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Zinc in PDB 5fz5: Transcription Initiation Complex Structures Elucidate Dna Opening (Cc)

Enzymatic activity of Transcription Initiation Complex Structures Elucidate Dna Opening (Cc)

All present enzymatic activity of Transcription Initiation Complex Structures Elucidate Dna Opening (Cc):
2.7.7.6; 3.6.4.12;

Other elements in 5fz5:

The structure of Transcription Initiation Complex Structures Elucidate Dna Opening (Cc) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Transcription Initiation Complex Structures Elucidate Dna Opening (Cc) (pdb code 5fz5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Transcription Initiation Complex Structures Elucidate Dna Opening (Cc), PDB code: 5fz5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 5fz5

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Zinc binding site 1 out of 10 in the Transcription Initiation Complex Structures Elucidate Dna Opening (Cc)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Transcription Initiation Complex Structures Elucidate Dna Opening (Cc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2453

b:0.3
occ:1.00
 SG A:CYS107 2.3 0.1 1.0
SG A:CYS148 2.4 0.2 1.0
SG A:CYS110 2.4 0.6 1.0
CB A:CYS148 2.7 0.9 1.0
CB A:CYS107 3.1 0.6 1.0
O A:CYS167 3.1 0.5 1.0
NE2 A:GLN171 3.4 0.2 1.0
CB A:CYS167 3.8 0.5 1.0
SG A:CYS167 3.9 0.6 1.0
O A:GLY166 3.9 0.4 1.0
CB A:CYS110 4.0 0.4 1.0
CA A:CYS148 4.2 0.7 1.0
C A:CYS167 4.2 0.6 1.0
N A:CYS110 4.3 1.0 1.0
CA A:CYS107 4.4 0.9 1.0
CD A:GLN171 4.5 0.3 1.0
CA A:CYS167 4.6 0.8 1.0
CA A:CYS110 4.7 0.6 1.0
C A:CYS148 4.9 0.8 1.0
N A:CYS148 4.9 0.9 1.0
C A:GLY166 5.0 0.4 1.0
O A:ASN169 5.0 0.4 1.0

Zinc binding site 2 out of 10 in 5fz5

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Zinc binding site 2 out of 10 in the Transcription Initiation Complex Structures Elucidate Dna Opening (Cc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Transcription Initiation Complex Structures Elucidate Dna Opening (Cc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2454

b:0.3
occ:1.00
 SG A:CYS70 2.3 0.8 1.0
SG A:CYS77 2.3 0.7 1.0
SG A:CYS67 2.4 0.7 1.0
CB A:CYS70 2.5 0.6 1.0
NE2 A:HIS80 2.8 69.4 1.0
CD2 A:HIS80 3.1 70.5 1.0
N A:CYS70 3.4 0.9 1.0
CB A:CYS77 3.4 95.7 1.0
CA A:CYS70 3.5 0.3 1.0
CG2 A:THR69 3.7 0.5 1.0
CB A:CYS67 3.8 0.6 1.0
CE1 A:HIS80 4.1 73.7 1.0
CA A:CYS77 4.2 76.7 1.0
O A:CYS67 4.3 0.4 1.0
O A:GLN71 4.3 0.0 1.0
CG A:HIS80 4.4 68.4 1.0
C A:CYS70 4.5 95.5 1.0
C A:THR69 4.6 0.0 1.0
CA A:GLY59 4.6 0.5 1.0
N A:GLN71 4.8 0.0 1.0
CD A:PRO78 4.8 74.2 1.0
ND1 A:HIS80 4.9 72.0 1.0
C A:CYS67 4.9 0.2 1.0
N A:GLY79 4.9 80.4 1.0
C A:CYS77 4.9 78.2 1.0
CA A:CYS67 5.0 0.9 1.0
CB A:THR69 5.0 0.1 1.0

