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Zinc in PDB 9mu8: Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk

Enzymatic activity of Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk

All present enzymatic activity of Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk:
2.7.7.6;

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk (pdb code 9mu8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk, PDB code: 9mu8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 9mu8

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Zinc binding site 1 out of 8 in the Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1501

b:127.7
occ:1.00
 NE2 A:HIS80 2.1 102.7 1.0
SG A:CYS77 2.3 107.4 1.0
SG A:CYS70 2.3 113.5 1.0
SG A:CYS67 2.3 112.7 1.0
CE1 A:HIS80 2.8 99.0 1.0
CB A:CYS67 3.0 107.9 1.0
CD2 A:HIS80 3.1 98.7 1.0
CB A:CYS77 3.5 101.3 1.0
CB A:CYS70 3.5 108.6 1.0
N A:CYS70 3.8 105.5 1.0
ND1 A:HIS80 3.9 93.1 1.0
CG A:HIS80 4.1 93.0 1.0
CA A:CYS77 4.2 100.6 1.0
CA A:CYS70 4.2 105.8 1.0
CA A:GLY59 4.5 98.0 1.0
CA A:CYS67 4.5 108.0 1.0
N A:GLY79 4.6 95.4 1.0
CD A:PRO78 4.6 97.0 1.0
CB A:THR69 4.6 99.6 1.0
O A:GLN58 4.8 98.1 1.0
C A:CYS70 4.8 106.5 1.0
C A:CYS77 4.9 98.1 1.0
C A:THR69 4.9 104.0 1.0
N A:PRO78 4.9 94.9 1.0
CA A:GLY79 5.0 91.9 1.0
N A:ALA71 5.0 105.1 1.0

Zinc binding site 2 out of 8 in 9mu8

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Zinc binding site 2 out of 8 in the Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1502

b:177.9
occ:1.00
 SG A:CYS107 2.3 149.1 1.0
SG A:CYS110 2.3 156.4 1.0
SG A:CYS150 2.3 171.4 1.0
SG A:CYS176 2.3 163.6 1.0
CB A:CYS107 3.1 137.7 1.0
CB A:CYS150 3.3 160.8 1.0
CB A:CYS110 3.4 147.5 1.0
CB A:CYS176 3.5 163.7 1.0
N A:CYS176 3.7 167.7 1.0
N A:CYS110 3.8 140.6 1.0
CA A:CYS176 4.2 165.6 1.0
CA A:CYS110 4.2 143.2 1.0
NE2 A:GLN180 4.5 148.6 1.0
CA A:CYS107 4.6 131.9 1.0
C A:GLY175 4.7 170.7 1.0
CA A:CYS150 4.7 161.6 1.0
CA A:GLY175 4.8 177.8 1.0
C A:CYS176 4.9 162.5 1.0
C A:CYS110 4.9 141.5 1.0
CB A:TYR109 4.9 138.2 1.0
N A:GLY177 4.9 162.1 1.0
C A:TYR109 4.9 137.0 1.0
N A:TYR109 5.0 133.8 1.0

Zinc binding site 3 out of 8 in 9mu8

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Zinc binding site 3 out of 8 in the Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:162.2
occ:1.00
 SG B:CYS1124 2.3 124.4 1.0
SG B:CYS1139 2.3 132.9 1.0
SG B:CYS1142 2.3 130.6 1.0
SG B:CYS1121 2.3 123.4 1.0
CB B:CYS1121 2.8 110.0 1.0
CB B:CYS1124 2.8 111.2 1.0
CB B:CYS1142 3.1 125.6 1.0
CB B:CYS1139 3.5 120.8 1.0
N B:CYS1124 3.7 107.8 1.0
CA B:CYS1124 3.8 106.1 1.0
N B:CYS1142 4.2 126.0 1.0
CA B:CYS1142 4.2 124.7 1.0
CA B:CYS1121 4.3 102.3 1.0
C B:CYS1124 4.7 103.1 1.0
C B:CYS1121 4.8 103.0 1.0
C B:GLY1141 4.8 127.8 1.0
C B:PHE1123 4.8 108.6 1.0
N B:GLY1125 4.8 102.6 1.0
CA B:CYS1139 4.9 118.7 1.0

Zinc binding site 4 out of 8 in 9mu8

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Zinc binding site 4 out of 8 in the Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:181.2
occ:1.00
 CB C:CYS97 2.0 135.3 1.0
SG C:CYS90 2.3 148.8 1.0
SG C:CYS88 2.3 156.1 1.0
SG C:CYS94 2.3 139.2 1.0
SG C:CYS97 2.3 140.7 1.0
CB C:CYS88 2.8 144.6 1.0
CA C:CYS97 3.4 123.1 1.0
CB C:CYS90 3.7 144.2 1.0
CB C:CYS94 3.8 127.3 1.0
N C:CYS97 4.0 124.6 1.0
N C:CYS94 4.1 125.9 1.0
CA C:CYS88 4.3 140.4 1.0
CA C:CYS94 4.4 124.4 1.0
C C:CYS97 4.5 114.9 1.0
O C:CYS94 4.5 122.5 1.0
C C:GLU96 4.5 122.1 1.0
O C:GLU96 4.7 121.3 1.0
O C:TYR84 4.8 127.9 1.0
C C:CYS94 4.8 121.5 1.0
CA C:CYS90 4.9 146.3 1.0
N C:CYS90 4.9 147.0 1.0

