Zinc in PDB 4c2m: Structure of Rna Polymerase I at 2.8 A Resolution

All present enzymatic activity of Structure of Rna Polymerase I at 2.8 A Resolution:
2.7.7.6;

The structure of Structure of Rna Polymerase I at 2.8 A Resolution, PDB code: 4c2m was solved by C.Engel, S.Sainsbury, A.C.Cheung, D.Kostrewa, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.292 / 2.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	122.740, 139.020, 209.550, 108.06, 95.40, 93.85
R / Rfree (%)	16.89 / 20.99

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Structure of Rna Polymerase I at 2.8 A Resolution (pdb code 4c2m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Structure of Rna Polymerase I at 2.8 A Resolution, PDB code: 4c2m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in the Structure of Rna Polymerase I at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Rna Polymerase I at 2.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 1:Zn3001 b:0.2 occ:1.00 SG 1:CYS48 2.3 0.1 1.0 SG 1:CYS34 2.3 0.7 1.0 SG 1:CYS51 2.3 0.7 1.0 SG 1:CYS31 2.3 1.0 1.0 CB 1:CYS51 2.6 0.9 1.0 CB 1:CYS48 2.8 0.5 1.0 CB 1:CYS31 3.3 0.7 1.0 CB 1:CYS34 3.4 0.2 1.0 N 1:CYS51 3.4 1.0 1.0 CA 1:CYS51 3.6 0.1 1.0 N 1:CYS34 3.9 0.1 1.0 CA 1:CYS34 4.2 0.2 1.0 CA 1:CYS48 4.3 0.8 1.0 C 1:ASP50 4.6 0.2 1.0 CB 1:ASP50 4.6 0.8 1.0 C 1:CYS51 4.7 0.8 1.0 N 1:GLY52 4.7 0.7 1.0 OG 1:SER36 4.7 0.9 1.0 CB 1:HIS53 4.7 0.8 1.0 CA 1:CYS31 4.8 0.8 1.0 CB 1:GLU33 4.9 0.1 1.0 N 1:HIS53 4.9 0.6 1.0 C 1:CYS48 4.9 0.3 1.0 C 1:CYS34 4.9 0.1 1.0 N 1:ASP50 4.9 0.8 1.0 CA 1:ASP50 4.9 0.7 1.0 N 1:SER35 4.9 0.6 1.0 C 1:GLU33 5.0 0.2 1.0

Zinc binding site 2 out of 14 in the Structure of Rna Polymerase I at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Rna Polymerase I at 2.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3001 b:75.2 occ:1.00 SG A:CYS65 2.0 55.2 1.0 NE2 A:HIS75 2.0 58.8 1.0 SG A:CYS62 2.1 59.2 1.0 SG A:CYS72 2.2 61.7 1.0 CD2 A:HIS75 2.8 57.5 1.0 CE1 A:HIS75 3.0 61.6 1.0 CB A:CYS62 3.2 64.9 1.0 CB A:CYS72 3.6 53.8 1.0 CB A:CYS65 3.6 61.9 1.0 CG A:HIS75 3.9 56.6 1.0 CD A:PRO73 3.9 51.5 1.0 ND1 A:HIS75 4.0 58.6 1.0 N A:CYS65 4.0 71.8 1.0 CA A:CYS72 4.2 53.1 1.0 N A:GLY74 4.2 56.6 1.0 CA A:GLY55 4.4 68.8 1.0 CA A:CYS65 4.4 70.8 1.0 N A:PRO73 4.5 53.4 1.0 C A:CYS72 4.6 55.6 1.0 CA A:GLY74 4.6 60.3 1.0 CA A:CYS62 4.7 66.4 1.0 CG A:PRO73 4.7 50.5 1.0 CB A:THR64 4.7 58.7 1.0 C A:GLY74 4.8 60.5 1.0 N A:ALA56 4.9 56.5 1.0 C A:THR64 5.0 67.2 1.0