Zinc binding site 3 out of 10 in 5fz5

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Zinc binding site 3 out of 10 in the Transcription Initiation Complex Structures Elucidate Dna Opening (Cc)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Transcription Initiation Complex Structures Elucidate Dna Opening (Cc) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2224

b:0.1
occ:1.00
 SG B:CYS1182 2.2 0.5 1.0
CB B:CYS1163 2.3 0.7 1.0
SG B:CYS1166 2.3 0.0 1.0
SG B:CYS1185 2.3 0.0 1.0
SG B:CYS1163 2.4 0.9 1.0
CB B:CYS1182 3.0 0.1 1.0
CA B:CYS1163 3.8 90.5 1.0
CB B:CYS1185 3.8 0.1 1.0
O B:CYS1166 3.9 0.3 1.0
CB B:CYS1166 4.0 0.4 1.0
N B:CYS1166 4.2 96.9 1.0
CA B:CYS1182 4.4 90.9 1.0
N B:CYS1163 4.4 88.0 1.0
CA B:CYS1166 4.5 96.8 1.0
C B:CYS1166 4.6 0.0 1.0
C B:CYS1163 4.7 93.1 1.0
O B:CYS1182 4.7 0.5 1.0
C B:CYS1182 4.8 99.5 1.0
CG2 B:VAL1171 4.9 78.6 1.0
CB B:THR1170 5.0 0.6 1.0

Zinc binding site 4 out of 10 in 5fz5

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Zinc binding site 4 out of 10 in the Transcription Initiation Complex Structures Elucidate Dna Opening (Cc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Transcription Initiation Complex Structures Elucidate Dna Opening (Cc) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1266

b:0.1
occ:1.00
 SG C:CYS88 2.2 0.9 1.0
SG C:CYS92 2.3 94.6 1.0
SG C:CYS86 2.3 0.7 1.0
SG C:CYS95 2.3 92.8 1.0
CB C:CYS86 3.0 0.2 1.0
CB C:CYS95 3.3 90.0 1.0
CB C:CYS92 3.5 91.6 1.0
N C:CYS92 3.7 90.0 1.0
CB C:CYS88 3.7 0.6 1.0
N C:CYS95 3.9 81.6 1.0
C C:HIS91 3.9 0.9 1.0
CA C:CYS92 4.2 89.2 1.0
CA C:CYS95 4.2 79.2 1.0
CA C:HIS91 4.3 0.4 1.0
O C:ASP90 4.4 0.9 1.0
CA C:CYS86 4.4 0.2 1.0
N C:CYS88 4.4 0.6 1.0
O C:HIS91 4.5 0.6 1.0
CB C:LYS94 4.6 68.8 1.0
C C:CYS86 4.6 0.7 1.0
CA C:CYS88 4.6 0.4 1.0
C C:CYS92 4.8 95.0 1.0
C C:LYS94 4.8 85.4 1.0
O C:CYS86 5.0 0.2 1.0
N C:LYS94 5.0 82.3 1.0

Zinc binding site 5 out of 10 in 5fz5

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Zinc binding site 5 out of 10 in the Transcription Initiation Complex Structures Elucidate Dna Opening (Cc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Transcription Initiation Complex Structures Elucidate Dna Opening (Cc) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1118

b:0.8
occ:1.00
 SG I:CYS7 2.3 0.6 1.0
SG I:CYS29 2.3 0.8 1.0
CB I:CYS10 2.4 0.6 1.0
SG I:CYS32 2.4 0.2 1.0
SG I:CYS10 2.4 0.0 1.0
CB I:CYS7 3.0 0.1 1.0
CB I:CYS29 3.1 0.8 1.0
OG1 I:THR31 3.3 0.2 1.0
CB I:CYS32 3.7 0.7 1.0
CA I:CYS10 3.8 0.8 1.0
N I:CYS10 4.2 0.3 1.0
N I:CYS32 4.4 0.7 1.0
CA I:CYS7 4.5 0.1 1.0
CA I:CYS29 4.5 0.7 1.0
CB I:TYR34 4.6 0.2 1.0
C I:CYS10 4.6 0.8 1.0
O I:CYS29 4.6 0.8 1.0
CB I:THR31 4.6 0.2 1.0
CA I:CYS32 4.7 0.8 1.0
O I:ARG8 4.7 0.3 1.0
C I:CYS29 4.8 0.6 1.0
C I:THR31 4.8 0.5 1.0
N I:ASN11 4.9 0.9 1.0

Zinc binding site 6 out of 10 in 5fz5

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Zinc binding site 6 out of 10 in the Transcription Initiation Complex Structures Elucidate Dna Opening (Cc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Transcription Initiation Complex Structures Elucidate Dna Opening (Cc) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1119

b:0.2
occ:1.00
 SG I:CYS106 2.3 0.6 1.0
SG I:CYS78 2.4 0.4 1.0
SG I:CYS75 2.4 0.2 1.0
SG I:CYS103 2.5 0.8 1.0
CB I:CYS75 2.8 0.4 1.0
CB I:CYS103 2.9 0.7 1.0
OG I:SER105 3.4 0.7 1.0
CB I:CYS106 3.9 0.0 1.0
CB I:CYS78 3.9 0.6 1.0
N I:CYS106 4.1 0.1 1.0
N I:CYS78 4.1 0.3 1.0
CA I:CYS75 4.3 0.4 1.0
CA I:CYS103 4.4 0.3 1.0
CA I:CYS106 4.5 0.5 1.0
CA I:CYS78 4.5 0.9 1.0
CB I:HIS108 4.6 0.2 1.0
CB I:SER105 4.7 0.6 1.0
CB I:SER80 4.8 0.8 1.0
N I:HIS79 4.9 0.3 1.0
CB I:LYS77 4.9 0.2 1.0
N I:SER80 4.9 0.9 1.0
N I:HIS108 5.0 0.8 1.0
C I:CYS78 5.0 0.6 1.0

Zinc binding site 7 out of 10 in 5fz5

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Zinc binding site 7 out of 10 in the Transcription Initiation Complex Structures Elucidate Dna Opening (Cc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Transcription Initiation Complex Structures Elucidate Dna Opening (Cc) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:0.1
occ:1.00
 N J:CYS46 2.1 54.2 1.0
SG J:CYS10 2.3 59.4 1.0
SG J:CYS46 2.3 97.9 1.0
SG J:CYS45 2.4 71.5 1.0
CA J:CYS46 2.6 54.1 1.0
C J:CYS45 2.8 63.6 1.0
CB J:CYS46 2.9 94.2 1.0
SG J:CYS7 3.0 72.8 1.0
CB J:CYS45 3.2 66.8 1.0
O J:CYS45 3.5 62.9 1.0
CA J:CYS45 3.5 59.7 1.0
CB J:CYS10 3.6 54.0 1.0
CB J:CYS7 4.0 69.0 1.0
C J:CYS46 4.1 58.4 1.0
N J:CYS45 4.2 62.0 1.0
N J:CYS10 4.3 46.5 1.0
NE J:ARG43 4.5 64.3 1.0
CA J:CYS10 4.6 49.0 1.0
NH2 J:ARG43 4.8 75.2 1.0
CB J:ARG43 4.8 55.5 1.0
N J:ARG47 4.8 58.8 1.0
O J:CYS46 4.9 58.7 1.0

