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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

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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

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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

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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

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