Zinc in PDB 8tvx: Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2)

Enzymatic activity of Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2)

All present enzymatic activity of Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2):
2.7.7.6;

Other elements in 8tvx:

The structure of Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2) (pdb code 8tvx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2), PDB code: 8tvx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8tvx

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Zinc binding site 1 out of 8 in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:265.6
occ:1.00
 HB2 A:CYS167 1.4 217.8 1.0
HB2 A:CYS110 2.0 204.8 1.0
CB A:CYS167 2.1 217.8 1.0
SG A:CYS167 2.3 217.8 1.0
HB3 A:CYS107 2.6 203.5 1.0
HB3 A:CYS167 2.7 217.8 1.0
O A:CYS107 2.7 203.5 1.0
H A:CYS167 2.7 217.8 1.0
SG A:CYS148 2.9 210.8 1.0
CB A:CYS110 2.9 204.8 1.0
HG A:CYS148 3.2 210.8 1.0
CA A:CYS167 3.2 217.8 1.0
N A:CYS167 3.3 217.8 1.0
HB3 A:CYS110 3.3 204.8 1.0
HG A:CYS110 3.5 204.8 1.0
CB A:CYS107 3.6 203.5 1.0
SG A:CYS110 3.6 204.8 1.0
OD1 A:ASN169 3.7 205.0 1.0
HE21 A:GLN171 3.7 203.8 1.0
C A:CYS107 3.7 203.5 1.0
H A:GLY168 3.8 209.7 1.0
HA A:CYS167 3.9 217.8 1.0
CA A:CYS110 4.0 204.8 1.0
HB2 A:CYS107 4.0 203.5 1.0
HB2 A:CYS148 4.0 210.8 1.0
HE22 A:GLN171 4.0 203.8 1.0
N A:CYS110 4.0 204.8 1.0
CB A:CYS148 4.1 210.8 1.0
O A:MET108 4.1 196.9 1.0
HA A:CYS110 4.1 204.8 1.0
C A:CYS167 4.2 217.8 1.0
NE2 A:GLN171 4.2 203.8 1.0
H A:CYS110 4.2 204.8 1.0
H A:ASN169 4.2 205.0 1.0
CA A:CYS107 4.2 203.5 1.0
N A:GLY168 4.2 209.7 1.0
HB3 A:CYS148 4.3 210.8 1.0
C A:HIS109 4.4 198.2 1.0
HA A:CYS107 4.5 203.5 1.0
O A:HIS109 4.5 198.2 1.0
SG A:CYS107 4.6 203.5 1.0
CG A:ASN169 4.6 205.0 1.0
C A:MET108 4.6 196.9 1.0
HG A:CYS107 4.6 203.5 1.0
C A:GLY166 4.6 213.2 1.0
HD21 A:ASN169 4.7 205.0 1.0
HB3 A:MET108 4.7 196.9 1.0
N A:MET108 4.8 196.9 1.0
H A:GLY166 5.0 213.2 1.0
HB2 A:HIS109 5.0 198.2 1.0

