Zinc in PDB 8uoq: Composite Map of PIC_DELTA_TFIIK FORM2

Enzymatic activity of Composite Map of PIC_DELTA_TFIIK FORM2

All present enzymatic activity of Composite Map of PIC_DELTA_TFIIK FORM2:
2.7.7.6; 3.6.4.12; 5.6.2.3;

Other elements in 8uoq:

The structure of Composite Map of PIC_DELTA_TFIIK FORM2 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 4 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Zinc atom in the Composite Map of PIC_DELTA_TFIIK FORM2 (pdb code 8uoq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 15 binding sites of Zinc where determined in the Composite Map of PIC_DELTA_TFIIK FORM2, PDB code: 8uoq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 15 in 8uoq

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Zinc binding site 1 out of 15 in the Composite Map of PIC_DELTA_TFIIK FORM2


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Composite Map of PIC_DELTA_TFIIK FORM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn401

b:291.8
occ:1.00
 SG M:CYS24 2.3 131.7 1.0
SG M:CYS48 2.3 125.3 1.0
SG M:CYS45 2.3 147.1 1.0
SG M:CYS27 2.3 140.1 1.0
CB M:CYS48 2.6 125.3 1.0
CB M:CYS45 3.0 147.1 1.0
CB M:CYS24 3.3 131.7 1.0
CB M:CYS27 3.4 140.1 1.0
N M:CYS48 3.4 125.3 1.0
CA M:CYS48 3.6 125.3 1.0
N M:CYS27 4.2 140.1 1.0
CA M:CYS45 4.4 147.1 1.0
O M:CYS45 4.4 147.1 1.0
CA M:CYS27 4.4 140.1 1.0
C M:CYS45 4.6 147.1 1.0
C M:LEU47 4.6 148.2 1.0
C M:CYS48 4.6 125.3 1.0
N M:GLY49 4.7 87.2 1.0
CB M:LEU47 4.7 148.2 1.0
CA M:CYS24 4.7 131.7 1.0
C M:GLU26 4.7 93.0 1.0
N M:LEU47 5.0 148.2 1.0

Zinc binding site 2 out of 15 in 8uoq

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Zinc binding site 2 out of 15 in the Composite Map of PIC_DELTA_TFIIK FORM2


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Composite Map of PIC_DELTA_TFIIK FORM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:299.6
occ:0.96
 SG A:CYS107 2.3 115.3 1.0
SG A:CYS148 2.3 133.1 1.0
SG A:CYS167 2.3 98.1 1.0
SG A:CYS110 2.3 80.0 1.0
CB A:CYS110 2.4 80.0 1.0
CB A:CYS148 2.8 133.1 1.0
CB A:CYS107 2.9 115.3 1.0
CA A:CYS110 3.8 80.0 1.0
CB A:CYS167 3.8 98.1 1.0
O A:CYS167 4.0 98.1 1.0
N A:CYS110 4.1 80.0 1.0
O A:MET108 4.1 94.2 1.0
N A:CYS167 4.2 98.1 1.0
CA A:CYS107 4.2 115.3 1.0
CA A:CYS148 4.3 133.1 1.0
CA A:CYS167 4.4 98.1 1.0
C A:CYS167 4.5 98.1 1.0
C A:CYS107 4.5 115.3 1.0
O A:CYS107 4.6 115.3 1.0
C A:CYS110 4.7 80.0 1.0
C A:CYS148 4.8 133.1 1.0
NE2 A:GLN171 4.8 118.1 1.0
O A:ASN169 4.9 108.6 1.0
N A:GLY111 5.0 66.8 1.0

