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Zinc in PDB 5xon: Rna Polymerase II Elongation Complex Bound with SPT4/5 and Tfiis

Enzymatic activity of Rna Polymerase II Elongation Complex Bound with SPT4/5 and Tfiis

All present enzymatic activity of Rna Polymerase II Elongation Complex Bound with SPT4/5 and Tfiis:
2.7.7.6;

Other elements in 5xon:

The structure of Rna Polymerase II Elongation Complex Bound with SPT4/5 and Tfiis 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 Tfiis (pdb code 5xon). 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 SPT4/5 and Tfiis, PDB code: 5xon:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 5xon

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Zinc binding site 1 out of 10 in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Tfiis


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 Tfiis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.4
occ:1.00
NE2 A:HIS80 2.2 60.5 1.0
CD2 A:HIS80 2.4 77.7 1.0
SG A:CYS67 2.5 96.3 1.0
SG A:CYS77 2.5 87.3 1.0
SG A:CYS70 2.6 92.3 1.0
CB A:CYS70 3.2 87.0 1.0
CE1 A:HIS80 3.5 85.4 1.0
CB A:CYS67 3.5 100.0 1.0
N A:CYS70 3.6 93.7 1.0
CG A:HIS80 3.7 74.2 1.0
CB A:CYS77 3.9 83.6 1.0
CA A:CYS70 4.0 83.5 1.0
CB A:THR69 4.1 81.9 1.0
ND1 A:HIS80 4.2 72.0 1.0
C A:THR69 4.6 88.6 1.0
O A:CYS67 4.6 0.5 1.0
CG2 A:THR69 4.6 81.3 1.0
CA A:CYS77 4.7 81.9 1.0
CA A:CYS67 4.8 0.7 1.0
CA A:THR69 4.8 88.4 1.0
N A:GLY79 4.9 75.7 1.0
CB A:HIS80 4.9 72.8 1.0
C A:CYS67 4.9 0.5 1.0
C A:GLY79 5.0 73.0 1.0
N A:THR69 5.0 90.5 1.0

Zinc binding site 2 out of 10 in 5xon

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Zinc binding site 2 out of 10 in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Tfiis


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 Tfiis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:0.9
occ:1.00
SG A:CYS168 2.4 0.6 1.0
SG A:CYS107 2.4 0.6 1.0
SG A:CYS148 2.4 0.4 1.0
SG A:CYS110 2.4 0.2 1.0
CB A:CYS148 3.2 99.5 1.0
N A:CYS168 3.2 0.3 1.0
CB A:CYS168 3.3 0.1 1.0
CB A:CYS107 3.5 0.9 1.0
N A:CYS110 3.6 0.2 1.0
CB A:CYS110 3.7 0.7 1.0
CA A:CYS168 3.9 0.7 1.0
CA A:CYS110 4.2 0.6 1.0
C A:GLY167 4.2 0.5 1.0
CA A:GLY167 4.3 0.8 1.0
CB A:ASN109 4.5 0.8 1.0
O A:CYS148 4.6 0.0 1.0
CA A:CYS148 4.6 0.3 1.0
N A:GLY111 4.6 0.5 1.0
C A:ASN109 4.7 0.8 1.0
C A:CYS168 4.7 0.1 1.0
C A:CYS110 4.7 0.3 1.0
N A:ASN109 4.7 0.7 1.0
N A:GLY169 4.8 0.8 1.0
CA A:ASN109 4.8 0.4 1.0
CA A:CYS107 4.9 0.1 1.0

Zinc binding site 3 out of 10 in 5xon

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Zinc binding site 3 out of 10 in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Tfiis


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

b:85.1
occ:1.00
SG B:CYS1182 2.4 76.4 1.0
SG B:CYS1166 2.5 85.9 1.0
SG B:CYS1163 3.0 79.1 1.0
SG B:CYS1185 3.2 0.5 1.0
CB B:CYS1166 3.2 78.3 1.0
CB B:CYS1185 3.4 0.7 1.0
CB B:CYS1163 3.6 87.2 1.0
CB B:CYS1182 3.7 78.9 1.0
N B:CYS1166 3.8 89.0 1.0
N B:CYS1185 4.1 1.0 1.0
CA B:CYS1166 4.2 91.9 1.0
CA B:CYS1185 4.4 99.0 1.0
CB B:SER1184 4.5 99.0 1.0
O B:CYS1182 4.6 93.4 1.0
C B:SER1184 4.6 95.6 1.0
CB B:ASN1187 4.8 88.4 1.0
CB B:ILE1165 4.8 91.4 1.0
CA B:CYS1182 4.9 80.9 1.0
C B:CYS1182 4.9 94.1 1.0
CA B:SER1184 5.0 96.5 1.0
C B:ILE1165 5.0 87.8 1.0
N B:SER1184 5.0 0.0 1.0
ND2 B:ASN1187 5.0 0.2 1.0

Zinc binding site 4 out of 10 in 5xon

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Zinc binding site 4 out of 10 in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Tfiis


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 Tfiis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:94.7
occ:1.00
SG C:CYS94 2.3 0.8 1.0
SG C:CYS87 2.4 98.9 1.0
SG C:CYS85 2.6 95.0 1.0
SG C:CYS91 2.8 0.4 1.0
CB C:CYS94 3.1 84.7 1.0
N C:CYS91 3.3 0.6 1.0
CB C:CYS85 3.4 89.3 1.0
CB C:CYS91 3.7 0.4 1.0
CB C:CYS87 3.9 0.7 1.0
CA C:TYR90 4.0 0.6 1.0
NZ W:LYS764 4.0 99.0 1.0
CA C:CYS91 4.0 0.0 1.0
C C:TYR90 4.1 0.4 1.0
CA C:CYS94 4.5 84.6 1.0
CE W:LYS764 4.5 93.7 1.0
N C:CYS94 4.6 0.3 1.0
C C:CYS91 4.7 0.8 1.0
CB C:TYR90 4.7 0.7 1.0
N C:CYS87 4.7 84.4 1.0
CA C:CYS85 4.7 92.8 1.0
CA C:CYS87 4.8 0.2 1.0
N C:ASP92 4.8 0.2 1.0
O C:ASP89 4.9 0.3 1.0
C C:CYS85 4.9 0.1 1.0
C C:GLU93 4.9 0.9 1.0
O C:CYS85 5.0 0.5 1.0

Zinc binding site 5 out of 10 in 5xon

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Zinc binding site 5 out of 10 in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Tfiis


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 Tfiis within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.2
occ:1.00
SG I:CYS106 2.1 70.7 1.0
SG I:CYS75 2.4 88.6 1.0
SG I:CYS103 2.5 0.0 1.0
SG I:CYS78 2.7 0.5 1.0
CB I:CYS75 2.8 73.3 1.0
CB I:CYS103 3.0 86.7 1.0
CB I:CYS106 3.3 66.5 1.0
N I:CYS106 3.9 87.9 1.0
N I:CYS78 3.9 0.4 1.0
CB I:CYS78 4.0 0.5 1.0
CA I:CYS106 4.1 66.2 1.0
CB I:GLU77 4.3 0.5 1.0
CA I:CYS75 4.4 90.1 1.0
CA I:CYS78 4.4 0.8 1.0
CA I:CYS103 4.5 96.2 1.0
CB I:SER80 4.7 90.2 1.0
C I:CYS106 4.8 76.3 1.0
CB I:ASN105 4.8 93.9 1.0
N I:SER80 4.9 0.3 1.0
C I:GLU77 4.9 0.9 1.0
N I:GLU77 4.9 97.5 1.0
N I:HIS79 4.9 0.4 1.0
C I:CYS78 4.9 0.4 1.0
CA I:GLU77 4.9 94.4 1.0
C I:CYS75 4.9 0.1 1.0
N I:LYS107 4.9 94.4 1.0
C I:ASN105 5.0 0.9 1.0

Zinc binding site 6 out of 10 in 5xon

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Zinc binding site 6 out of 10 in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Tfiis


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 Tfiis within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.1
occ:1.00
CB I:CYS10 2.1 0.5 1.0
SG I:CYS7 2.7 0.7 1.0
SG I:CYS29 2.7 0.7 1.0
CB I:CYS32 3.1 0.8 1.0
SG I:CYS32 3.2 0.9 1.0
CA I:CYS10 3.3 0.8 1.0
CB I:CYS7 3.3 0.7 1.0
SG I:CYS10 3.3 0.1 1.0
N I:CYS10 3.4 0.6 1.0
N I:CYS32 3.8 0.5 1.0
CB I:CYS29 3.8 0.3 1.0
C I:GLU9 3.9 0.1 1.0
CA I:CYS32 4.1 0.2 1.0
C I:CYS10 4.1 0.2 1.0
O I:GLU9 4.3 0.8 1.0
CB I:ASN31 4.4 0.9 1.0
N I:ASN11 4.4 0.9 1.0
C I:ASN31 4.5 0.8 1.0
N I:ASN12 4.7 0.1 1.0
CA I:GLU9 4.7 0.1 1.0
N I:GLU9 4.7 1.0 1.0
CB I:ASN12 4.7 83.4 1.0
CA I:CYS7 4.8 0.7 1.0
O I:CYS10 4.8 0.8 1.0
CB I:GLU9 4.9 0.3 1.0
CA I:ASN31 4.9 0.3 1.0

Zinc binding site 7 out of 10 in 5xon

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Zinc binding site 7 out of 10 in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Tfiis


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 Tfiis within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:85.8
occ:1.00
SG J:CYS10 2.4 66.7 1.0
SG J:CYS44 2.4 70.8 1.0
SG J:CYS7 2.5 67.3 1.0
SG J:CYS45 2.7 71.3 1.0
CB J:CYS7 3.4 67.7 1.0
N J:CYS45 3.4 73.2 1.0
CB J:CYS10 3.6 69.3 1.0
CB J:CYS44 3.6 75.6 1.0
N J:CYS10 3.8 59.7 1.0
CB J:CYS45 3.9 66.0 1.0
CA J:CYS45 3.9 62.4 1.0
C J:CYS44 4.0 74.1 1.0
CA J:CYS10 4.3 68.7 1.0
CA J:CYS44 4.4 75.3 1.0
N J:GLY11 4.6 65.8 1.0
N J:SER9 4.6 65.4 1.0
O J:CYS44 4.7 71.1 1.0
CB J:SER9 4.7 65.0 1.0
C J:SER9 4.8 66.8 1.0
CA J:CYS7 4.8 57.6 1.0
C J:CYS10 4.9 66.4 1.0
CA J:SER9 4.9 67.3 1.0
N J:LYS12 5.0 66.4 1.0

Zinc binding site 8 out of 10 in 5xon

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Zinc binding site 8 out of 10 in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Tfiis


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 Tfiis within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:98.2
occ:1.00
SG L:CYS50 2.6 86.4 1.0
SG L:CYS36 2.6 0.0 1.0
CB L:CYS50 2.6 90.5 1.0
N L:CYS53 2.7 93.0 1.0
CB L:GLU52 2.7 0.3 1.0
N L:GLU52 3.1 0.4 1.0
CA L:GLU52 3.1 0.6 1.0
C L:GLU52 3.2 98.5 1.0
SG L:CYS53 3.4 0.7 1.0
N L:GLY54 3.5 91.3 1.0
C L:CYS50 3.7 0.1 1.0
CA L:CYS53 3.7 0.9 1.0
CA L:CYS50 3.7 95.7 1.0
CG L:GLU52 3.8 0.9 1.0
SG L:CYS33 3.9 92.1 1.0
O L:CYS50 3.9 0.5 1.0
CB L:CYS36 4.0 91.9 1.0
CB L:CYS53 4.0 0.1 1.0
C L:CYS53 4.1 0.2 1.0
N L:LYS51 4.2 0.7 1.0
CB L:CYS33 4.2 74.3 1.0
O L:GLU52 4.3 0.6 1.0
C L:LYS51 4.3 0.5 1.0
N L:CYS50 4.5 88.5 1.0
CA L:GLY54 4.6 97.0 1.0
N L:HIS55 4.7 93.6 1.0
CB L:HIS38 4.9 0.6 1.0
CA L:LYS51 4.9 0.1 1.0

Zinc binding site 9 out of 10 in 5xon

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Zinc binding site 9 out of 10 in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Tfiis


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 Tfiis within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Zn301

b:0.8
occ:1.00
SG U:CYS247 1.8 0.9 1.0
SG U:CYS278 2.3 0.3 1.0
CB U:CYS247 2.9 86.6 1.0
SG U:CYS250 3.0 0.8 1.0
N U:CYS250 3.2 0.4 1.0
SG U:CYS275 3.4 0.7 1.0
CB U:LYS249 3.5 0.4 1.0
CB U:CYS250 3.8 0.4 1.0
CB U:CYS278 3.8 0.5 1.0
CB U:CYS275 3.9 92.1 1.0
CB U:ASN280 4.0 91.2 1.0
N U:LYS249 4.0 0.7 1.0
CA U:CYS250 4.0 1.0 1.0
CA U:LYS249 4.1 0.5 1.0
C U:LYS249 4.1 1.0 1.0
CA U:CYS247 4.3 0.4 1.0
N U:LYS251 4.5 0.3 1.0
C U:CYS247 4.6 0.4 1.0
C U:CYS250 4.7 0.8 1.0
ND2 U:ASN280 4.7 78.4 1.0
CG U:LYS249 4.7 0.8 1.0
N U:GLY248 4.8 0.8 1.0
N U:CYS278 4.8 0.8 1.0
CA U:CYS278 4.9 0.2 1.0
CG U:ASN280 4.9 97.4 1.0
N U:ASN280 4.9 92.1 1.0

Zinc binding site 10 out of 10 in 5xon

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Zinc binding site 10 out of 10 in the Rna Polymerase II Elongation Complex Bound with SPT4/5 and Tfiis


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 SPT4/5 and Tfiis 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.Yokoyama, H.Shigematsu, S.Yokoyama, M.Shirouzu, S.I.Sekine. Structure of the Complete Elongation Complex of Rna Polymerase II with Basal Factors Science V. 357 921 2017.
ISSN: ESSN 1095-9203
PubMed: 28775211
DOI: 10.1126/SCIENCE.AAN8552
Page generated: Wed Dec 16 11:20:58 2020

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