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Zinc in PDB 6j50: Rna Polymerase II Elongation Complex Bound with SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation)

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

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

Other elements in 6j50:

The structure of Rna Polymerase II Elongation Complex Bound with SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation) 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 SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation) (pdb code 6j50). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation), PDB code: 6j50:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 6j50

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


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 SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation) 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 3.9 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 9 in 6j50

Go back to Zinc Binding Sites List in 6j50
Zinc binding site 2 out of 9 in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation)


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 SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation) 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 9 in 6j50

Go back to Zinc Binding Sites List in 6j50
Zinc binding site 3 out of 9 in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation)


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 SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation) 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 9 in 6j50

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Zinc binding site 4 out of 9 in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation)


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 SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation) 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 9 in 6j50

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


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 SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation) 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 3.2 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 9 in 6j50

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Zinc binding site 6 out of 9 in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation)


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 SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation) 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 9 in 6j50

Go back to Zinc Binding Sites List in 6j50
Zinc binding site 7 out of 9 in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation)


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 SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation) 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 9 in 6j50

Go back to Zinc Binding Sites List in 6j50
Zinc binding site 8 out of 9 in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation)


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 SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation) 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 9 in 6j50

Go back to Zinc Binding Sites List in 6j50
Zinc binding site 9 out of 9 in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation)


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 SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (Tilted Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Zn300

b:17.1
occ:1.00
 SG V:CYS29 1.3 18.0 1.0
CB V:CYS29 2.3 17.4 1.0
CB V:CYS12 2.8 14.9 1.0
SG V:CYS12 2.9 34.8 1.0
SG V:CYS15 3.1 22.8 1.0
CG2 V:ILE17 3.3 11.7 1.0
CA V:CYS29 3.4 18.3 1.0
CE1 V:PHE24 3.7 15.7 1.0
SG V:CYS32 4.0 25.4 1.0
C V:CYS29 4.1 16.6 1.0
CB V:CYS32 4.2 17.2 1.0
CA V:CYS12 4.3 13.8 1.0
CD V:PRO30 4.5 18.7 1.0
CB V:CYS15 4.5 14.4 1.0
CZ V:PHE24 4.6 15.1 1.0
CB V:ILE17 4.6 14.9 1.0
N V:PRO30 4.6 17.1 1.0
N V:CYS32 4.6 16.6 1.0
CD1 V:PHE24 4.6 18.1 1.0
N V:CYS29 4.6 18.4 1.0
N V:ASN31 4.7 16.2 1.0
O V:CYS29 4.8 19.7 1.0
CB V:ASN31 4.9 15.9 1.0
N V:CYS12 5.0 15.2 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 00:47:01 2024

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