Zinc binding site 3 out of 15 in 8uoq

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Zinc binding site 3 out of 15 in the Composite Map of PIC_DELTA_TFIIK FORM2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Composite Map of PIC_DELTA_TFIIK FORM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:63.5
occ:1.00
 CB A:CYS67 1.9 62.9 1.0
NE2 A:HIS80 2.0 32.4 1.0
O A:CYS67 2.3 62.9 1.0
SG A:CYS67 2.3 62.9 1.0
SG A:CYS70 2.3 74.1 1.0
SG A:CYS77 2.3 43.6 1.0
CA A:CYS67 2.8 62.9 1.0
C A:CYS67 2.8 62.9 1.0
CD2 A:HIS80 3.0 32.4 1.0
CE1 A:HIS80 3.0 32.4 1.0
CB A:CYS77 3.5 43.6 1.0
CB A:CYS70 3.7 74.1 1.0
N A:CYS67 4.0 62.9 1.0
ND1 A:HIS80 4.1 32.4 1.0
N A:GLN68 4.1 60.5 1.0
CG A:HIS80 4.1 32.4 1.0
N A:CYS70 4.1 74.1 1.0
CA A:CYS70 4.3 74.1 1.0
O A:LYS66 4.3 54.9 1.0
C A:CYS70 4.5 74.1 1.0
CA A:CYS77 4.5 43.6 1.0
CB A:GLU72 4.6 66.9 1.0
C A:LYS66 4.6 54.9 1.0
N A:GLN71 4.6 63.6 1.0
N A:GLU72 4.7 66.9 1.0
CG A:GLN68 4.8 60.5 1.0
NE2 A:GLN68 4.8 60.5 1.0
CA A:GLY59 4.9 47.5 1.0
CG A:GLU72 5.0 66.9 1.0

Zinc binding site 4 out of 15 in 8uoq

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Zinc binding site 4 out of 15 in the Composite Map of PIC_DELTA_TFIIK FORM2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Composite Map of PIC_DELTA_TFIIK FORM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:268.2
occ:1.00
 CB B:CYS1185 2.2 109.0 1.0
SG B:CYS1185 2.3 109.0 1.0
SG B:CYS1166 2.3 86.0 1.0
SG B:CYS1182 2.3 80.5 1.0
SG B:CYS1163 2.3 98.4 1.0
CB B:CYS1163 3.1 98.4 1.0
CB B:CYS1166 3.2 86.0 1.0
OD1 B:ASN1187 3.3 99.9 1.0
N B:CYS1166 3.5 86.0 1.0
CA B:CYS1185 3.8 109.0 1.0
CB B:CYS1182 3.8 80.5 1.0
ND2 B:ASN1187 3.8 99.9 1.0
CA B:CYS1166 3.8 86.0 1.0
CG B:ASN1187 3.9 99.9 1.0
N B:CYS1185 4.4 109.0 1.0
C B:ILE1165 4.5 86.7 1.0
C B:CYS1185 4.5 109.0 1.0
O B:CYS1163 4.5 98.4 1.0
CA B:CYS1163 4.5 98.4 1.0
CB B:ILE1165 4.7 86.7 1.0
O B:CYS1185 4.7 109.0 1.0
C B:CYS1163 4.8 98.4 1.0
O B:CYS1182 5.0 80.5 1.0

Zinc binding site 5 out of 15 in 8uoq

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Zinc binding site 5 out of 15 in the Composite Map of PIC_DELTA_TFIIK FORM2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Composite Map of PIC_DELTA_TFIIK FORM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:220.4
occ:1.00
 SG C:CYS92 2.3 81.8 1.0
SG C:CYS88 2.3 212.6 1.0
SG C:CYS86 2.3 236.3 1.0
SG C:CYS95 2.3 76.3 1.0
CB C:CYS95 3.0 76.3 1.0
CB C:CYS86 3.3 236.3 1.0
CB C:CYS92 3.5 81.8 1.0
CB C:CYS88 3.6 212.6 1.0
N C:CYS92 3.7 81.8 1.0
CA C:CYS92 4.1 81.8 1.0
CA C:CYS95 4.2 76.3 1.0
N C:CYS95 4.2 76.3 1.0
N C:CYS88 4.5 212.6 1.0
CA C:CYS88 4.5 212.6 1.0
O C:CYS92 4.6 81.8 1.0
CA C:CYS86 4.6 236.3 1.0
C C:CYS92 4.7 81.8 1.0
C C:HIS91 4.8 100.8 1.0
C C:CYS88 4.8 212.6 1.0
CA C:HIS91 4.9 100.8 1.0
C C:CYS86 5.0 236.3 1.0
N C:HIS91 5.0 100.8 1.0

