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Zinc in PDB 4c3j: Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90

Enzymatic activity of Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90

All present enzymatic activity of Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90:
2.7.7.6;

Protein crystallography data

The structure of Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90, PDB code: 4c3j was solved by C.Fernandez-Tornero, M.Moreno-Morcillo, U.J.Rashid, N.M.I.Taylor, F.M.Ruiz, T.Gruene, P.Legrand, U.Steuerwald, C.W.Muller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.05 / 3.35
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 401.020, 139.840, 140.940, 90.00, 90.39, 90.00
R / Rfree (%) 21.3 / 22.04

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90 (pdb code 4c3j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90, PDB code: 4c3j:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 4c3j

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Zinc binding site 1 out of 7 in the Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2664

b:0.3
occ:1.00
 SG A:CYS105 2.2 0.1 1.0
SG A:CYS233 2.4 0.7 1.0
SG A:CYS102 2.4 0.2 1.0
SG A:CYS236 2.4 0.1 1.0
CB A:CYS102 3.1 0.9 1.0
CB A:CYS233 3.3 0.8 1.0
CB A:CYS105 3.4 0.5 1.0
O A:CYS236 3.6 0.6 1.0
N A:CYS236 3.7 0.5 1.0
CB A:CYS236 3.8 0.8 1.0
N A:CYS105 3.9 0.7 1.0
CA A:CYS236 4.1 0.6 1.0
CA A:CYS105 4.2 0.3 1.0
C A:CYS236 4.3 0.2 1.0
CB A:ASN235 4.5 0.8 1.0
CA A:CYS102 4.6 0.3 1.0
CA A:CYS233 4.8 0.8 1.0
C A:ASN235 4.8 0.8 1.0
C A:CYS105 4.9 0.8 1.0
N A:HIS106 5.0 0.1 1.0
CB A:PHE104 5.0 0.6 1.0

Zinc binding site 2 out of 7 in 4c3j

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Zinc binding site 2 out of 7 in the Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2665

b:0.5
occ:1.00
 NE2 A:HIS75 2.0 0.9 1.0
SG A:CYS65 2.2 0.9 1.0
SG A:CYS72 2.3 0.7 1.0
SG A:CYS62 2.3 0.6 1.0
CD2 A:HIS75 2.7 0.0 1.0
CB A:CYS62 3.1 0.8 1.0
CE1 A:HIS75 3.2 0.2 1.0
CB A:CYS65 3.3 0.2 1.0
N A:CYS65 3.7 0.2 1.0
CB A:CYS72 3.7 0.3 1.0
CG A:HIS75 3.9 0.9 1.0
CA A:CYS65 4.0 0.5 1.0
ND1 A:HIS75 4.2 0.5 1.0
CA A:GLY55 4.3 0.7 1.0
CA A:CYS72 4.4 0.8 1.0
CD A:PRO73 4.4 0.4 1.0
CA A:CYS62 4.5 0.9 1.0
C A:CYS65 4.6 1.0 1.0
N A:GLY66 4.6 0.6 1.0
N A:GLY74 4.7 0.3 1.0
CB A:THR64 4.7 0.4 1.0
C A:THR64 4.8 0.5 1.0
N A:PRO73 4.9 0.8 1.0
N A:ALA56 4.9 0.5 1.0
C A:CYS72 4.9 0.2 1.0
CA A:GLY74 5.0 0.4 1.0
N A:GLY55 5.0 0.7 1.0

Zinc binding site 3 out of 7 in 4c3j

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Zinc binding site 3 out of 7 in the Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2204

b:0.4
occ:1.00
 SG B:CYS1131 2.2 1.0 1.0
SG B:CYS1104 2.3 0.9 1.0
SG B:CYS1128 2.3 0.2 1.0
SG B:CYS1107 2.4 0.4 1.0
CB B:CYS1104 3.3 0.7 1.0
CB B:CYS1107 3.3 0.9 1.0
CB B:CYS1131 3.3 0.0 1.0
CB B:CYS1128 3.3 0.1 1.0
N B:CYS1107 3.7 0.0 1.0
N B:CYS1131 3.8 0.5 1.0
CA B:CYS1107 4.1 0.8 1.0
CA B:CYS1131 4.1 0.6 1.0
CB B:ARG1130 4.3 0.9 1.0
OG1 B:THR1112 4.4 0.0 1.0
CB B:GLU1106 4.4 0.8 1.0
CG B:ARG1130 4.5 0.1 1.0
C B:GLU1106 4.6 0.0 1.0
CA B:CYS1104 4.7 0.6 1.0
C B:ARG1130 4.7 0.5 1.0
OG B:SER1109 4.8 1.0 1.0
CA B:CYS1128 4.8 0.6 1.0
CA B:ARG1130 4.9 0.0 1.0
CA B:GLU1106 4.9 0.9 1.0
C B:CYS1107 5.0 0.5 1.0

Zinc binding site 4 out of 7 in 4c3j

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Zinc binding site 4 out of 7 in the Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1126

b:0.2
occ:1.00
 SG I:CYS13 2.3 0.0 1.0
SG I:CYS33 2.5 0.6 1.0
SG I:CYS30 2.7 1.0 1.0
SG I:CYS10 2.9 0.0 1.0
CB I:CYS30 3.2 0.2 1.0
CB I:CYS10 3.4 0.3 1.0
CB I:CYS13 3.7 0.6 1.0
N I:CYS33 3.8 0.3 1.0
O I:CYS33 3.8 0.1 1.0
CB I:CYS33 4.0 0.2 1.0
N I:CYS13 4.2 0.3 1.0
CA I:CYS33 4.3 0.5 1.0
CB I:GLN32 4.4 0.1 1.0
C I:CYS33 4.5 0.5 1.0
CA I:CYS13 4.5 0.4 1.0
CA I:CYS30 4.6 1.0 1.0
CB I:ALA35 4.8 0.5 1.0
CB I:ASP15 4.9 0.1 1.0
CA I:CYS10 4.9 0.5 1.0
C I:GLN32 4.9 0.6 1.0
N I:GLY14 5.0 0.8 1.0