Zinc binding site 2 out of 8 in 8tvx

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Zinc binding site 2 out of 8 in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:218.9
occ:1.00
 O A:PRO78 2.1 155.6 1.0
HB3 A:CYS67 2.1 187.7 1.0
NE2 A:HIS80 2.3 162.2 1.0
SG A:CYS77 2.3 172.9 1.0
CE1 A:HIS80 2.9 162.2 1.0
O A:CYS67 3.0 187.7 1.0
HE1 A:HIS80 3.0 162.2 1.0
CB A:CYS67 3.1 187.7 1.0
CD2 A:HIS80 3.1 162.2 1.0
HA2 A:GLY79 3.2 161.1 1.0
C A:PRO78 3.3 155.6 1.0
HD2 A:HIS80 3.5 162.2 1.0
HB2 A:CYS67 3.5 187.7 1.0
HB2 A:CYS70 3.5 186.6 1.0
C A:CYS67 3.7 187.7 1.0
ND1 A:HIS80 3.8 162.2 1.0
CA A:CYS67 3.8 187.7 1.0
CA A:GLY79 3.9 161.1 1.0
HA A:CYS67 3.9 187.7 1.0
CG A:HIS80 4.0 162.2 1.0
CB A:CYS77 4.0 172.9 1.0
HA2 A:GLY59 4.0 171.5 1.0
N A:GLY79 4.0 161.1 1.0
SG A:CYS70 4.1 186.6 1.0
C A:GLY79 4.1 161.1 1.0
SG A:CYS67 4.2 187.7 1.0
CB A:CYS70 4.2 186.6 1.0
HB3 A:CYS77 4.2 172.9 1.0
HG A:CYS67 4.2 187.7 1.0
N A:PRO78 4.2 155.6 1.0
C A:CYS77 4.3 172.9 1.0
O A:GLY79 4.3 161.1 1.0
HB3 A:CYS70 4.3 186.6 1.0
CA A:PRO78 4.4 155.6 1.0
HD2 A:PRO78 4.4 155.6 1.0
HD1 A:HIS80 4.5 162.2 1.0
HB3 A:GLN68 4.5 179.5 1.0
O A:CYS77 4.5 172.9 1.0
HB2 A:CYS77 4.6 172.9 1.0
HG2 A:PRO78 4.6 155.6 1.0
CA A:CYS77 4.7 172.9 1.0
HA3 A:GLY79 4.7 161.1 1.0
N A:HIS80 4.8 162.2 1.0
HA A:CYS77 4.8 172.9 1.0
CD A:PRO78 4.8 155.6 1.0
H A:GLY79 4.9 161.1 1.0
N A:GLN68 4.9 179.5 1.0
CA A:GLY59 4.9 171.5 1.0
O A:LEU58 4.9 170.5 1.0
HA A:PRO78 5.0 155.6 1.0
H A:HIS80 5.0 162.2 1.0

Zinc binding site 3 out of 8 in 8tvx

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Zinc binding site 3 out of 8 in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:270.0
occ:1.00
 SG B:CYS1182 2.3 175.3 1.0
SG B:CYS1166 2.3 171.1 1.0
SG B:CYS1163 2.3 166.9 1.0
SG B:CYS1185 2.3 180.3 1.0
HB3 B:CYS1163 2.8 166.9 1.0
CB B:CYS1163 3.0 166.9 1.0
H B:CYS1166 3.0 171.1 1.0
HB2 B:CYS1185 3.0 180.3 1.0
HB2 B:CYS1163 3.0 166.9 1.0
CB B:CYS1185 3.3 180.3 1.0
HB3 B:CYS1182 3.4 175.3 1.0
HB B:ILE1165 3.4 175.5 1.0
CB B:CYS1182 3.5 175.3 1.0
HB3 B:CYS1166 3.5 171.1 1.0
CB B:CYS1166 3.5 171.1 1.0
N B:CYS1166 3.6 171.1 1.0
HB2 B:CYS1182 3.8 175.3 1.0
HB3 B:CYS1185 3.8 180.3 1.0
O B:CYS1166 4.0 171.1 1.0
CA B:CYS1166 4.1 171.1 1.0
HG1 B:THR1170 4.1 156.1 1.0
CB B:ILE1165 4.3 175.5 1.0
HB2 B:CYS1166 4.3 171.1 1.0
OG1 B:THR1170 4.4 156.1 1.0
CA B:CYS1163 4.5 166.9 1.0
H B:CYS1185 4.5 180.3 1.0
H B:ILE1165 4.5 175.5 1.0
HG22 B:ILE1165 4.5 175.5 1.0
C B:CYS1166 4.5 171.1 1.0
CA B:CYS1185 4.6 180.3 1.0
C B:ILE1165 4.6 175.5 1.0
N B:CYS1185 4.6 180.3 1.0
O B:CYS1182 4.7 175.3 1.0
HB3 B:ASN1187 4.8 175.7 1.0
CA B:CYS1182 4.8 175.3 1.0
CA B:ILE1165 4.8 175.5 1.0
N B:ILE1165 4.9 175.5 1.0
HA B:CYS1163 4.9 166.9 1.0
CG2 B:ILE1165 4.9 175.5 1.0
C B:CYS1163 4.9 166.9 1.0
HA B:CYS1166 5.0 171.1 1.0

Zinc binding site 4 out of 8 in 8tvx

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Zinc binding site 4 out of 8 in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:226.7
occ:1.00
 H C:CYS95 1.6 155.7 1.0
O C:CYS92 2.1 166.2 1.0
N C:CYS95 2.2 155.7 1.0
H C:CYS92 2.3 166.2 1.0
SG C:CYS92 2.4 166.2 1.0
SG C:CYS95 2.4 155.7 1.0
C C:CYS92 2.6 166.2 1.0
H C:LYS94 2.8 153.2 1.0
N C:CYS92 2.8 166.2 1.0
CA C:CYS95 2.9 155.7 1.0
CA C:CYS92 3.0 166.2 1.0
CB C:CYS95 3.0 155.7 1.0
N C:LYS94 3.1 153.2 1.0
HB3 C:CYS95 3.1 155.7 1.0
C C:LYS94 3.2 153.2 1.0
HB2 C:LYS94 3.2 153.2 1.0
CB C:CYS92 3.2 166.2 1.0
H C:SER96 3.3 141.6 1.0
HG C:SER96 3.4 141.6 1.0
SG C:CYS88 3.4 161.2 1.0
C C:CYS95 3.5 155.7 1.0
CA C:LYS94 3.5 153.2 1.0
N C:ASP93 3.6 149.6 1.0
N C:SER96 3.6 141.6 1.0
HB3 C:CYS92 3.7 166.2 1.0
SG C:CYS86 3.7 146.4 1.0
C C:ASP93 3.8 149.6 1.0
CB C:LYS94 3.8 153.2 1.0
HA C:CYS95 3.8 155.7 1.0
HB2 C:CYS92 3.9 166.2 1.0
HB2 C:CYS95 3.9 155.7 1.0
HA C:CYS92 3.9 166.2 1.0
C C:HIS91 4.0 147.6 1.0
HA C:HIS91 4.1 147.6 1.0
H C:ASP93 4.1 149.6 1.0
CA C:ASP93 4.2 149.6 1.0
OG C:SER96 4.2 141.6 1.0
O C:LYS94 4.2 153.2 1.0
O C:CYS95 4.3 155.7 1.0
HB3 C:SER96 4.4 141.6 1.0
HB3 C:LYS94 4.4 153.2 1.0
HA C:LYS94 4.4 153.2 1.0
HB3 C:CYS86 4.4 146.4 1.0
HA C:ASP93 4.5 149.6 1.0
HB3 C:CYS88 4.5 161.2 1.0
HB2 C:CYS86 4.5 146.4 1.0
CB C:CYS86 4.5 146.4 1.0
CA C:HIS91 4.6 147.6 1.0
O C:ASP93 4.6 149.6 1.0
HB2 C:HIS91 4.6 147.6 1.0
CB C:SER96 4.6 141.6 1.0
CB C:CYS88 4.7 161.2 1.0
CA C:SER96 4.7 141.6 1.0
HG3 C:LYS94 4.8 153.2 1.0
O C:HIS91 4.9 147.6 1.0
CG C:LYS94 4.9 153.2 1.0
HB2 C:CYS88 5.0 161.2 1.0

Zinc binding site 5 out of 8 in 8tvx

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Zinc binding site 5 out of 8 in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:340.2
occ:1.00
 O I:THR31 2.3 263.2 1.0
C I:THR31 3.4 263.2 1.0
CB I:CYS10 3.5 272.9 1.0
CA I:CYS32 3.7 270.8 1.0
CB I:CYS7 3.9 269.8 1.0
N I:CYS10 4.0 272.9 1.0
N I:CYS32 4.0 270.8 1.0
C I:ASP9 4.2 272.7 1.0
CA I:CYS10 4.3 272.9 1.0
CB I:ASP9 4.3 272.7 1.0
CB I:CYS32 4.3 270.8 1.0
N I:ASP9 4.5 272.7 1.0
CB I:THR31 4.6 263.2 1.0
CA I:ASP9 4.6 272.7 1.0
CA I:THR31 4.6 263.2 1.0
O I:ASP9 4.6 272.7 1.0
N I:SER33 4.8 262.0 1.0
C I:CYS32 4.9 270.8 1.0

