Zinc in PDB 8wav: De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss

Enzymatic activity of De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss

All present enzymatic activity of De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss:
2.7.7.6; 3.6.4.12;

Other elements in 8wav:

The structure of De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss (pdb code 8wav). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss, PDB code: 8wav:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8wav

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Zinc binding site 1 out of 8 in the De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Zn2001

b:126.1
occ:1.00
 NE2 o:HIS84 2.1 127.0 1.0
SG o:CYS71 2.3 141.6 1.0
SG o:CYS74 2.3 137.3 1.0
SG o:CYS81 2.3 138.7 1.0
CD2 o:HIS84 3.0 127.0 1.0
CE1 o:HIS84 3.0 127.0 1.0
OG1 o:THR73 3.4 132.3 1.0
CB o:CYS81 3.5 138.7 1.0
CB o:CYS74 3.8 137.3 1.0
CB o:CYS71 3.8 141.6 1.0
N o:CYS74 3.9 136.6 1.0
ND1 o:HIS84 4.1 127.0 1.0
CG o:HIS84 4.2 127.0 1.0
O o:CYS74 4.2 136.6 1.0
CA o:CYS74 4.2 136.6 1.0
CA o:CYS81 4.3 136.2 1.0
C o:CYS74 4.5 136.6 1.0
CB o:THR73 4.6 132.3 1.0
C o:THR73 4.8 134.0 1.0
CD o:PRO82 4.8 128.1 1.0
N o:GLY83 4.8 128.4 1.0
C o:CYS81 5.0 136.2 1.0
CG2 o:VAL64 5.0 146.2 1.0

Zinc binding site 2 out of 8 in 8wav

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Zinc binding site 2 out of 8 in the De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Zn2002

b:126.1
occ:1.00
 SG o:CYS111 2.3 164.4 1.0
SG o:CYS184 2.3 171.8 1.0
SG o:CYS114 2.3 163.7 1.0
CB o:CYS114 2.4 163.7 1.0
O o:GLY183 3.1 175.3 1.0
SG o:CYS154 3.4 174.7 1.0
CB o:CYS184 3.5 171.8 1.0
CB o:CYS111 3.5 164.4 1.0
CA o:CYS114 3.9 156.0 1.0
CB o:CYS154 3.9 174.7 1.0
O o:CYS184 4.0 172.2 1.0
C o:GLY183 4.2 175.3 1.0
CA o:CYS184 4.4 172.2 1.0
O o:PHE112 4.5 152.2 1.0
NE2 o:GLN188 4.5 158.9 1.0
C o:CYS184 4.5 172.2 1.0
N o:CYS114 4.5 156.0 1.0
N o:CYS184 4.8 172.2 1.0
C o:CYS114 4.8 156.0 1.0
CA o:CYS111 4.9 151.6 1.0

Zinc binding site 3 out of 8 in 8wav

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Zinc binding site 3 out of 8 in the De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss within 5.0Å range:
probe atom residue distance (Å) B Occ
p:Zn1202

b:126.1
occ:1.00
 SG p:CYS1122 2.3 142.6 1.0
SG p:CYS1137 2.3 148.7 1.0
SG p:CYS1140 2.3 153.0 1.0
SG p:CYS1119 2.3 141.6 1.0
CB p:CYS1119 3.0 141.6 1.0
CB p:CYS1122 3.4 142.6 1.0
CB p:CYS1137 3.6 148.7 1.0
CB p:CYS1140 3.6 153.0 1.0
N p:CYS1122 3.6 134.3 1.0
O p:CYS1122 4.0 134.3 1.0
CA p:CYS1122 4.0 134.3 1.0
C p:CYS1122 4.4 134.3 1.0
N p:CYS1140 4.5 144.2 1.0
CA p:CYS1119 4.5 135.0 1.0
CB p:LEU1121 4.7 131.9 1.0
CA p:CYS1140 4.7 144.2 1.0
CB p:ASN1142 4.7 141.6 1.0
O p:ARG1138 4.8 140.2 1.0
C p:LEU1121 4.8 132.4 1.0
ND2 p:ASN1142 4.9 141.6 1.0
CA p:CYS1137 4.9 138.5 1.0
N p:LEU1121 5.0 132.4 1.0