Zinc binding site 5 out of 7 in 4c3j

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Zinc binding site 5 out of 7 in the Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1127

b:0.3
occ:1.00
 SG I:CYS86 3.1 0.7 1.0
SG I:CYS89 3.1 0.7 1.0
SG I:CYS114 3.3 0.4 1.0
CB I:GLN88 3.7 0.0 1.0
CB I:SER116 3.7 0.5 1.0
CB I:CYS86 4.0 0.2 1.0
N I:CYS89 4.1 0.6 1.0
CB I:ASN91 4.1 0.9 1.0
OG I:SER116 4.2 0.9 1.0
CG I:GLN88 4.3 0.0 1.0
CB I:CYS89 4.4 0.5 1.0
SG I:CYS117 4.6 0.9 1.0
N I:GLY90 4.6 0.3 1.0
CA I:GLN88 4.6 0.7 1.0
C I:GLN88 4.7 0.4 1.0
CA I:CYS89 4.8 0.4 1.0
CA I:SER116 4.8 0.8 1.0
N I:ASN91 4.8 0.9 1.0
N I:CYS117 4.9 0.4 1.0
CB I:CYS114 4.9 0.7 1.0
CG I:ASN91 4.9 0.3 1.0
N I:GLN88 5.0 0.7 1.0
N I:SER116 5.0 0.9 1.0

Zinc binding site 6 out of 7 in 4c3j

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Zinc binding site 6 out of 7 in the Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1070

b:0.5
occ:1.00
 SG J:CYS7 2.2 0.9 1.0
SG J:CYS45 2.3 0.2 1.0
SG J:CYS46 2.3 0.8 1.0
SG J:CYS10 2.5 1.0 1.0
CB J:CYS7 3.1 0.3 1.0
N J:CYS46 3.3 0.1 1.0
CB J:CYS45 3.5 0.8 1.0
CB J:CYS46 3.6 0.2 1.0
CA J:CYS46 3.7 0.3 1.0
CB J:CYS10 3.7 0.2 1.0
C J:CYS45 3.7 0.9 1.0
N J:CYS10 3.7 0.6 1.0
NE J:ARG43 4.2 0.5 1.0
CA J:CYS45 4.2 0.9 1.0
O J:CYS45 4.3 1.0 1.0
CA J:CYS10 4.3 0.1 1.0
CB J:SER9 4.4 0.2 1.0
CA J:CYS7 4.5 0.3 1.0
N J:GLY11 4.7 0.5 1.0
C J:SER9 4.8 0.5 1.0
CB J:ARG43 4.8 0.2 1.0
C J:CYS7 4.9 0.2 1.0
NH2 J:ARG43 4.9 0.2 1.0
N J:SER9 4.9 0.2 1.0
CA J:SER9 4.9 0.1 1.0
O J:CYS7 4.9 0.9 1.0
CD J:ARG43 4.9 0.8 1.0
N J:CYS45 5.0 0.5 1.0
CB J:LYS12 5.0 0.6 1.0
OG J:SER9 5.0 0.2 1.0
N J:LYS12 5.0 0.8 1.0

Zinc binding site 7 out of 7 in 4c3j

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Zinc binding site 7 out of 7 in the Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of 14-Subunit Rna Polymerase I at 3.35 A Resolution, Crystal Form C2-90 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.1
occ:1.00
 SG L:CYS34 2.4 0.5 1.0
SG L:CYS51 2.4 0.9 1.0
SG L:CYS31 2.4 0.2 1.0
SG L:CYS48 2.5 0.8 1.0
CB L:CYS48 2.9 0.4 1.0
CB L:CYS31 3.3 0.8 1.0
CB L:CYS51 3.6 0.5 1.0
CB L:CYS34 3.6 0.2 1.0
O L:CYS51 3.7 0.4 1.0
N L:CYS51 3.7 0.8 1.0
OG L:SER36 4.0 0.9 1.0
CA L:CYS51 4.0 0.4 1.0
N L:CYS34 4.0 0.4 1.0
C L:CYS51 4.2 0.4 1.0
CA L:CYS34 4.4 0.0 1.0
CA L:CYS48 4.4 0.1 1.0
CB L:HIS53 4.4 0.1 1.0
CB L:ASP50 4.7 0.6 1.0
CA L:CYS31 4.7 0.1 1.0
C L:ASP50 4.7 0.8 1.0
C L:CYS48 4.9 0.6 1.0

Reference:

C.Fernandez-Tornero, M.Moreno-Morcillo, U.J.Rashid, N.M.I.Taylor, F.M.Ruiz, T.Gruene, P.Legrand, U.Steuerwald, C.W.Muller. Crystal Structure of the 14-Subunit Rna Polymerase I Nature V. 502 644 2013.
ISSN: ISSN 0028-0836
PubMed: 24153184
DOI: 10.1038/NATURE12636
Page generated: Sat Oct 26 20:23:39 2024

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