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Zinc in PDB 4y7n: The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.

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

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

Protein crystallography data

The structure of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation., PDB code: 4y7n 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) 48.88 / 3.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.181, 222.614, 192.829, 90.00, 101.59, 90.00
R / Rfree (%) 20.7 / 25

Other elements in 4y7n:

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

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. (pdb code 4y7n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation., PDB code: 4y7n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4y7n

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Zinc binding site 1 out of 8 in the The Structure Insight Into 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 The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.1
occ:0.96
 SG A:CYS110 2.3 0.7 1.0
SG A:CYS167 2.3 0.5 1.0
SG A:CYS148 2.4 0.2 1.0
SG A:CYS107 2.4 0.6 1.0
N A:CYS110 2.8 0.1 1.0
CB A:CYS110 3.0 0.9 1.0
CB A:CYS167 3.4 0.0 1.0
CA A:CYS110 3.4 0.2 1.0
CB A:HIS109 3.5 0.3 1.0
CB A:CYS148 3.7 0.8 1.0
CB A:CYS107 3.8 0.0 1.0
N A:GLY111 3.8 0.7 1.0
C A:HIS109 3.9 0.8 1.0
C A:CYS110 4.0 1.0 1.0
CA A:HIS109 4.1 0.3 1.0
N A:CYS167 4.2 0.1 1.0
OD1 A:ASN169 4.2 0.2 1.0
N A:HIS109 4.3 0.0 1.0
CA A:CYS167 4.3 0.3 1.0
CG A:HIS109 4.6 0.7 1.0
O A:CYS167 4.7 1.0 1.0
C A:CYS167 4.9 1.0 1.0
CA A:GLY111 4.9 0.7 1.0
O A:HIS109 5.0 0.7 1.0
CA A:CYS148 5.0 0.4 1.0

Zinc binding site 2 out of 8 in 4y7n

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Zinc binding site 2 out of 8 in the The Structure Insight Into 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 The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:0.7
occ:1.00
 SG A:CYS67 2.3 0.8 1.0
NE2 A:HIS80 2.3 0.4 1.0
SG A:CYS70 2.4 0.2 1.0
SG A:CYS77 2.4 0.6 1.0
OE1 A:GLN68 2.7 0.8 1.0
CE1 A:HIS80 3.1 0.6 1.0
CD2 A:HIS80 3.4 0.4 1.0
CB A:CYS67 3.5 0.8 1.0
CB A:CYS77 3.5 0.5 1.0
CD A:GLN68 3.5 0.7 1.0
NE2 A:GLN68 3.6 0.5 1.0
CB A:CYS70 3.7 0.8 1.0
O A:CYS67 3.9 0.1 1.0
ND1 A:HIS80 4.2 0.4 1.0
CA A:CYS77 4.4 0.5 1.0
CG A:HIS80 4.4 0.3 1.0
CD A:PRO78 4.4 0.5 1.0
C A:CYS67 4.5 0.5 1.0
O A:GLN71 4.6 0.9 1.0
CA A:CYS67 4.6 0.9 1.0
CG A:GLN68 4.9 0.8 1.0
N A:PRO78 5.0 0.9 1.0
C A:CYS77 5.0 0.4 1.0

Zinc binding site 3 out of 8 in 4y7n

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Zinc binding site 3 out of 8 in the The Structure Insight Into 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 The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.1
occ:1.00
 SG B:CYS1182 2.3 0.2 1.0
SG B:CYS1163 2.3 0.4 1.0
SG B:CYS1166 2.4 0.8 1.0
SG B:CYS1185 2.4 0.1 1.0
CB B:CYS1166 2.8 0.4 1.0
CB B:CYS1163 3.0 0.8 1.0
N B:CYS1166 3.2 0.4 1.0
CA B:CYS1166 3.6 0.1 1.0
CB B:CYS1182 3.9 0.1 1.0
CB B:ILE1165 4.2 0.9 1.0
CB B:CYS1185 4.2 0.6 1.0
N B:CYS1185 4.2 0.5 1.0
C B:ILE1165 4.3 0.6 1.0
CA B:GLY1184 4.3 0.8 1.0
C B:GLY1184 4.4 0.1 1.0
N B:GLY1167 4.5 0.5 1.0
CA B:CYS1163 4.5 0.4 1.0
C B:CYS1166 4.6 0.4 1.0
CA B:ILE1165 4.6 0.7 1.0
O B:CYS1182 4.6 0.9 1.0
N B:ILE1165 4.7 0.3 1.0
CG1 B:ILE1165 4.8 0.3 1.0
N B:GLY1184 4.8 0.5 1.0
C B:CYS1163 4.9 0.6 1.0
CA B:CYS1185 5.0 0.8 1.0

