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Zinc in PDB 6j4y: Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome (+1B)

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

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

Other elements in 6j4y:

The structure of Rna Polymerase II Elongation Complex Bound with ELF1 and SPT4/5, Stalled at Shl(-1) of the Nucleosome (+1B) 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 (+1B) (pdb code 6j4y). 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 (+1B), PDB code: 6j4y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 6j4y

Go back to Zinc Binding Sites List in 6j4y
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 (+1B)


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 (+1B) 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 6j4y

Go back to Zinc Binding Sites List in 6j4y
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 (+1B)


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 (+1B) 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 6j4y

Go back to Zinc Binding Sites List in 6j4y
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 (+1B)


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 (+1B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.8
occ:1.00
 SG B:CYS1182 2.4 0.4 1.0
SG B:CYS1185 2.4 0.6 1.0
SG B:CYS1163 2.4 76.1 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 6j4y

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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 (+1B)


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 (+1B) 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 6j4y

Go back to Zinc Binding Sites List in 6j4y
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 (+1B)


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 (+1B) 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 6j4y

Go back to Zinc Binding Sites List in 6j4y
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 (+1B)


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 (+1B) 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 6j4y

Go back to Zinc Binding Sites List in 6j4y
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 (+1B)


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 (+1B) 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 6j4y

Go back to Zinc Binding Sites List in 6j4y
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 (+1B)


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 (+1B) 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 6j4y

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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 (+1B)


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 (+1B) 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 3.2 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
CD1 M:LEU54 4.5 30.0 1.0
CA M:CYS28 4.5 0.3 1.0
N M:ASN53 4.6 0.1 1.0
CB M:LEU54 4.7 30.0 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 6j4y

Go back to Zinc Binding Sites List in 6j4y
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 (+1B)


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 (+1B) 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 00:46:59 2024

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