Zinc binding site 3 out of 14 in the Structure of Rna Polymerase I at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Rna Polymerase I at 2.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3002 b:77.5 occ:1.00 SG A:CYS105 2.2 72.6 1.0 SG A:CYS233 2.3 73.0 1.0 SG A:CYS236 2.3 79.3 1.0 SG A:CYS102 2.4 75.2 1.0 CB A:CYS105 3.2 74.3 1.0 CB A:CYS233 3.2 81.4 1.0 CB A:CYS102 3.3 77.8 1.0 CB A:CYS236 3.5 80.5 1.0 N A:CYS105 3.7 81.3 1.0 N A:CYS236 3.8 86.4 1.0 CA A:CYS105 3.9 73.5 1.0 CA A:CYS236 4.2 86.5 1.0 C A:CYS105 4.7 75.7 1.0 CA A:CYS233 4.7 80.0 1.0 CB A:ASN235 4.7 79.7 1.0 C A:ASN235 4.7 84.7 1.0 CA A:CYS102 4.7 73.9 1.0 N A:HIS106 4.8 78.2 1.0 C A:PHE104 4.8 80.0 1.0 C A:CYS236 4.9 92.1 1.0 N A:GLY237 4.9 91.9 1.0 CB A:PHE104 4.9 76.7 1.0

Zinc binding site 4 out of 14 in the Structure of Rna Polymerase I at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Rna Polymerase I at 2.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3001 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:CYS1104 2.3 49.9 1.0 SG B:CYS1107 2.3 53.4 1.0 CB B:CYS1104 3.1 50.2 1.0 CB B:CYS1107 3.1 31.5 1.0 CB B:CYS1128 3.3 53.8 1.0 CB B:CYS1131 3.3 66.3 1.0 N B:CYS1107 3.6 44.8 1.0 N B:CYS1131 3.9 53.4 1.0 CA B:CYS1107 3.9 37.3 1.0 CA B:CYS1131 4.2 62.9 1.0 CB B:ARG1130 4.3 68.5 1.0 CB B:GLU1106 4.5 71.6 1.0 OG1 B:THR1112 4.5 47.5 1.0 CA B:CYS1104 4.5 48.7 1.0 C B:GLU1106 4.6 52.4 1.0 CD B:ARG1130 4.7 69.5 1.0 C B:ARG1130 4.7 62.2 1.0 CA B:CYS1128 4.7 48.6 1.0 C B:CYS1107 4.8 43.6 1.0 CG B:ARG1130 4.9 68.2 1.0 CA B:ARG1130 4.9 64.0 1.0 N B:ARG1130 4.9 57.1 1.0 CA B:GLU1106 4.9 61.1 1.0 N B:GLU1106 5.0 58.5 1.0 C B:CYS1104 5.0 55.9 1.0 O B:CYS1104 5.0 64.2 1.0

Zinc binding site 5 out of 14 in the Structure of Rna Polymerase I at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Rna Polymerase I at 2.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn3001 b:74.0 occ:1.00 SG I:CYS13 2.2 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 3.2 74.2 1.0 CB I:CYS30 3.3 73.1 1.0 CB I:CYS13 3.5 85.7 1.0 CB I:CYS33 3.6 74.0 1.0 N I:CYS13 3.6 91.4 1.0 N I:CYS33 3.9 85.7 1.0 CA I:CYS13 4.0 85.0 1.0 CA I:CYS33 4.3 82.2 1.0 CB I:GLN32 4.4 71.9 1.0 C I:CYS13 4.4 95.5 1.0 CB I:ALA35 4.4 72.7 1.0 CB I:ASP12 4.5 89.0 1.0 O I:CYS13 4.6 0.2 1.0 CA I:CYS10 4.6 76.6 1.0 CA I:CYS30 4.7 80.6 1.0 C I:ASP12 4.8 88.5 1.0 C I:GLN32 4.9 82.8 1.0 C I:CYS33 4.9 82.5 1.0 N I:ASP12 4.9 85.6 1.0 CB I:ASP15 5.0 81.7 1.0 CA I:ASP12 5.0 86.9 1.0 N I:ASP15 5.0 72.6 1.0 N I:ALA35 5.0 86.7 1.0

