Atomistry » Zinc » PDB 6j4f-6jes » 6j4z
Atomistry »
  Zinc »
    PDB 6j4f-6jes »
      6j4z »

Zinc in PDB 6j4z: Rna Polymerase II Elongation Complex Bound with SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome

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

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

Other elements in 6j4z:

The structure of Rna Polymerase II Elongation Complex Bound with SPT4/5 and Foreign Dna, 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 SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (pdb code 6j4z). 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, PDB code: 6j4z:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 6j4z

Go back to Zinc Binding Sites List in 6j4z
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


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 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 6j4z

Go back to Zinc Binding Sites List in 6j4z
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


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 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 4.6 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 6j4z

Go back to Zinc Binding Sites List in 6j4z
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


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 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 6j4z

Go back to Zinc Binding Sites List in 6j4z
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


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 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 6j4z

Go back to Zinc Binding Sites List in 6j4z
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


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 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 6j4z

Go back to Zinc Binding Sites List in 6j4z
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


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 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 6j4z

Go back to Zinc Binding Sites List in 6j4z
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


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 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 6j4z

Go back to Zinc Binding Sites List in 6j4z
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


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 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 6j4z

Go back to Zinc Binding Sites List in 6j4z
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


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 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 00:46:58 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy