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Zinc in PDB 6ir9: Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome

Enzymatic activity of Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome

All present enzymatic activity of Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome:
2.7.7.6;

Other elements in 6ir9:

The structure of Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome (pdb code 6ir9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome, PDB code: 6ir9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 6ir9

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Zinc binding site 1 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:96.9
occ:1.00
 NE2 A:HIS80 2.1 61.9 1.0
SG A:CYS70 2.4 94.7 1.0
SG A:CYS77 2.4 74.5 1.0
SG A:CYS67 2.4 0.2 1.0
CD2 A:HIS80 3.1 61.9 1.0
CE1 A:HIS80 3.1 61.9 1.0
CB A:CYS67 3.2 0.2 1.0
CB A:CYS70 3.4 94.7 1.0
CB A:CYS77 3.7 74.5 1.0
N A:CYS70 3.8 94.7 1.0
ND1 A:HIS80 4.2 61.9 1.0
CG A:HIS80 4.2 61.9 1.0
CA A:CYS70 4.2 94.7 1.0
CA A:CYS77 4.4 74.5 1.0
N A:GLY79 4.6 63.4 1.0
CD A:PRO78 4.6 62.1 1.0
CB A:THR69 4.6 85.3 1.0
CA A:CYS67 4.7 0.2 1.0
C A:THR69 4.8 85.3 1.0
C A:CYS77 4.9 74.5 1.0
N A:PRO78 4.9 62.1 1.0

Zinc binding site 2 out of 10 in 6ir9

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Zinc binding site 2 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:0.5
occ:1.00
 SG A:CYS110 2.5 0.4 1.0
SG A:CYS107 2.5 0.7 1.0
N A:CYS110 2.7 0.4 1.0
CB A:CYS168 2.8 0.4 1.0
SG A:CYS168 3.0 0.4 1.0
CB A:CYS110 3.0 0.4 1.0
CB A:ASN109 3.1 0.4 1.0
CA A:CYS110 3.4 0.4 1.0
C A:ASN109 3.5 0.4 1.0
N A:CYS168 3.6 0.4 1.0
CA A:ASN109 3.7 0.4 1.0
CG A:ASN109 3.8 0.4 1.0
CA A:CYS168 3.8 0.4 1.0
CB A:CYS107 3.9 0.7 1.0
ND2 A:ASN109 4.0 0.4 1.0
N A:ASN109 4.0 0.4 1.0
C A:GLY167 4.3 0.2 1.0
C A:CYS110 4.4 0.4 1.0
O A:ASN109 4.5 0.4 1.0
N A:GLY111 4.5 0.2 1.0
OD1 A:ASN109 4.6 0.4 1.0
CA A:GLY167 4.7 0.2 1.0
O A:GLY166 4.7 0.2 1.0
C A:CYS168 4.9 0.4 1.0

Zinc binding site 3 out of 10 in 6ir9

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Zinc binding site 3 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.8
occ:1.00
 SG B:CYS1185 2.4 0.6 1.0
SG B:CYS1163 2.4 76.1 1.0
SG B:CYS1182 2.4 0.4 1.0
SG B:CYS1166 2.4 77.9 1.0
CB B:CYS1163 3.0 76.1 1.0
CB B:CYS1166 3.3 77.9 1.0
CB B:CYS1185 3.3 0.6 1.0
CB B:CYS1182 3.6 0.4 1.0
N B:CYS1166 3.8 77.9 1.0
N B:CYS1185 4.0 0.6 1.0
CA B:CYS1166 4.1 77.9 1.0
CA B:CYS1185 4.3 0.6 1.0
OG B:SER1170 4.4 77.3 1.0
CA B:CYS1163 4.5 76.1 1.0
CB B:ILE1165 4.7 81.2 1.0
CB B:SER1184 4.8 0.3 1.0
C B:CYS1166 4.8 77.9 1.0
C B:ILE1165 4.9 81.2 1.0
CA B:CYS1182 5.0 0.4 1.0
N B:GLY1167 5.0 72.9 1.0
C B:SER1184 5.0 0.3 1.0
C B:CYS1163 5.0 76.1 1.0

Zinc binding site 4 out of 10 in 6ir9

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Zinc binding site 4 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:0.4
occ:1.00
 SG C:CYS91 2.6 0.1 1.0
SG C:CYS94 2.6 0.1 1.0
CB C:CYS94 2.8 0.1 1.0
SG C:CYS85 2.9 0.1 1.0
N C:CYS94 3.0 0.1 1.0
SG C:CYS87 3.4 0.8 1.0
CA C:CYS94 3.5 0.1 1.0
C C:GLU93 3.6 0.7 1.0
CB C:GLU93 3.7 0.7 1.0
CB C:CYS85 3.8 0.1 1.0
CB C:CYS91 4.0 0.1 1.0
N C:GLU93 4.0 0.7 1.0
CA C:GLU93 4.0 0.7 1.0
N C:CYS91 4.3 0.1 1.0
O C:GLU93 4.4 0.7 1.0
CB C:CYS87 4.5 0.8 1.0
CA C:CYS91 4.5 0.1 1.0
C C:CYS91 4.5 0.1 1.0
O C:CYS91 4.5 0.1 1.0
C C:CYS94 4.6 0.1 1.0
CG C:GLU93 4.8 0.7 1.0
OE1 C:GLU93 4.8 0.7 1.0
N C:ASP92 5.0 0.3 1.0

Zinc binding site 5 out of 10 in 6ir9

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Zinc binding site 5 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.9
occ:1.00
 SG I:CYS103 2.5 0.6 1.0
N I:CYS106 2.6 0.9 1.0
SG I:CYS78 2.7 0.6 1.0
CB I:ASN105 2.9 0.3 1.0
SG I:CYS106 3.2 0.9 1.0
SG I:CYS75 3.3 0.7 1.0
CB I:CYS106 3.4 0.9 1.0
C I:ASN105 3.5 0.3 1.0
CA I:ASN105 3.5 0.3 1.0
CB I:CYS103 3.5 0.6 1.0
CA I:CYS106 3.6 0.9 1.0
CB I:CYS78 3.6 0.6 1.0
N I:ASN105 3.7 0.3 1.0
CG I:ASN105 3.8 0.3 1.0
N I:CYS78 4.2 0.6 1.0
OD1 I:ASN105 4.2 0.3 1.0
CB I:CYS75 4.2 0.7 1.0
CA I:CYS78 4.5 0.6 1.0
C I:CYS106 4.6 0.9 1.0
CB I:GLU77 4.6 0.2 1.0
O I:ASN105 4.6 0.3 1.0
N I:LYS107 4.7 0.8 1.0
ND2 I:ASN105 4.7 0.3 1.0
CA I:CYS103 4.8 0.6 1.0
C I:CYS103 4.8 0.6 1.0
O I:CYS103 4.9 0.6 1.0

Zinc binding site 6 out of 10 in 6ir9

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Zinc binding site 6 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.8
occ:1.00
 SG I:CYS29 2.6 0.7 1.0
CB I:CYS10 2.6 0.8 1.0
SG I:CYS32 2.7 0.6 1.0
SG I:CYS10 3.0 0.8 1.0
CB I:CYS32 3.4 0.6 1.0
N I:CYS32 3.6 0.6 1.0
CB I:CYS29 3.8 0.7 1.0
SG I:CYS7 3.9 0.6 1.0
CA I:CYS32 4.1 0.6 1.0
CA I:CYS10 4.1 0.8 1.0
C I:ASN31 4.1 0.3 1.0
CB I:ASN31 4.3 0.3 1.0
CB I:CYS7 4.3 0.6 1.0
N I:ASN31 4.5 0.3 1.0
CA I:ASN31 4.5 0.3 1.0
N I:CYS10 4.6 0.8 1.0
C I:CYS32 4.7 0.6 1.0
O I:ASN31 4.8 0.3 1.0
C I:CYS10 4.9 0.8 1.0
O I:CYS32 4.9 0.6 1.0
CB I:ASN12 5.0 0.3 1.0

Zinc binding site 7 out of 10 in 6ir9

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Zinc binding site 7 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:68.2
occ:1.00
 N J:CYS45 2.2 40.5 1.0
SG J:CYS7 2.4 34.6 1.0
SG J:CYS45 2.4 40.5 1.0
SG J:CYS44 2.5 41.0 1.0
CA J:CYS45 2.6 40.5 1.0
C J:CYS44 2.7 41.0 1.0
SG J:CYS10 2.9 33.6 1.0
CB J:CYS45 2.9 40.5 1.0
CB J:CYS44 3.1 41.0 1.0
O J:CYS44 3.2 41.0 1.0
CB J:CYS7 3.3 34.6 1.0
CA J:CYS44 3.4 41.0 1.0
C J:CYS45 4.1 40.5 1.0
CB J:CYS10 4.2 33.6 1.0
N J:CYS44 4.2 41.0 1.0
N J:CYS10 4.5 33.6 1.0
O J:ARG42 4.7 36.8 1.0
CA J:CYS7 4.8 34.6 1.0
N J:ARG46 4.8 37.0 1.0
O J:CYS45 4.8 40.5 1.0
NE J:ARG42 4.9 36.8 1.0
CA J:CYS10 5.0 33.6 1.0

Zinc binding site 8 out of 10 in 6ir9

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Zinc binding site 8 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.6
occ:1.00
 SG L:CYS50 2.4 0.6 1.0
SG L:CYS53 2.5 0.7 1.0
SG L:CYS33 2.5 0.6 1.0
SG L:CYS36 2.5 0.3 1.0
CB L:CYS36 3.3 0.3 1.0
N L:CYS53 3.3 0.7 1.0
CB L:CYS50 3.4 0.6 1.0
CB L:CYS33 3.4 0.6 1.0
CB L:CYS53 3.5 0.7 1.0
CB L:GLU52 3.6 0.4 1.0
N L:CYS36 3.9 0.3 1.0
CA L:CYS53 4.0 0.7 1.0
CA L:CYS36 4.2 0.3 1.0
C L:GLU52 4.2 0.4 1.0
CA L:GLU52 4.3 0.4 1.0
N L:GLU52 4.4 0.4 1.0
CG L:GLU52 4.7 0.4 1.0
C L:CYS53 4.7 0.7 1.0
CA L:CYS50 4.7 0.6 1.0
C L:CYS36 4.8 0.3 1.0
CB L:ALA35 4.8 0.1 1.0
N L:GLY54 4.8 0.2 1.0
CA L:CYS33 4.8 0.6 1.0
CB L:HIS38 4.9 0.1 1.0
CB L:HIS55 4.9 0.3 1.0
N L:ALA37 4.9 0.2 1.0
C L:ALA35 5.0 0.1 1.0

Zinc binding site 9 out of 10 in 6ir9

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Zinc binding site 9 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:0.7
occ:1.00
 SG M:CYS52 2.2 0.4 1.0
SG M:CYS25 2.3 0.3 1.0
SG M:CYS49 2.3 0.6 1.0
SG M:CYS28 2.9 0.8 1.0
CB M:CYS49 2.9 0.7 1.0
CD2 M:LEU54 3.1 30.0 1.0
CB M:CYS25 3.3 0.5 1.0
CG M:LEU54 3.5 30.0 1.0
CB M:CYS28 3.7 1.0 1.0
CB M:CYS52 3.7 0.1 1.0
N M:CYS28 4.1 0.5 1.0
N M:CYS52 4.1 1.0 1.0
CA M:CYS52 4.4 0.6 1.0
CA M:CYS49 4.4 0.4 1.0
CA M:CYS28 4.5 0.3 1.0
CB M:LEU54 4.5 30.0 1.0
CD1 M:LEU54 4.5 30.0 1.0
N M:ASN53 4.7 0.1 1.0
CA M:CYS25 4.7 0.7 1.0
N M:LEU54 4.7 0.6 1.0
C M:CYS52 4.7 0.3 1.0
CB M:PHE27 4.9 0.7 1.0

Zinc binding site 10 out of 10 in 6ir9

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Zinc binding site 10 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Zn300

b:17.1
occ:1.00
 SG V:CYS12 2.2 34.8 1.0
SG V:CYS15 2.3 22.8 1.0
SG V:CYS29 2.4 18.0 1.0
SG V:CYS32 2.4 25.4 1.0
CB V:CYS12 3.0 14.9 1.0
CB V:CYS15 3.1 14.4 1.0
CB V:CYS32 3.3 17.2 1.0
N V:CYS15 3.5 15.3 1.0
CB V:CYS29 3.5 17.4 1.0
CA V:CYS15 3.8 14.2 1.0
N V:CYS32 4.2 16.6 1.0
CB V:ASN31 4.3 15.9 1.0
CB V:LEU14 4.4 13.2 1.0
CA V:CYS32 4.4 17.2 1.0
CG2 V:ILE17 4.4 11.7 1.0
CA V:CYS12 4.5 13.8 1.0
C V:LEU14 4.5 18.1 1.0
C V:CYS15 4.6 17.6 1.0
N V:GLY16 4.6 14.7 1.0
N V:LEU14 4.7 17.1 1.0
CD1 V:LEU36 4.7 19.9 1.0
CA V:LEU14 4.8 17.6 1.0
CA V:CYS29 4.9 18.3 1.0
C V:ASN31 4.9 16.7 1.0
C V:CYS12 4.9 16.8 1.0
ND2 V:ASN31 4.9 14.9 1.0
CA V:ASN31 5.0 14.6 1.0

Reference:

H.Ehara, T.Kujirai, Y.Fujino, M.Shirouzu, H.Kurumizaka, S.I.Sekine. Structural Insight Into Nucleosome Transcription By Rna Polymerase II with Elongation Factors. Science V. 363 744 2019.
ISSN: ESSN 1095-9203
PubMed: 30733384
DOI: 10.1126/SCIENCE.AAV8912
Page generated: Tue Oct 29 00:01:48 2024

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