Zinc binding site 4 out of 8 in 4y7n

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Zinc binding site 4 out of 8 in the The Structure Insight Into 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 The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:0.4
occ:1.00
 SG C:CYS92 2.2 76.6 1.0
SG C:CYS86 2.4 91.5 1.0
SG C:CYS88 2.4 79.6 1.0
SG C:CYS95 2.4 90.7 1.0
CB C:CYS92 2.9 83.2 1.0
N C:CYS92 3.3 90.1 1.0
CB C:CYS95 3.4 81.0 1.0
CB C:CYS86 3.5 83.3 1.0
CB C:CYS88 3.6 86.7 1.0
CA C:CYS92 3.7 84.7 1.0
C C:HIS91 3.7 94.0 1.0
CA C:HIS91 4.1 89.7 1.0
O C:ASP90 4.3 85.1 1.0
O C:HIS91 4.4 89.9 1.0
N C:CYS95 4.4 92.5 1.0
C C:CYS92 4.4 85.0 1.0
CA C:CYS95 4.5 86.1 1.0
N C:CYS88 4.6 84.7 1.0
CA C:CYS88 4.7 87.0 1.0
CA C:CYS86 4.8 86.1 1.0
C C:CYS86 4.9 86.8 1.0
N C:ASP93 5.0 80.9 1.0

Zinc binding site 5 out of 8 in 4y7n

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Zinc binding site 5 out of 8 in the The Structure Insight Into 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 The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.1
occ:1.00
 SG I:CYS29 2.2 97.2 1.0
SG I:CYS32 2.2 0.4 1.0
SG I:CYS10 2.3 98.7 1.0
SG I:CYS7 2.4 89.5 1.0
CB I:CYS10 2.8 88.6 1.0
CB I:CYS7 3.0 90.3 1.0
CB I:CYS29 3.3 93.7 1.0
CB I:CYS32 3.5 0.5 1.0
N I:CYS32 3.8 0.6 1.0
N I:CYS10 4.0 98.5 1.0
CA I:CYS10 4.0 93.7 1.0
CA I:CYS32 4.2 0.9 1.0
CB I:THR31 4.3 0.3 1.0
CB I:TYR34 4.5 80.6 1.0
CA I:CYS7 4.5 96.4 1.0
C I:THR31 4.6 0.7 1.0
N I:SER33 4.7 0.4 1.0
CA I:CYS29 4.7 93.0 1.0
OG1 I:THR31 4.7 0.9 1.0
N I:THR31 4.7 0.6 1.0
N I:TYR34 4.8 84.3 1.0
CB I:ASP9 4.8 0.5 1.0
CA I:THR31 4.8 0.3 1.0
C I:CYS29 4.9 99.1 1.0
C I:ASP9 4.9 0.2 1.0
O I:CYS29 4.9 0.1 1.0
C I:CYS10 5.0 94.2 1.0