Zinc binding site 4 out of 8 in 8wav

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Zinc binding site 4 out of 8 in the De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss within 5.0Å range:
probe atom residue distance (Å) B Occ
q:Zn301

b:126.1
occ:1.00
 SG q:CYS94 2.3 133.0 1.0
SG q:CYS88 2.3 138.1 1.0
SG q:CYS90 2.3 147.2 1.0
SG q:CYS97 2.3 132.4 1.0
CB q:CYS94 2.8 133.0 1.0
N q:CYS94 3.4 122.6 1.0
CB q:CYS97 3.5 132.4 1.0
CB q:CYS88 3.6 138.1 1.0
CB q:CYS90 3.6 147.2 1.0
CA q:CYS94 3.6 122.6 1.0
N q:CYS97 4.0 117.8 1.0
C q:CYS94 4.2 122.6 1.0
C q:PHE93 4.2 128.4 1.0
O q:CYS94 4.4 122.6 1.0
CA q:CYS97 4.4 117.8 1.0
N q:CYS90 4.5 143.5 1.0
CA q:CYS90 4.5 143.5 1.0
CA q:PHE93 4.5 128.4 1.0
O q:CYS90 4.5 143.5 1.0
O q:GLU92 4.7 134.8 1.0
C q:CYS90 4.8 143.5 1.0
N q:GLU96 4.8 122.0 1.0
CB q:GLU96 4.9 131.8 1.0
CA q:CYS88 4.9 140.3 1.0
C q:GLU96 4.9 122.0 1.0

Zinc binding site 5 out of 8 in 8wav

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Zinc binding site 5 out of 8 in the De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss within 5.0Å range:
probe atom residue distance (Å) B Occ
w:Zn201

b:126.1
occ:1.00
 SG w:CYS20 2.3 163.9 1.0
SG w:CYS42 2.3 167.8 1.0
SG w:CYS17 2.3 161.5 1.0
SG w:CYS39 2.3 169.3 1.0
CB w:CYS39 2.8 169.3 1.0
CB w:CYS17 3.0 161.5 1.0
CB w:CYS42 3.9 167.8 1.0
CB w:CYS20 4.0 163.9 1.0
N w:CYS20 4.1 156.2 1.0
CA w:CYS39 4.3 161.3 1.0
N w:CYS42 4.4 163.9 1.0
CA w:CYS17 4.5 153.9 1.0
CA w:CYS20 4.6 156.2 1.0
CA w:CYS42 4.7 163.9 1.0
CB w:TYR44 4.7 153.5 1.0
CB w:GLU19 4.7 158.2 1.0
CB w:ASN22 4.8 154.4 1.0
ND2 w:ASN22 4.8 154.4 1.0
OE1 w:GLU19 4.9 158.2 1.0
N w:ASN22 4.9 153.2 1.0
C w:CYS39 4.9 161.3 1.0
N w:GLU19 5.0 155.9 1.0
C w:ASN41 5.0 162.3 1.0

Zinc binding site 6 out of 8 in 8wav

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Zinc binding site 6 out of 8 in the De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss within 5.0Å range:
probe atom residue distance (Å) B Occ
w:Zn202

b:126.1
occ:1.00
 SG w:CYS119 2.3 152.4 1.0
SG w:CYS86 2.3 150.4 1.0
SG w:CYS89 2.3 155.6 1.0
SG w:CYS114 2.3 146.3 1.0
CB w:CYS86 2.8 150.4 1.0
CB w:CYS114 3.2 146.3 1.0
CB w:CYS119 3.4 152.4 1.0
CB w:CYS89 3.8 155.6 1.0
N w:CYS89 4.0 150.2 1.0
CA w:CYS86 4.3 144.4 1.0
CA w:CYS89 4.4 150.2 1.0
CB w:HIS91 4.4 143.6 1.0
CB w:HIS121 4.6 136.5 1.0
O w:THR115 4.7 137.4 1.0
CA w:CYS114 4.7 133.3 1.0
N w:HIS91 4.7 143.4 1.0
CA w:CYS119 4.8 143.7 1.0
CB w:LYS88 4.8 142.6 1.0
N w:GLY90 4.8 146.3 1.0
N w:LYS88 4.9 146.1 1.0
C w:CYS89 4.9 150.2 1.0
C w:CYS86 4.9 144.4 1.0