Zinc binding site 8 out of 10 in 5fz5

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Zinc binding site 8 out of 10 in the Transcription Initiation Complex Structures Elucidate Dna Opening (Cc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Transcription Initiation Complex Structures Elucidate Dna Opening (Cc) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.2
occ:1.00
 SG L:CYS51 2.2 0.5 1.0
SG L:CYS34 2.2 0.4 1.0
SG L:CYS31 2.3 0.6 1.0
SG L:CYS48 2.3 0.1 1.0
CB L:CYS31 2.9 0.9 1.0
CB L:CYS48 3.4 1.0 1.0
OG L:SER36 3.9 0.9 1.0
CB L:CYS51 3.9 0.3 1.0
CB L:CYS34 3.9 0.8 1.0
O L:LYS49 4.2 0.7 1.0
N L:CYS51 4.3 0.5 1.0
N L:CYS34 4.3 0.5 1.0
CA L:CYS31 4.4 0.7 1.0
CA L:CYS51 4.6 0.2 1.0
CG L:GLU33 4.6 0.3 1.0
CA L:CYS34 4.6 0.6 1.0
O L:CYS51 4.7 0.6 1.0
CA L:CYS48 4.8 0.2 1.0
C L:CYS51 4.9 0.4 1.0
C L:ASP50 4.9 0.1 1.0
OE2 L:GLU33 5.0 0.8 1.0

Zinc binding site 9 out of 10 in 5fz5

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Zinc binding site 9 out of 10 in the Transcription Initiation Complex Structures Elucidate Dna Opening (Cc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Transcription Initiation Complex Structures Elucidate Dna Opening (Cc) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn1327

b:0.6
occ:1.00
 SG M:CYS48 2.3 0.8 1.0
SG M:CYS27 2.3 0.8 1.0
SG M:CYS45 2.3 0.0 1.0
SG M:CYS24 2.5 0.8 1.0
CB M:CYS45 3.0 1.0 1.0
CB M:CYS24 3.1 0.2 1.0
CB M:CYS27 3.4 0.1 1.0
CB M:CYS48 3.6 0.8 1.0
N M:CYS48 3.7 0.2 1.0
CA M:CYS48 4.3 0.8 1.0
N M:CYS27 4.3 0.4 1.0
CA M:CYS45 4.5 0.0 1.0
CA M:CYS27 4.5 0.8 1.0
CB M:LEU47 4.5 0.6 1.0
CA M:CYS24 4.6 0.6 1.0
CB M:LEU50 4.7 90.9 1.0
C M:LEU47 4.8 0.7 1.0
N M:LEU47 4.8 0.7 1.0
C M:CYS45 4.9 0.3 1.0
C M:CYS48 4.9 0.1 1.0
N M:GLY49 4.9 0.8 1.0
CA M:LEU47 5.0 0.3 1.0
O M:CYS45 5.0 0.6 1.0
N M:LEU50 5.0 0.9 1.0

Zinc binding site 10 out of 10 in 5fz5

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Zinc binding site 10 out of 10 in the Transcription Initiation Complex Structures Elucidate Dna Opening (Cc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Transcription Initiation Complex Structures Elucidate Dna Opening (Cc) within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn1192

b:57.4
occ:1.00
 CB W:CYS127 1.7 0.2 1.0
CB W:CYS124 3.0 0.8 1.0
CA W:CYS127 3.1 0.4 1.0
CB W:CYS149 3.4 0.6 1.0
N W:CYS127 3.5 0.4 1.0
CB W:CYS152 3.9 0.6 1.0
C W:CYS127 4.0 0.4 1.0
CB W:THR129 4.3 0.9 1.0
CB W:GLU154 4.4 0.2 1.0
N W:LEU128 4.4 0.6 1.0
CA W:CYS124 4.5 0.8 1.0
N W:THR129 4.6 0.5 1.0
O W:CYS127 4.7 0.4 1.0
N W:CYS152 4.8 0.8 1.0
CA W:CYS149 4.8 0.5 1.0
C W:ILE126 4.9 0.2 1.0
CA W:CYS152 4.9 0.8 1.0
C W:CYS124 4.9 0.8 1.0
O W:CYS124 5.0 0.8 1.0

Reference:

C.Plaschka, M.Hantsche, C.Dienemann, C.Burzinski, J.Plitzko, P.Cramer. Transcription Initiation Complex Structures Elucidate Dna Opening Nature V. 533 353 2016.
ISSN: ISSN 0028-0836
PubMed: 27193681
DOI: 10.1038/NATURE17990
Page generated: Sun Oct 27 16:42:14 2024

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