Zinc binding site 6 out of 8 in 8tvx

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Zinc binding site 6 out of 8 in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:330.1
occ:1.00
 H I:CYS106 1.9 270.8 1.0
OG I:SER105 2.0 264.1 1.0
N I:CYS106 2.2 270.8 1.0
SG I:CYS78 2.4 255.2 1.0
SG I:CYS106 2.4 270.8 1.0
SG I:CYS103 2.4 260.0 1.0
HB3 I:CYS106 2.5 270.8 1.0
CB I:CYS106 2.7 270.8 1.0
HG I:CYS75 2.9 253.7 1.0
HB3 I:CYS103 2.9 260.0 1.0
CA I:CYS106 2.9 270.8 1.0
C I:SER105 3.0 264.1 1.0
HB2 I:CYS78 3.1 255.2 1.0
CB I:SER105 3.1 264.1 1.0
CB I:CYS103 3.2 260.0 1.0
CB I:CYS78 3.3 255.2 1.0
CA I:SER105 3.4 264.1 1.0
H I:SER105 3.4 264.1 1.0
HB2 I:SER105 3.6 264.1 1.0
HB3 I:CYS78 3.6 255.2 1.0
HB2 I:CYS106 3.6 270.8 1.0
N I:SER105 3.6 264.1 1.0
HA I:CYS106 3.7 270.8 1.0
O I:CYS103 3.7 260.0 1.0
H I:SER107 3.7 248.3 1.0
C I:CYS106 3.8 270.8 1.0
HB3 I:SER105 3.9 264.1 1.0
O I:SER105 3.9 264.1 1.0
HB2 I:CYS103 3.9 260.0 1.0
H I:HIS108 3.9 243.9 1.0
N I:SER107 4.0 248.3 1.0
SG I:CYS75 4.0 253.7 1.0
C I:CYS103 4.1 260.0 1.0
HB3 I:HIS108 4.2 243.9 1.0
CA I:CYS103 4.3 260.0 1.0
HA I:SER105 4.3 264.1 1.0
H I:CYS78 4.3 255.2 1.0
HB2 I:CYS75 4.6 253.7 1.0
C I:LEU104 4.6 234.3 1.0
O I:CYS106 4.7 270.8 1.0
CA I:CYS78 4.7 255.2 1.0
HB3 I:CYS75 4.7 253.7 1.0
N I:HIS108 4.7 243.9 1.0
CB I:CYS75 4.8 253.7 1.0
HA I:CYS103 4.8 260.0 1.0
N I:LEU104 4.8 234.3 1.0
HB2 I:HIS108 4.9 243.9 1.0
N I:CYS78 4.9 255.2 1.0
CB I:HIS108 4.9 243.9 1.0

Zinc binding site 7 out of 8 in 8tvx

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Zinc binding site 7 out of 8 in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:196.1
occ:1.00
 SG J:CYS45 2.3 108.5 1.0
SG J:CYS10 2.3 111.4 1.0
SG J:CYS46 2.3 111.7 1.0
SG J:CYS7 2.3 107.0 1.0
HB2 J:CYS10 2.5 111.4 1.0
CB J:CYS10 2.9 111.4 1.0
H J:CYS10 3.0 111.4 1.0
HE J:ARG43 3.2 107.9 1.0
H J:CYS46 3.3 111.7 1.0
N J:CYS46 3.4 111.7 1.0
OG J:SER9 3.5 103.6 1.0
HB2 J:CYS7 3.5 107.0 1.0
HH21 J:ARG43 3.5 107.9 1.0
CB J:CYS7 3.5 107.0 1.0
HA J:CYS46 3.5 111.7 1.0
HG J:SER9 3.6 103.6 1.0
HB3 J:CYS10 3.6 111.4 1.0
CB J:CYS46 3.6 111.7 1.0
N J:CYS10 3.7 111.4 1.0
HB3 J:CYS7 3.7 107.0 1.0
CA J:CYS46 3.7 111.7 1.0
CB J:CYS45 3.8 108.5 1.0
HB2 J:CYS45 3.8 108.5 1.0
CA J:CYS10 3.9 111.4 1.0
C J:CYS45 3.9 108.5 1.0
HE1 J:MET49 4.0 102.7 1.0
NE J:ARG43 4.1 107.9 1.0
HB2 J:CYS46 4.1 111.7 1.0
HB2 J:ARG43 4.1 107.9 1.0
HB3 J:LYS12 4.2 105.3 1.0
NH2 J:ARG43 4.3 107.9 1.0
HB3 J:CYS46 4.3 111.7 1.0
HA J:CYS10 4.4 111.4 1.0
HB3 J:CYS45 4.5 108.5 1.0
CA J:CYS45 4.5 108.5 1.0
O J:CYS45 4.5 108.5 1.0
HB3 J:ARG43 4.6 107.9 1.0
H J:LYS12 4.6 105.3 1.0
CZ J:ARG43 4.7 107.9 1.0
H J:SER9 4.7 103.6 1.0
CB J:ARG43 4.8 107.9 1.0
H J:GLY11 4.8 103.8 1.0
CB J:SER9 4.8 103.6 1.0
CE J:MET49 4.8 102.7 1.0
HB2 J:LYS12 4.9 105.3 1.0
HD2 J:ARG43 4.9 107.9 1.0
C J:SER9 4.9 103.6 1.0
CA J:CYS7 4.9 107.0 1.0
HE2 J:MET49 4.9 102.7 1.0
HH22 J:ARG43 5.0 107.9 1.0
CB J:LYS12 5.0 105.3 1.0