Zinc binding site 6 out of 14 in the Structure of Rna Polymerase I at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Rna Polymerase I at 2.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn3002 b:77.9 occ:0.75 SG I:CYS114 2.2 74.3 1.0 SG I:CYS86 2.2 77.8 1.0 SG I:CYS117 2.3 87.3 1.0 SG I:CYS89 2.4 90.7 1.0 CB I:CYS86 2.9 95.0 1.0 CB I:CYS114 3.2 85.7 1.0 CB I:CYS89 3.2 0.5 1.0 CB I:CYS117 3.2 84.5 1.0 N I:CYS89 3.6 0.3 1.0 CA I:CYS89 3.9 0.2 1.0 CB I:ASN91 4.1 88.0 1.0 N I:CYS117 4.1 0.7 1.0 CA I:CYS117 4.2 94.7 1.0 CA I:CYS86 4.4 92.9 1.0 N I:GLY90 4.5 93.2 1.0 CA I:CYS114 4.6 80.4 1.0 C I:CYS89 4.6 95.4 1.0 N I:ASN91 4.6 88.8 1.0 CB I:GLN88 4.7 89.3 1.0 C I:GLN88 4.8 0.1 1.0 OG I:SER116 4.8 86.3 1.0 C I:CYS117 4.8 96.4 1.0 CB I:TYR119 4.9 75.0 1.0 C I:CYS86 4.9 95.6 1.0

Zinc binding site 7 out of 14 in the Structure of Rna Polymerase I at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Rna Polymerase I at 2.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn3001 b:0.2 occ:1.01 CA J:CYS46 1.7 79.5 1.0 N J:CYS46 1.8 84.7 1.0 SG J:CYS7 2.2 59.1 1.0 SG J:CYS46 2.3 61.8 1.0 CB J:CYS46 2.3 75.7 1.0 SG J:CYS45 2.3 99.9 1.0 C J:CYS45 2.3 81.9 1.0 SG J:CYS10 2.4 55.2 1.0 O J:CYS45 2.8 75.8 1.0 CB J:CYS7 3.1 60.2 1.0 C J:CYS46 3.2 75.5 1.0 CB J:CYS45 3.4 53.5 1.0 CA J:CYS45 3.4 81.3 1.0 O J:CYS46 3.8 75.8 1.0 CG J:MET49 4.0 70.0 1.0 N J:ARG47 4.1 70.8 1.0 CB J:CYS10 4.1 56.0 1.0 NH1 J:ARG48 4.4 54.6 1.0 CA J:CYS7 4.4 59.1 1.0 N J:CYS45 4.4 73.2 1.0 O J:ARG43 4.5 61.5 1.0 CB J:MET49 4.9 54.8 1.0 N J:CYS10 4.9 70.0 1.0 C J:TYR44 4.9 60.0 1.0 O J:TYR44 4.9 56.4 1.0