Zinc binding site 6 out of 15 in 8uoq

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Zinc binding site 6 out of 15 in the Composite Map of PIC_DELTA_TFIIK FORM2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Composite Map of PIC_DELTA_TFIIK FORM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:153.1
occ:1.00
 SG I:CYS10 2.3 95.0 1.0
SG I:CYS32 2.3 109.5 1.0
SG I:CYS7 2.3 95.4 1.0
SG I:CYS29 2.3 115.0 1.0
CB I:CYS7 3.0 95.4 1.0
CB I:CYS29 3.1 115.0 1.0
CB I:CYS32 3.2 109.5 1.0
N I:CYS32 3.5 109.5 1.0
CA I:CYS32 3.8 109.5 1.0
CB I:CYS10 4.0 95.0 1.0
O I:CYS10 4.0 95.0 1.0
N I:CYS10 4.2 95.0 1.0
C I:CYS32 4.2 109.5 1.0
O I:CYS32 4.4 109.5 1.0
CB I:TYR34 4.4 75.7 1.0
CB I:THR31 4.5 114.9 1.0
CA I:CYS7 4.5 95.4 1.0
CA I:CYS10 4.5 95.0 1.0
CA I:CYS29 4.6 115.0 1.0
ND2 I:ASN12 4.6 72.3 1.0
C I:THR31 4.6 114.9 1.0
CB I:ASP9 4.7 124.0 1.0
C I:CYS10 4.7 95.0 1.0
N I:TYR34 4.8 75.7 1.0
CG2 I:THR31 4.9 114.9 1.0
CA I:THR31 5.0 114.9 1.0
C I:ASP9 5.0 124.0 1.0

Zinc binding site 7 out of 15 in 8uoq

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Zinc binding site 7 out of 15 in the Composite Map of PIC_DELTA_TFIIK FORM2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Composite Map of PIC_DELTA_TFIIK FORM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:183.3
occ:1.00
 N I:CYS78 2.2 126.2 1.0
SG I:CYS78 2.3 126.2 1.0
SG I:CYS106 2.3 104.4 1.0
SG I:CYS75 2.3 127.4 1.0
CB I:CYS106 2.7 104.4 1.0
CB I:CYS75 2.8 127.4 1.0
CB I:CYS78 2.8 126.2 1.0
CA I:CYS78 3.0 126.2 1.0
C I:LYS77 3.1 86.8 1.0
N I:LYS77 3.2 86.8 1.0
CB I:LYS77 3.3 86.8 1.0
CA I:LYS77 3.3 86.8 1.0
O I:CYS75 3.6 127.4 1.0
C I:CYS75 3.7 127.4 1.0
CA I:CYS75 3.8 127.4 1.0
C I:CYS78 4.0 126.2 1.0
N I:HIS79 4.0 123.1 1.0
CA I:CYS106 4.0 104.4 1.0
O I:LYS77 4.2 86.8 1.0
N I:PRO76 4.3 87.8 1.0
N I:CYS106 4.3 104.4 1.0
C I:PRO76 4.4 87.8 1.0
CG I:LYS77 4.5 86.8 1.0
OG I:SER105 4.6 109.8 1.0
CE I:LYS77 4.8 86.8 1.0
N I:CYS75 4.8 127.4 1.0
CA I:PRO76 4.9 87.8 1.0

Zinc binding site 8 out of 15 in 8uoq

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Zinc binding site 8 out of 15 in the Composite Map of PIC_DELTA_TFIIK FORM2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Composite Map of PIC_DELTA_TFIIK FORM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:194.3
occ:1.00
 SG J:CYS10 2.3 30.6 1.0
SG J:CYS46 2.3 57.5 1.0
SG J:CYS45 2.3 42.5 1.0
SG J:CYS7 2.3 21.1 1.0
CB J:CYS10 2.4 30.6 1.0
N J:CYS10 2.7 30.6 1.0
CA J:CYS10 3.0 30.6 1.0
N J:CYS46 3.1 57.5 1.0
CB J:CYS7 3.2 21.1 1.0
C J:CYS45 3.2 42.5 1.0
O J:CYS45 3.4 42.5 1.0
CA J:CYS46 3.4 57.5 1.0
CB J:CYS46 3.5 57.5 1.0
CB J:CYS45 3.5 42.5 1.0
C J:SER9 3.9 23.9 1.0
N J:GLY11 3.9 23.5 1.0
CA J:CYS45 4.0 42.5 1.0
C J:CYS10 4.0 30.6 1.0
CB J:SER9 4.1 23.9 1.0
CA J:SER9 4.4 23.9 1.0
N J:SER9 4.6 23.9 1.0
CA J:CYS7 4.6 21.1 1.0
C J:CYS7 4.8 21.1 1.0
O J:SER9 4.9 23.9 1.0
N J:CYS45 4.9 42.5 1.0
C J:CYS46 4.9 57.5 1.0
OG J:SER9 5.0 23.9 1.0

Zinc binding site 9 out of 15 in 8uoq

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Zinc binding site 9 out of 15 in the Composite Map of PIC_DELTA_TFIIK FORM2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Composite Map of PIC_DELTA_TFIIK FORM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn201

b:212.9
occ:1.00
 CB L:CYS51 2.3 236.0 1.0
SG L:CYS48 2.3 174.8 1.0
SG L:CYS31 2.4 118.6 1.0
SG L:CYS51 2.4 236.0 1.0
CB L:ALA32 2.5 119.3 1.0
CB L:CYS48 2.9 174.8 1.0
CA L:CYS51 3.7 236.0 1.0
CA L:ALA32 3.9 119.3 1.0
ND1 L:HIS53 3.9 111.3 1.0
CB L:CYS31 4.0 118.6 1.0
C L:CYS31 4.0 118.6 1.0
O L:ILE30 4.1 79.7 1.0
N L:ALA32 4.1 119.3 1.0
CB L:HIS53 4.2 111.3 1.0
CG L:HIS53 4.2 111.3 1.0
SG L:CYS34 4.2 168.0 1.0
O L:CYS31 4.3 118.6 1.0
N L:CYS51 4.4 236.0 1.0
CA L:CYS48 4.4 174.8 1.0
N L:GLY52 4.4 163.4 1.0
C L:CYS51 4.4 236.0 1.0
N L:HIS53 4.5 111.3 1.0
CA L:CYS31 4.6 118.6 1.0
CE1 L:HIS53 4.7 111.3 1.0
C L:ALA32 4.8 119.3 1.0
C L:CYS48 4.9 174.8 1.0
CA L:HIS53 5.0 111.3 1.0
N L:CYS48 5.0 174.8 1.0

Zinc binding site 10 out of 15 in 8uoq

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Zinc binding site 10 out of 15 in the Composite Map of PIC_DELTA_TFIIK FORM2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Composite Map of PIC_DELTA_TFIIK FORM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn401

b:539.9
occ:1.00
 SG S:CYS271 2.3 316.9 1.0
SG S:CYS274 2.3 384.6 1.0
SG S:CYS302 2.3 334.4 1.0
SG S:CYS299 2.3 344.4 1.0
CB S:CYS299 3.0 344.4 1.0
CB S:CYS271 3.0 316.9 1.0
CB S:CYS302 3.6 334.4 1.0
CB S:CYS274 3.7 384.6 1.0
N S:CYS302 3.8 334.4 1.0
N S:CYS274 3.9 384.6 1.0
CB S:ASN304 4.3 306.2 1.0
CA S:CYS274 4.3 384.6 1.0
CA S:CYS302 4.3 334.4 1.0
CB S:ALA301 4.3 321.6 1.0
CA S:CYS299 4.4 344.4 1.0
CA S:CYS271 4.4 316.9 1.0
C S:ALA301 4.6 321.6 1.0
N S:LYS275 4.6 274.3 1.0
N S:ASN304 4.6 306.2 1.0
N S:ALA301 4.7 321.6 1.0
N S:GLY303 4.7 317.6 1.0
CB S:LYS273 4.7 340.2 1.0
C S:CYS274 4.8 384.6 1.0
CA S:ALA301 4.8 321.6 1.0
N S:GLU276 4.8 281.3 1.0
C S:CYS299 4.8 344.4 1.0
N S:LYS273 4.9 340.2 1.0
CB S:GLU276 4.9 281.3 1.0
C S:CYS302 5.0 334.4 1.0
C S:LYS273 5.0 340.2 1.0

Reference:

C.Yang, P.Basnet, S.Sharmin, H.Shen, C.D.Kaplan, K.Murakami. Transcription Start Site Scanning Requires the Fungi-Specific Hydrophobic Loop of TFB3. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 39287137
DOI: 10.1093/NAR/GKAE805
Page generated: Thu Oct 31 12:24:40 2024

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