Zinc binding site 6 out of 8 in 4y7n

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Zinc binding site 6 out of 8 in the The Structure Insight Into 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 The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:93.9
occ:1.00
 SG I:CYS78 2.2 0.5 1.0
SG I:CYS106 2.2 0.3 1.0
SG I:CYS103 2.4 91.0 1.0
SG I:CYS75 2.4 0.4 1.0
CB I:CYS78 2.7 0.7 1.0
CB I:CYS75 2.8 95.3 1.0
N I:CYS78 3.4 0.2 1.0
CA I:CYS78 3.6 0.7 1.0
CB I:CYS106 3.6 0.3 1.0
CB I:CYS103 3.7 92.2 1.0
N I:CYS106 3.7 0.2 1.0
CB I:SER105 4.1 0.0 1.0
CA I:CYS106 4.3 99.8 1.0
CA I:CYS75 4.3 95.3 1.0
C I:LYS77 4.3 83.3 1.0
C I:CYS78 4.4 0.7 1.0
N I:HIS79 4.4 0.9 1.0
N I:LYS77 4.6 88.1 1.0
CB I:LYS77 4.6 90.4 1.0
N I:SER80 4.7 77.4 1.0
CA I:LYS77 4.8 87.4 1.0
CB I:SER80 4.8 71.0 1.0
C I:SER105 4.8 0.3 1.0
C I:CYS75 4.8 99.0 1.0
CA I:SER105 4.9 0.9 1.0
CB I:HIS108 4.9 91.7 1.0
C I:CYS106 4.9 0.1 1.0
N I:SER105 4.9 0.6 1.0

Zinc binding site 7 out of 8 in 4y7n

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Zinc binding site 7 out of 8 in the The Structure Insight Into 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 The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:92.2
occ:1.00
 SG J:CYS10 2.2 83.2 1.0
SG J:CYS7 2.2 76.5 1.0
SG J:CYS45 2.2 93.4 1.0
SG J:CYS46 2.2 67.4 1.0
CB J:CYS46 2.5 77.4 1.0
N J:CYS46 2.8 91.5 1.0
CA J:CYS46 2.9 88.0 1.0
CB J:CYS7 3.1 77.5 1.0
C J:CYS45 3.2 88.2 1.0
CB J:CYS10 3.4 68.3 1.0
O J:CYS45 3.6 83.7 1.0
CB J:CYS45 3.6 86.1 1.0
N J:CYS10 3.7 69.3 1.0
CA J:CYS45 4.1 80.5 1.0
CA J:CYS10 4.1 72.5 1.0
NH2 J:ARG43 4.3 92.7 1.0
C J:CYS46 4.4 84.5 1.0
CB J:SER9 4.4 70.8 1.0
CA J:CYS7 4.5 75.6 1.0
OG J:SER9 4.6 67.4 1.0
N J:GLY11 4.7 60.7 1.0
N J:CYS45 4.7 77.9 1.0
C J:SER9 4.8 60.3 1.0
CB J:LYS12 4.8 52.2 1.0
N J:SER9 4.8 61.1 1.0
CA J:SER9 4.9 60.1 1.0
C J:CYS7 5.0 77.6 1.0
C J:CYS10 5.0 69.6 1.0

Zinc binding site 8 out of 8 in 4y7n

Go back to Zinc Binding Sites List in 4y7n
Zinc binding site 8 out of 8 in the The Structure Insight Into 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 The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.5
occ:1.00
 SG L:CYS48 2.3 0.8 1.0
SG L:CYS51 2.4 0.4 1.0
SG L:CYS31 2.4 0.1 1.0
SG L:CYS34 2.4 0.9 1.0
CB L:CYS51 2.5 0.4 1.0
CB L:CYS34 2.7 0.1 1.0
CB L:CYS31 3.4 0.5 1.0
CB L:CYS48 3.8 0.9 1.0
O L:LYS49 3.9 0.7 1.0
CA L:CYS51 3.9 0.1 1.0
CA L:CYS34 4.0 0.8 1.0
N L:CYS51 4.2 0.7 1.0
N L:CYS34 4.3 0.2 1.0
O L:ASP50 4.4 0.3 1.0
C L:ASP50 4.5 0.2 1.0
O L:CYS34 4.6 0.4 1.0
C L:CYS34 4.6 0.9 1.0
C L:LYS49 4.7 0.8 1.0
N L:LYS49 4.7 0.9 1.0
CA L:CYS31 4.8 0.0 1.0
C L:CYS51 5.0 0.7 1.0
O L:HIS53 5.0 0.9 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 10:58:16 2024

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