.9 1.0
ND2 A:ASN235 4.6 73.7 1.0
CG A:ASN235 4.7 77.4 1.0
C A:PHE104 4.7 80.0 1.0
CB A:PHE104 4.7 76.7 1.0
C A:CYS236 4.9 92.1 1.0
C A:CYS105 4.9 75.7 1.0
CA A:CYS233 5.0 80.0 1.0

Zinc binding site 3 out of 6 in 5m3f

Go back to Zinc Binding Sites List in 5m3f
Zinc binding site 3 out of 6 in the Yeast Rna Polymerase I Elongation Complex at 3.8A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast Rna Polymerase I Elongation Complex at 3.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1302

b:53.6
occ:1.00
 SG B:CYS1131 2.3 75.4 1.0
SG B:CYS1128 2.3 43.2 1.0
SG B:CYS1107 2.3 53.4 1.0
SG B:CYS1104 2.3 49.9 1.0
CB B:CYS1131 2.7 66.3 1.0
CB B:CYS1128 2.9 53.8 1.0
CB B:CYS1107 3.3 31.5 1.0
N B:CYS1131 3.5 53.4 1.0
CA B:CYS1131 3.7 62.9 1.0
CB B:CYS1104 3.8 50.2 1.0
N B:CYS1107 4.1 44.8 1.0
CA B:CYS1107 4.3 37.3 1.0
CA B:CYS1128 4.3 48.6 1.0
C B:ARG1130 4.6 62.2 1.0
CB B:ARG1130 4.6 68.5 1.0
C B:CYS1128 4.7 55.4 1.0
N B:ARG1130 4.8 57.1 1.0
C B:CYS1131 4.8 66.8 1.0
O B:CYS1128 4.8 66.7 1.0
CA B:ARG1130 4.9 64.0 1.0
CA B:CYS1104 5.0 48.7 1.0

Zinc binding site 4 out of 6 in 5m3f

Go back to Zinc Binding Sites List in 5m3f
Zinc binding site 4 out of 6 in the Yeast Rna Polymerase I Elongation Complex at 3.8A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast Rna Polymerase I Elongation Complex at 3.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3001

b:74.0
occ:1.00
 CB I:CYS30 1.9 73.1 1.0
SG I:CYS13 2.3 73.5 1.0
SG I:CYS33 2.3 71.0 1.0
SG I:CYS30 2.3 67.0 1.0
SG I:CYS10 2.3 78.7 1.0
CB I:CYS10 2.5 74.2 1.0
CA I:CYS30 3.3 80.6 1.0
N I:CYS30 3.9 84.5 1.0
CA I:CYS10 4.1 76.6 1.0
CB I:CYS13 4.1 85.7 1.0
CB I:CYS33 4.1 74.0 1.0
N I:CYS33 4.4 85.7 1.0
C I:CYS30 4.4 78.0 1.0
N I:CYS13 4.4 91.4 1.0
CB I:ALA35 4.6 72.7 1.0
N I:ALA35 4.6 86.7 1.0
CA I:CYS13 4.7 85.0 1.0
CA I:CYS33 4.7 82.2 1.0
O I:CYS13 4.7 0.2 1.0
N I:CYS10 4.8 73.3 1.0
N I:LYS34 4.8 84.1 1.0
CD2 I:LEU17 4.8 71.7 1.0
C I:CYS13 4.8 95.5 1.0
C I:CYS10 4.9 79.3 1.0
N I:SER31 5.0 71.7 1.0

Zinc binding site 5 out of 6 in 5m3f

Go back to Zinc Binding Sites List in 5m3f
Zinc binding site 5 out of 6 in the Yeast Rna Polymerase I Elongation Complex at 3.8A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Yeast Rna Polymerase I Elongation Complex at 3.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3001

b:0.2
occ:1.01
 CB J:CYS10 2.2 56.0 1.0
SG J:CYS10 2.3 55.2 1.0
SG J:CYS46 2.3 61.8 1.0
SG J:CYS45 2.3 99.9 1.0
SG J:CYS7 2.3 59.1 1.0
CB J:CYS7 3.0 60.2 1.0
N J:CYS10 3.0 70.0 1.0
CA J:CYS10 3.1 63.8 1.0
N J:CYS46 3.5 84.7 1.0
CB J:CYS46 3.5 75.7 1.0
CA J:CYS46 3.5 79.5 1.0
CB J:CYS45 3.7 53.5 1.0
C J:CYS45 3.9 81.9 1.0
N J:GLY11 4.0 72.9 1.0
C J:CYS10 4.1 69.6 1.0
CA J:CYS7 4.2 59.1 1.0
C J:SER9 4.2 68.0 1.0
C J:CYS7 4.3 59.0 1.0
O J:CYS7 4.4 59.4 1.0
O J:CYS45 4.4 75.8 1.0
CA J:CYS45 4.4 81.3 1.0
N J:SER9 4.6 63.5 1.0
CA J:SER9 4.8 67.8 1.0
N J:PHE8 4.8 53.1 1.0
CB J:SER9 4.8 73.9 1.0
N J:LYS12 4.9 68.5 1.0

Zinc binding site 6 out of 6 in 5m3f

Go back to Zinc Binding Sites List in 5m3f
Zinc binding site 6 out of 6 in the Yeast Rna Polymerase I Elongation Complex at 3.8A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Yeast Rna Polymerase I Elongation Complex at 3.8A within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn3001

b:87.2
occ:1.00
 SG L:CYS34 2.3 85.1 1.0
CB L:CYS51 2.4 87.7 1.0
SG L:CYS51 2.5 0.1 1.0
N L:CYS51 2.8 90.7 1.0
CA L:CYS51 3.1 88.9 1.0
CB L:CYS34 3.2 73.9 1.0
SG L:CYS48 3.3 79.1 1.0
SG L:CYS31 3.7 82.4 1.0
N L:CYS34 3.9 82.0 1.0
C L:ASP50 4.0 0.1 1.0
CB L:CYS48 4.0 0.7 1.0
CB L:ASP50 4.0 0.3 1.0
C L:CYS51 4.1 94.1 1.0
CA L:CYS34 4.2 79.3 1.0
N L:GLY52 4.3 99.2 1.0
CA L:ASP50 4.4 0.6 1.0
CB L:HIS53 4.5 0.6 1.0
N L:HIS53 4.5 99.0 1.0
N L:ASP50 4.6 0.2 1.0
CB L:CYS31 4.7 74.2 1.0
CB L:GLU33 4.8 84.5 1.0
O L:CYS51 5.0 91.5 1.0
O L:ASP50 5.0 0.8 1.0

Reference:

S.Neyer, M.Kunz, C.Geiss, M.Hantsche, V.V.Hodirnau, A.Seybert, C.Engel, M.P.Scheffer, P.Cramer, A.S.Frangakis. Structure of Rna Polymerase I Transcribing Ribosomal Dna Genes. Nature V. 540 607 2016.
ISSN: ISSN 0028-0836
PubMed: 27842382
DOI: 10.1038/NATURE20561
Page generated: Sun Oct 27 21:42:14 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy