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Zinc in PDB 4y52: Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.

Enzymatic activity of Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.

All present enzymatic activity of Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation., PDB code: 4y52 was solved by L.Wang, J.Chong, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.27 / 3.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 166.703, 221.644, 192.410, 90.00, 100.35, 90.00
R / Rfree (%) 20.1 / 23.2

Other elements in 4y52:

The structure of Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. (pdb code 4y52). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation., PDB code: 4y52:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4y52

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Zinc binding site 1 out of 8 in the Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.7
occ:1.00
 SG A:CYS167 2.3 0.0 1.0
SG A:CYS110 2.4 0.5 1.0
SG A:CYS148 2.4 0.0 1.0
SG A:CYS107 2.4 0.5 1.0
CB A:CYS107 2.6 0.3 1.0
CB A:CYS110 4.0 0.0 1.0
CB A:CYS167 4.0 0.2 1.0
O A:CYS167 4.0 0.8 1.0
CB A:CYS148 4.1 0.3 1.0
CA A:CYS107 4.2 0.9 1.0
N A:CYS110 4.3 0.2 1.0
C A:CYS167 4.5 0.1 1.0
CA A:CYS167 4.6 0.3 1.0
CA A:CYS110 4.7 0.2 1.0
N A:CYS167 4.7 0.2 1.0
C A:CYS107 4.8 0.4 1.0
N A:CYS107 4.9 0.9 1.0
CB A:HIS109 4.9 0.4 1.0

Zinc binding site 2 out of 8 in 4y52

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Zinc binding site 2 out of 8 in the Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:0.9
occ:1.00
 SG A:CYS67 2.2 0.1 1.0
NE2 A:HIS80 2.2 0.1 1.0
SG A:CYS77 2.3 0.1 1.0
CE1 A:HIS80 2.4 0.7 1.0
SG A:CYS70 2.4 0.3 1.0
CB A:CYS77 3.1 0.8 1.0
O A:CYS67 3.3 0.7 1.0
CB A:CYS67 3.4 0.3 1.0
CD2 A:HIS80 3.6 0.9 1.0
CB A:CYS70 3.7 0.4 1.0
ND1 A:HIS80 3.7 90.7 1.0
C A:CYS67 3.8 0.3 1.0
CA A:CYS67 4.2 0.4 1.0
CG A:HIS80 4.3 0.7 1.0
CB A:GLN68 4.4 0.7 1.0
CA A:CYS77 4.5 0.6 1.0
N A:GLN68 4.7 0.1 1.0
O A:GLN71 4.8 0.6 1.0
CA A:CYS70 4.9 0.7 1.0

Zinc binding site 3 out of 8 in 4y52

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Zinc binding site 3 out of 8 in the Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:1.0
occ:1.00
 SG B:CYS1166 2.3 78.4 1.0
SG B:CYS1163 2.3 0.7 1.0
SG B:CYS1185 2.3 0.8 1.0
SG B:CYS1182 2.4 0.4 1.0
CB B:CYS1163 3.1 0.7 1.0
CB B:CYS1185 3.4 0.7 1.0
CB B:CYS1166 3.6 96.9 1.0
N B:CYS1166 3.8 0.4 1.0
CB B:CYS1182 4.0 0.0 1.0
CB B:ILE1165 4.2 0.1 1.0
O B:CYS1182 4.3 0.6 1.0
CA B:CYS1166 4.4 0.2 1.0
N B:CYS1185 4.5 0.6 1.0
CA B:CYS1185 4.6 0.7 1.0
CA B:CYS1163 4.6 0.3 1.0
CG1 B:ILE1165 4.8 0.3 1.0
C B:ILE1165 4.9 0.3 1.0
CA B:ILE1165 5.0 0.2 1.0

Zinc binding site 4 out of 8 in 4y52

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Zinc binding site 4 out of 8 in the Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:96.1
occ:1.00
 SG C:CYS86 2.2 62.8 1.0
SG C:CYS92 2.2 49.8 1.0
SG C:CYS95 2.2 79.5 1.0
SG C:CYS88 2.3 53.1 1.0
CB C:CYS86 2.9 76.2 1.0
CB C:CYS92 3.2 54.4 1.0
N C:CYS92 3.4 93.6 1.0
CB C:CYS95 3.5 86.9 1.0
C C:HIS91 3.8 0.9 1.0
CA C:CYS92 3.8 73.7 1.0
CB C:CYS88 3.9 0.0 1.0
CA C:HIS91 4.1 87.8 1.0
O C:ASP90 4.2 75.7 1.0
CA C:CYS86 4.4 67.3 1.0
N C:CYS95 4.4 94.7 1.0
CA C:CYS95 4.5 71.9 1.0
O C:HIS91 4.5 93.4 1.0
C C:CYS92 4.6 73.0 1.0
N C:CYS88 4.7 67.8 1.0
CA C:CYS88 4.8 87.3 1.0
O C:CYS88 4.9 83.7 1.0
O C:CYS92 4.9 75.8 1.0
C C:CYS95 4.9 47.5 1.0
C C:CYS86 4.9 77.9 1.0
CA C:SER83 5.0 45.5 1.0

Zinc binding site 5 out of 8 in 4y52

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Zinc binding site 5 out of 8 in the Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.4
occ:1.00
 SG I:CYS10 2.3 65.1 1.0
SG I:CYS29 2.3 0.4 1.0
SG I:CYS32 2.4 77.1 1.0
SG I:CYS7 2.4 74.6 1.0
CB I:CYS29 3.1 68.1 1.0
CB I:CYS7 3.1 63.8 1.0
CB I:CYS32 3.6 95.4 1.0
CB I:CYS10 3.7 88.2 1.0
N I:CYS32 3.8 91.4 1.0
CB I:THR31 4.1 85.6 1.0
CB I:TYR34 4.1 48.4 1.0
CA I:CYS32 4.3 0.1 1.0
N I:CYS10 4.3 0.7 1.0
C I:THR31 4.4 1.0 1.0
CA I:CYS29 4.5 70.4 1.0
N I:TYR34 4.5 55.7 1.0
CA I:CYS7 4.6 81.0 1.0
N I:SER33 4.6 0.9 1.0
CA I:CYS10 4.6 0.0 1.0
CA I:THR31 4.6 73.9 1.0
N I:THR31 4.6 94.3 1.0
OG1 I:THR31 4.7 0.9 1.0
CB I:ASP9 4.8 0.7 1.0
C I:CYS29 4.9 0.1 1.0
C I:CYS32 4.9 0.4 1.0
CA I:TYR34 5.0 59.0 1.0

Zinc binding site 6 out of 8 in 4y52

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Zinc binding site 6 out of 8 in the Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:96.1
occ:1.00
 SG I:CYS78 2.2 73.7 1.0
SG I:CYS103 2.3 91.2 1.0
SG I:CYS106 2.3 40.8 1.0
SG I:CYS75 2.4 94.4 1.0
CB I:CYS103 2.7 66.9 1.0
CB I:CYS75 3.0 81.1 1.0
CB I:CYS106 3.6 22.1 1.0
CB I:CYS78 3.6 56.3 1.0
N I:CYS78 3.7 61.5 1.0
N I:CYS106 3.9 80.7 1.0
CA I:CYS103 4.1 56.1 1.0
CA I:CYS78 4.1 23.9 1.0
CB I:LYS77 4.2 0.1 1.0
CA I:CYS106 4.3 42.4 1.0
CB I:HIS108 4.4 81.0 1.0
CA I:CYS75 4.5 59.4 1.0
CB I:SER80 4.6 36.9 1.0
C I:CYS78 4.7 65.0 1.0
C I:LYS77 4.7 79.7 1.0
CD2 I:HIS108 4.8 84.7 1.0
N I:HIS108 4.8 70.3 1.0
CA I:LYS77 4.9 60.4 1.0
N I:HIS79 4.9 85.7 1.0
C I:CYS106 4.9 48.7 1.0
N I:LYS77 4.9 87.9 1.0
C I:CYS103 4.9 70.7 1.0
N I:SER107 4.9 1.0 1.0
N I:SER80 5.0 43.2 1.0
CG I:HIS108 5.0 90.0 1.0
N I:CYS103 5.0 58.5 1.0

