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Zinc in PDB 7b0y: Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex

Enzymatic activity of Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex

All present enzymatic activity of Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex:
2.7.7.6;

Other elements in 7b0y:

The structure of Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex (pdb code 7b0y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex, PDB code: 7b0y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7b0y

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Zinc binding site 1 out of 8 in the Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:76.0
occ:1.00
 NE2 A:HIS84 2.1 39.6 1.0
SG A:CYS74 2.4 48.5 1.0
SG A:CYS81 2.4 43.1 1.0
SG A:CYS71 2.5 51.9 1.0
CB A:CYS71 2.6 51.9 1.0
CD2 A:HIS84 2.7 39.6 1.0
CE1 A:HIS84 3.3 39.6 1.0
CB A:CYS74 3.5 48.5 1.0
CA A:GLY63 3.8 48.2 1.0
N A:CYS74 3.8 48.5 1.0
CB A:CYS81 3.9 43.1 1.0
CG A:HIS84 4.0 39.6 1.0
CA A:CYS71 4.2 51.9 1.0
N A:GLY63 4.2 48.2 1.0
CA A:CYS74 4.2 48.5 1.0
ND1 A:HIS84 4.3 39.6 1.0
C A:GLY63 4.5 48.2 1.0
O A:PRO82 4.5 38.6 1.0
CB A:THR73 4.6 44.5 1.0
CA A:CYS81 4.6 43.1 1.0
N A:ALA75 4.7 50.9 1.0
C A:CYS71 4.8 51.9 1.0
O A:GLY63 4.8 48.2 1.0
C A:CYS74 4.8 48.5 1.0
C A:THR73 4.9 44.5 1.0
N A:CYS71 4.9 51.9 1.0
C A:CYS81 4.9 43.1 1.0
O A:ARG61 4.9 44.8 1.0
N A:THR73 4.9 44.5 1.0

Zinc binding site 2 out of 8 in 7b0y

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Zinc binding site 2 out of 8 in the Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:85.1
occ:1.00
 SG A:CYS111 2.4 61.1 1.0
SG A:CYS114 2.5 63.0 1.0
SG A:CYS154 2.5 75.4 1.0
CB A:CYS184 2.9 80.0 1.0
CB A:CYS114 3.0 63.0 1.0
CB A:CYS154 3.0 75.4 1.0
N A:CYS184 3.1 80.0 1.0
CA A:CYS184 3.5 80.0 1.0
CB A:CYS111 3.5 61.1 1.0
N A:CYS114 3.9 63.0 1.0
CA A:CYS114 4.0 63.0 1.0
C A:GLY183 4.2 79.7 1.0
CA A:GLY183 4.4 79.7 1.0
SG A:CYS184 4.4 80.0 1.0
C A:CYS184 4.5 80.0 1.0
NE2 A:GLN188 4.5 68.8 1.0
CA A:CYS154 4.5 75.4 1.0
N A:GLY185 4.7 80.8 1.0
C A:CYS114 4.9 63.0 1.0
CA A:CYS111 4.9 61.1 1.0

Zinc binding site 3 out of 8 in 7b0y

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Zinc binding site 3 out of 8 in the Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:111.3
occ:1.00
 SG B:CYS1122 2.4 38.6 1.0
SG B:CYS1119 2.5 43.2 1.0
SG B:CYS1137 2.5 47.0 1.0
SG B:CYS1140 2.5 46.8 1.0
CB B:CYS1119 2.7 43.2 1.0
CB B:CYS1140 3.2 46.8 1.0
CB B:CYS1137 3.2 47.0 1.0
CB B:CYS1122 3.5 38.6 1.0
N B:CYS1140 3.8 46.8 1.0
N B:CYS1122 3.9 38.6 1.0
OD1 B:ASN1142 4.0 43.9 1.0
CA B:CYS1140 4.1 46.8 1.0
CA B:CYS1119 4.2 43.2 1.0
CA B:CYS1122 4.3 38.6 1.0
CA B:CYS1137 4.6 47.0 1.0
CG B:ASN1142 4.7 43.9 1.0
CB B:LEU1121 4.7 40.5 1.0
ND2 B:ASN1142 4.7 43.9 1.0
C B:CYS1119 4.8 43.2 1.0
O B:CYS1137 5.0 47.0 1.0
O B:CYS1119 5.0 43.2 1.0
C B:GLY1139 5.0 43.4 1.0
N B:CYS1119 5.0 43.2 1.0

Zinc binding site 4 out of 8 in 7b0y

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Zinc binding site 4 out of 8 in the Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:82.7
occ:1.00
 SG C:CYS90 2.3 46.5 1.0
SG C:CYS97 2.4 34.9 1.0
SG C:CYS88 2.4 43.1 1.0
SG C:CYS94 2.4 36.1 1.0
CB C:CYS97 2.4 34.9 1.0
CB C:CYS88 3.2 43.1 1.0
N C:CYS97 3.5 34.9 1.0
CB C:CYS90 3.5 46.5 1.0
CA C:CYS97 3.5 34.9 1.0
CB C:CYS94 3.6 36.1 1.0
C C:GLU96 4.3 33.0 1.0
N C:CYS94 4.4 36.1 1.0
C C:CYS97 4.5 34.9 1.0
CA C:CYS94 4.5 36.1 1.0
CA C:CYS90 4.7 46.5 1.0
CA C:CYS88 4.7 43.1 1.0
N C:CYS90 4.7 46.5 1.0
CB C:GLU96 4.7 33.0 1.0
O C:CYS94 4.9 36.1 1.0
C C:CYS94 4.9 36.1 1.0
C C:PHE93 4.9 34.4 1.0
CA C:GLU96 4.9 33.0 1.0
N C:GLU96 4.9 33.0 1.0
O C:GLU91 5.0 45.7 1.0

Zinc binding site 5 out of 8 in 7b0y

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Zinc binding site 5 out of 8 in the Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:91.6
occ:1.00
 SG I:CYS20 2.4 52.5 1.0
SG I:CYS42 2.5 60.0 1.0
SG I:CYS39 2.5 60.2 1.0
SG I:CYS17 2.5 54.8 1.0
CB I:CYS17 2.7 54.8 1.0
CB I:CYS39 2.8 60.2 1.0
CB I:CYS42 3.8 60.0 1.0
CB I:CYS20 4.1 52.5 1.0
N I:CYS20 4.2 52.5 1.0
CA I:CYS17 4.2 54.8 1.0
CA I:CYS39 4.3 60.2 1.0
N I:CYS42 4.4 60.0 1.0
CB I:TYR44 4.4 55.8 1.0
CB I:ASN22 4.6 51.2 1.0
CA I:CYS42 4.6 60.0 1.0
CA I:CYS20 4.6 52.5 1.0
N I:ASN22 4.7 51.2 1.0
CD2 I:LEU24 4.7 55.3 1.0
O I:ASN22 4.9 51.2 1.0
N I:CYS17 4.9 54.8 1.0
CB I:GLU19 5.0 56.8 1.0
N I:ASN21 5.0 47.9 1.0
C I:CYS17 5.0 54.8 1.0

Zinc binding site 6 out of 8 in 7b0y

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Zinc binding site 6 out of 8 in the Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:69.3
occ:1.00
 SG I:CYS114 2.4 40.5 1.0
SG I:CYS119 2.4 45.0 1.0
SG I:CYS86 2.4 43.5 1.0
SG I:CYS89 2.4 45.8 1.0
CB I:CYS114 2.8 40.5 1.0
CB I:CYS86 3.0 43.5 1.0
CB I:CYS119 3.4 45.0 1.0
CB I:CYS89 3.8 45.8 1.0
CB I:HIS121 4.0 40.9 1.0
N I:CYS89 4.3 45.8 1.0
CA I:CYS114 4.3 40.5 1.0
CB I:HIS91 4.5 43.1 1.0
CA I:CYS86 4.5 43.5 1.0
CB I:ALA116 4.5 42.9 1.0
N I:HIS121 4.5 40.9 1.0
CA I:CYS89 4.7 45.8 1.0
CA I:CYS119 4.8 45.0 1.0
CA I:HIS121 4.9 40.9 1.0
CB I:LYS88 5.0 45.5 1.0
C I:CYS114 5.0 40.5 1.0
CG I:HIS121 5.0 40.9 1.0
N I:HIS91 5.0 43.1 1.0

Zinc binding site 7 out of 8 in 7b0y

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Zinc binding site 7 out of 8 in the Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:25.2
occ:1.00
 SG J:CYS44 2.4 23.8 1.0
SG J:CYS45 2.4 22.0 1.0
SG J:CYS7 2.4 23.7 1.0
SG J:CYS10 2.5 22.2 1.0
CB J:CYS7 2.9 23.7 1.0
N J:CYS45 3.2 22.0 1.0
CB J:CYS10 3.2 22.2 1.0
CB J:CYS44 3.5 23.8 1.0
CA J:CYS45 3.5 22.0 1.0
CB J:CYS45 3.5 22.0 1.0
C J:CYS44 3.7 23.8 1.0
N J:CYS10 3.7 22.2 1.0
CA J:CYS10 4.1 22.2 1.0
CA J:CYS44 4.2 23.8 1.0
O J:CYS44 4.3 23.8 1.0
CA J:CYS7 4.4 23.7 1.0
N J:GLY11 4.5 24.1 1.0
CB J:THR9 4.6 23.1 1.0
NE J:ARG42 4.7 26.5 1.0
CB J:LYS12 4.7 24.5 1.0
N J:LYS12 4.8 24.5 1.0
C J:THR9 4.8 23.1 1.0
C J:CYS10 4.8 22.2 1.0
C J:CYS7 4.9 23.7 1.0
N J:CYS44 5.0 23.8 1.0
N J:THR9 5.0 23.1 1.0

Zinc binding site 8 out of 8 in 7b0y

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Zinc binding site 8 out of 8 in the Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:65.7
occ:1.00
 SG L:CYS19 2.3 44.7 1.0
SG L:CYS36 2.3 55.5 1.0
SG L:CYS22 2.3 47.2 1.0
SG L:CYS39 2.4 59.8 1.0
CB L:CYS19 2.4 44.7 1.0
CB L:CYS36 3.0 55.5 1.0
CB L:CYS22 3.7 47.2 1.0
CB L:CYS39 3.9 59.8 1.0
CA L:CYS19 3.9 44.7 1.0
N L:CYS22 4.1 47.2 1.0
CB L:TYR41 4.1 47.8 1.0
CE L:MET44 4.1 42.0 1.0
N L:CYS39 4.3 59.8 1.0
CA L:CYS22 4.4 47.2 1.0
CA L:CYS36 4.5 55.5 1.0
N L:HIS23 4.6 43.7 1.0
CA L:CYS39 4.6 59.8 1.0
CB L:THR24 4.6 48.4 1.0
N L:THR24 4.6 48.4 1.0
N L:CYS19 4.7 44.7 1.0
OG1 L:THR24 4.7 48.4 1.0
N L:TYR41 4.7 47.8 1.0
C L:CYS19 4.8 44.7 1.0
OE1 L:GLU38 4.8 62.9 1.0
C L:CYS22 4.8 47.2 1.0
N L:GLY20 5.0 41.5 1.0

Reference:

S.Zhang, S.Aibara, S.M.Vos, D.E.Agafonov, R.Luehrmann, P.Cramer. Structure of A Transcribing Rna Polymerase II-U1 Snrnp Complex Science 2021.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ABF1870
Page generated: Tue Oct 29 17:17:10 2024

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