Zinc binding site 7 out of 8 in 8wav

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Zinc binding site 7 out of 8 in the De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss within 5.0Å range:
probe atom residue distance (Å) B Occ
x:Zn101

b:126.1
occ:1.00
 SG x:CYS10 2.3 95.3 1.0
SG x:CYS45 2.3 108.2 1.0
SG x:CYS44 2.3 107.5 1.0
SG x:CYS7 2.3 98.6 1.0
CB x:CYS7 3.1 98.6 1.0
N x:CYS45 3.3 97.0 1.0
CB x:CYS10 3.4 95.3 1.0
CB x:CYS44 3.5 107.5 1.0
CB x:CYS45 3.5 108.2 1.0
CA x:CYS45 3.6 97.0 1.0
C x:CYS44 3.7 97.9 1.0
N x:CYS10 3.8 93.8 1.0
O x:CYS44 4.2 97.9 1.0
CA x:CYS44 4.2 97.9 1.0
CA x:CYS10 4.2 93.8 1.0
NE x:ARG42 4.4 100.3 1.0
CA x:CYS7 4.6 91.5 1.0
CB x:THR9 4.6 92.6 1.0
NH2 x:ARG42 4.6 100.3 1.0
N x:GLY11 4.7 93.3 1.0
C x:THR9 4.8 91.2 1.0
N x:THR9 4.9 91.2 1.0
C x:CYS10 4.9 93.8 1.0
C x:CYS7 4.9 91.5 1.0
N x:CYS44 4.9 97.9 1.0
CZ x:ARG42 5.0 100.3 1.0

Zinc binding site 8 out of 8 in 8wav

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Zinc binding site 8 out of 8 in the De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of De Novo Transcribing Complex 12 (TC12), the Early Elongation Complex with Pol II Positioned 12NT Downstream of Tss within 5.0Å range:
probe atom residue distance (Å) B Occ
z:Zn101

b:126.1
occ:1.00
 SG z:CYS39 2.3 150.7 1.0
SG z:CYS19 2.3 146.6 1.0
SG z:CYS22 2.3 145.8 1.0
SG z:CYS36 2.3 153.0 1.0
CB z:CYS19 2.8 146.6 1.0
CB z:CYS36 2.9 153.0 1.0
CB z:CYS39 3.4 150.7 1.0
CB z:CYS22 3.6 145.8 1.0
OG1 z:THR24 3.9 140.9 1.0
N z:CYS22 4.1 140.7 1.0
CA z:CYS19 4.3 135.2 1.0
CA z:CYS36 4.3 148.9 1.0
CA z:CYS22 4.4 140.7 1.0
O z:ARG37 4.5 150.1 1.0
CA z:CYS39 4.5 151.2 1.0
N z:CYS39 4.6 151.2 1.0
CB z:TYR41 4.7 143.2 1.0
C z:CYS36 4.8 148.9 1.0
CE z:MET44 4.8 136.6 1.0
O z:THR24 4.8 139.0 1.0
C z:CYS22 4.8 140.7 1.0
ND2 z:ASN26 4.8 139.2 1.0
N z:HIS23 4.9 140.8 1.0
N z:TYR41 4.9 145.1 1.0
N z:GLY40 4.9 148.8 1.0

Reference:

X.Chen, W.Liu, Q.Wang, X.Wang, Y.Ren, X.Qu, W.Li, Y.Xu. Structural Visualization of De Novo Transcription Initiation. Science.
ISSN: ESSN 1095-9203
Page generated: Thu Oct 31 13:17:16 2024

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