Zinc binding site 7 out of 8 in 4y52

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Zinc binding site 7 out of 8 in the Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:76.2
occ:1.00
 SG J:CYS46 2.3 48.6 1.0
SG J:CYS10 2.3 62.7 1.0
SG J:CYS7 2.3 36.9 1.0
SG J:CYS45 2.3 72.2 1.0
CB J:CYS46 2.9 32.4 1.0
N J:CYS46 2.9 37.9 1.0
CA J:CYS46 3.2 43.3 1.0
N J:CYS10 3.4 54.8 1.0
CB J:SER9 3.5 70.1 1.0
CB J:CYS7 3.6 52.8 1.0
CB J:CYS45 3.6 61.9 1.0
CB J:CYS10 3.7 70.2 1.0
C J:CYS45 3.8 57.8 1.0
CD J:ARG43 4.1 86.5 1.0
CA J:CYS10 4.1 69.3 1.0
CA J:CYS45 4.3 47.5 1.0
N J:GLY11 4.3 81.8 1.0
CG J:ARG43 4.3 78.5 1.0
C J:SER9 4.3 57.1 1.0
CA J:SER9 4.3 59.0 1.0
NE J:ARG43 4.4 50.9 1.0
OG J:SER9 4.5 69.3 1.0
O J:CYS45 4.6 61.5 1.0
N J:SER9 4.6 65.9 1.0
C J:CYS46 4.7 40.2 1.0
C J:CYS10 4.7 57.5 1.0
CB J:LYS12 4.7 72.3 1.0
N J:LYS12 4.7 66.8 1.0
CA J:CYS7 4.9 51.3 1.0
N J:CYS45 5.0 50.1 1.0

Zinc binding site 8 out of 8 in 4y52

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Zinc binding site 8 out of 8 in the Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.2
occ:1.00
 SG L:CYS31 2.3 0.3 1.0
SG L:CYS51 2.3 0.5 1.0
SG L:CYS48 2.4 0.8 1.0
SG L:CYS34 2.4 0.6 1.0
CB L:CYS34 2.7 0.3 1.0
CB L:CYS51 2.8 0.8 1.0
CB L:CYS31 2.9 0.4 1.0
CB L:CYS48 3.7 0.3 1.0
O L:LYS49 3.8 0.5 1.0
CA L:CYS51 4.0 0.7 1.0
CA L:CYS34 4.0 0.5 1.0
N L:CYS51 4.2 0.2 1.0
C L:CYS34 4.3 0.5 1.0
CA L:CYS31 4.4 0.8 1.0
OG L:SER36 4.5 77.0 1.0
N L:LYS49 4.5 0.0 1.0
N L:CYS34 4.6 0.8 1.0
O L:CYS34 4.7 0.7 1.0
C L:LYS49 4.7 0.3 1.0
CB L:SER36 4.8 0.0 1.0
N L:SER35 4.8 0.0 1.0

Reference:

L.Wang, Y.Zhou, L.Xu, R.Xiao, X.Lu, L.Chen, J.Chong, H.Li, C.He, X.D.Fu, D.Wang. Molecular Basis For 5-Carboxycytosine Recognition By Rna Polymerase II Elongation Complex. Nature V. 523 621 2015.
ISSN: ESSN 1476-4687
PubMed: 26123024
DOI: 10.1038/NATURE14482
Page generated: Sun Oct 27 10:55:43 2024

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