Zinc binding site 8 out of 8 in 8tvx

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Zinc binding site 8 out of 8 in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:251.6
occ:1.00
 HB2 L:CYS34 1.7 200.8 1.0
O L:CYS31 1.9 193.4 1.0
H L:CYS34 1.9 200.8 1.0
N L:CYS34 2.1 200.8 1.0
SG L:CYS51 2.2 191.8 1.0
CB L:CYS34 2.3 200.8 1.0
CA L:CYS34 2.5 200.8 1.0
O L:ALA32 2.6 175.6 1.0
C L:CYS31 2.6 193.4 1.0
SG L:CYS31 2.6 193.4 1.0
HB3 L:CYS31 2.9 193.4 1.0
C L:ALA32 2.9 175.6 1.0
SG L:CYS34 2.9 200.8 1.0
C L:GLU33 2.9 180.6 1.0
CB L:CYS31 3.1 193.4 1.0
O L:CYS34 3.1 200.8 1.0
HB3 L:CYS34 3.2 200.8 1.0
C L:CYS34 3.2 200.8 1.0
N L:GLU33 3.3 180.6 1.0
HA L:CYS34 3.4 200.8 1.0
CA L:CYS31 3.4 193.4 1.0
N L:ALA32 3.4 175.6 1.0
CA L:GLU33 3.6 180.6 1.0
HB2 L:GLU33 3.6 180.6 1.0
O L:GLU33 3.7 180.6 1.0
CA L:ALA32 3.7 175.6 1.0
CB L:CYS51 3.8 191.8 1.0
HA L:CYS31 4.0 193.4 1.0
H L:GLU33 4.0 180.6 1.0
HB2 L:CYS31 4.0 193.4 1.0
HB3 L:CYS51 4.0 191.8 1.0
HA L:ALA32 4.0 175.6 1.0
HB2 L:CYS51 4.1 191.8 1.0
CB L:GLU33 4.1 180.6 1.0
H L:ALA32 4.1 175.6 1.0
HA L:GLU33 4.4 180.6 1.0
OG L:SER36 4.4 195.0 1.0
N L:SER35 4.5 197.6 1.0
N L:CYS31 4.5 193.4 1.0
H L:SER36 4.5 195.0 1.0
HG L:SER36 4.7 195.0 1.0
H L:CYS31 4.7 193.4 1.0
HB3 L:GLU33 4.8 180.6 1.0
HG2 L:GLU33 4.9 180.6 1.0
H L:SER35 4.9 197.6 1.0
O L:SER36 4.9 195.0 1.0

Reference:

R.D.Sarsam, J.Xu, I.Lahiri, W.Gong, Q.Li, J.Oh, Z.Zhou, P.Hou, J.Chong, N.Hao, S.Li, D.Wang, A.E.Leschziner. ELF1 Promotes RAD26'S Interaction with Lesion-Arrested Pol II For Transcription-Coupled Repair. Proc.Natl.Acad.Sci.Usa V. 121 45121 2024.
ISSN: ESSN 1091-6490
PubMed: 38194460
DOI: 10.1073/PNAS.2314245121
Page generated: Thu Oct 31 11:52:58 2024

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