Zinc binding site 8 out of 14 in the Structure of Rna Polymerase I at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Rna Polymerase I at 2.8 A Resolution 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 SG L:CYS51 2.3 0.1 1.0 SG L:CYS31 2.3 82.4 1.0 SG L:CYS48 2.3 79.1 1.0 CB L:CYS51 2.6 87.7 1.0 CB L:CYS48 2.9 0.7 1.0 CB L:CYS31 3.3 74.2 1.0 CB L:CYS34 3.3 73.9 1.0 N L:CYS51 3.5 90.7 1.0 CA L:CYS51 3.7 88.9 1.0 N L:CYS34 3.8 82.0 1.0 CA L:CYS34 4.1 79.3 1.0 CA L:CYS48 4.4 0.3 1.0 CB L:ASP50 4.7 0.3 1.0 C L:ASP50 4.7 0.1 1.0 CA L:CYS31 4.7 76.8 1.0 OG L:SER36 4.7 0.3 1.0 C L:CYS51 4.8 94.1 1.0 N L:GLY52 4.8 99.2 1.0 CB L:HIS53 4.8 0.6 1.0 CB L:GLU33 4.8 84.5 1.0 C L:CYS34 4.8 85.2 1.0 N L:SER35 4.9 85.9 1.0 C L:GLU33 4.9 79.3 1.0 N L:HIS53 4.9 99.0 1.0 C L:CYS48 5.0 0.5 1.0

Zinc binding site 9 out of 14 in the Structure of Rna Polymerase I at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Rna Polymerase I at 2.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn3001 b:70.6 occ:1.00 NE2 P:HIS75 2.0 64.5 1.0 SG P:CYS65 2.1 63.7 1.0 SG P:CYS72 2.2 69.7 1.0 SG P:CYS62 2.2 65.2 1.0 CD2 P:HIS75 2.8 62.6 1.0 CE1 P:HIS75 3.0 66.1 1.0 CB P:CYS62 3.1 68.2 1.0 CB P:CYS72 3.5 68.0 1.0 CB P:CYS65 3.6 78.3 1.0 CG P:HIS75 4.0 63.4 1.0 CD P:PRO73 4.0 62.1 1.0 N P:CYS65 4.0 72.0 1.0 ND1 P:HIS75 4.0 61.1 1.0 CA P:CYS72 4.2 64.6 1.0 N P:GLY74 4.3 64.3 1.0 CA P:GLY55 4.3 78.8 1.0 CA P:CYS65 4.4 71.3 1.0 N P:PRO73 4.5 59.1 1.0 C P:CYS72 4.5 65.2 1.0 CA P:CYS62 4.6 69.2 1.0 CA P:GLY74 4.6 67.6 1.0 CG P:PRO73 4.8 59.7 1.0 CB P:THR64 4.8 76.9 1.0 N P:ALA56 4.8 69.9 1.0 C P:GLY74 4.8 70.7 1.0 C P:THR64 4.9 74.7 1.0

Zinc binding site 10 out of 14 in the Structure of Rna Polymerase I at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Rna Polymerase I at 2.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn3002 b:83.4 occ:1.00 SG P:CYS105 2.2 89.6 1.0 SG P:CYS236 2.3 87.5 1.0 SG P:CYS102 2.3 85.1 1.0 SG P:CYS233 2.3 82.5 1.0 CB P:CYS105 3.2 84.1 1.0 CB P:CYS233 3.2 96.2 1.0 CB P:CYS102 3.2 91.0 1.0 CB P:CYS236 3.4 0.0 1.0 N P:CYS105 3.6 88.4 1.0 N P:CYS236 3.9 91.9 1.0 CA P:CYS105 3.9 88.3 1.0 CA P:CYS236 4.2 0.5 1.0 C P:CYS105 4.6 89.4 1.0 CA P:CYS233 4.7 93.4 1.0 CA P:CYS102 4.7 88.2 1.0 N P:HIS106 4.7 94.5 1.0 C P:PHE104 4.8 99.7 1.0 C P:ASN235 4.8 95.8 1.0 CB P:ASN235 4.8 84.0 1.0 CB P:PHE104 4.8 0.4 1.0 C P:CYS236 4.9 0.3 1.0 N P:GLY237 4.9 99.1 1.0

C.Engel, S.Sainsbury, A.C.Cheung, D.Kostrewa, P.Cramer. Rna Polymerase I Structure and Transcription Regulation. Nature V. 502 502 2013.
ISSN: ISSN 0028-0836
PubMed: 24153182
DOI: 10.1038/NATURE12712