Zinc binding site 5 out of 8 in 9mu8

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Zinc binding site 5 out of 8 in the Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:164.8
occ:1.00
 CB I:CYS46 1.9 131.1 1.0
SG I:CYS21 2.3 116.1 1.0
SG I:CYS24 2.3 123.5 1.0
SG I:CYS43 2.3 134.4 1.0
SG I:CYS46 2.3 123.2 1.0
CB I:CYS21 3.3 104.9 1.0
CA I:CYS46 3.4 122.3 1.0
CB I:CYS43 3.4 117.7 1.0
CB I:CYS24 3.9 109.3 1.0
N I:CYS46 3.9 119.8 1.0
N I:CYS24 3.9 108.1 1.0
C I:CYS46 4.2 119.2 1.0
CB I:TYR48 4.3 116.2 1.0
CB I:GLU23 4.3 117.9 1.0
N I:ASP47 4.4 114.7 1.0
CA I:CYS24 4.5 105.1 1.0
N I:TYR48 4.5 110.4 1.0
C I:GLU23 4.7 110.2 1.0
CA I:CYS21 4.7 102.8 1.0
N I:GLU23 4.8 109.3 1.0
C I:ASN45 4.8 116.2 1.0
CA I:GLU23 4.9 110.9 1.0
CA I:CYS43 4.9 110.5 1.0
CB I:ASN26 5.0 103.2 1.0
CG I:GLU23 5.0 121.5 1.0

Zinc binding site 6 out of 8 in 9mu8

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Zinc binding site 6 out of 8 in the Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:143.0
occ:1.00
 SG I:CYS93 2.3 119.3 1.0
SG I:CYS123 2.3 116.7 1.0
SG I:CYS118 2.3 111.7 1.0
SG I:CYS90 2.3 112.8 1.0
CB I:CYS123 3.2 110.4 1.0
CB I:CYS118 3.2 94.9 1.0
CB I:CYS90 3.2 102.1 1.0
CB I:CYS93 3.4 113.0 1.0
N I:CYS93 3.7 108.1 1.0
CA I:CYS93 4.1 112.4 1.0
CB I:HIS125 4.2 86.1 1.0
CB I:HIS95 4.4 101.4 1.0
N I:HIS125 4.5 93.1 1.0
CA I:CYS123 4.6 105.9 1.0
C I:CYS93 4.6 113.8 1.0
CB I:ASN120 4.6 100.7 1.0
CB I:LYS92 4.6 93.9 1.0
CA I:CYS118 4.7 83.1 1.0
CA I:CYS90 4.7 99.0 1.0
N I:HIS95 4.7 106.1 1.0
N I:THR124 4.7 95.3 1.0
N I:SER94 4.8 108.9 1.0
C I:LYS92 4.8 103.5 1.0
C I:CYS123 4.9 100.4 1.0

Zinc binding site 7 out of 8 in 9mu8

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Zinc binding site 7 out of 8 in the Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:152.5
occ:1.00
 CB J:CYS10 2.0 104.5 1.0
SG J:CYS45 2.3 115.3 1.0
SG J:CYS44 2.3 124.4 1.0
SG J:CYS7 2.3 109.3 1.0
SG J:CYS10 2.3 120.0 1.0
CB J:CYS7 3.2 91.9 1.0
CA J:CYS10 3.4 88.8 1.0
N J:CYS45 3.6 96.6 1.0
CB J:CYS45 3.7 97.0 1.0
CB J:CYS44 3.8 95.5 1.0
C J:CYS44 3.9 94.5 1.0
CA J:CYS45 3.9 93.6 1.0
N J:CYS10 3.9 91.2 1.0
C J:CYS10 4.2 90.2 1.0
O J:CYS44 4.3 95.0 1.0
OG1 J:THR9 4.3 105.3 1.0
CB J:LYS12 4.4 88.9 1.0
CA J:CYS44 4.5 92.2 1.0
N J:GLY11 4.5 87.7 1.0
N J:LYS12 4.6 89.6 1.0
CA J:CYS7 4.7 86.6 1.0
CZ J:ARG42 4.8 117.2 1.0
NH1 J:ARG42 5.0 122.1 1.0
NE J:ARG42 5.0 111.1 1.0
O J:CYS10 5.0 97.6 1.0

Zinc binding site 8 out of 8 in 9mu8

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Zinc binding site 8 out of 8 in the Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of A Native Drosophila Melanogaster Pol II Elongation Complex Without RPB4/RPB7 Stalk within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn201

b:143.1
occ:1.00
 SG L:CYS38 2.3 132.3 1.0
SG L:CYS21 2.3 120.7 1.0
SG L:CYS35 2.3 119.5 1.0
SG L:CYS18 2.3 117.9 1.0
CB L:CYS21 2.9 106.6 1.0
CB L:CYS38 3.3 120.1 1.0
CB L:CYS35 3.3 109.2 1.0
CB L:CYS18 3.5 103.1 1.0
N L:CYS38 3.7 115.8 1.0
N L:CYS21 3.8 107.2 1.0
CA L:CYS21 3.9 107.0 1.0
CA L:CYS38 4.0 116.5 1.0
N L:GLY39 4.3 110.9 1.0
CB L:TYR40 4.4 100.6 1.0
C L:CYS38 4.5 113.8 1.0
CG L:GLU20 4.5 113.6 1.0
N L:TYR40 4.6 108.2 1.0
CA L:CYS35 4.7 108.7 1.0
C L:GLU37 4.7 115.4 1.0
CA L:CYS18 4.9 91.7 1.0
C L:GLU20 4.9 109.3 1.0
CB L:GLU37 4.9 113.8 1.0

Reference:

N.L.Venette-Smith, R.K.Vishwakarma, R.Dollinger, J.Schultz, V.Venkatakrishnan, P.Babitzke, G.Anand, D.S.Gilmour, J.-P.Armache, K.Murakami. Structural Characterization of Native Rna Polymerase II Transcription Complexes in Drosophila Melanogaster To Be Published.
Page generated: Fri Aug 22 18:43:48 2025

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