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Zinc in PDB 9fd2: Structure of Pol II-Tc-Ner-STK19 Complex

Enzymatic activity of Structure of Pol II-Tc-Ner-STK19 Complex

All present enzymatic activity of Structure of Pol II-Tc-Ner-STK19 Complex:
2.7.7.6;

Other elements in 9fd2:

The structure of Structure of Pol II-Tc-Ner-STK19 Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Pol II-Tc-Ner-STK19 Complex (pdb code 9fd2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Structure of Pol II-Tc-Ner-STK19 Complex, PDB code: 9fd2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 9fd2

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Zinc binding site 1 out of 10 in the Structure of Pol II-Tc-Ner-STK19 Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Pol II-Tc-Ner-STK19 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:92.2
occ:1.00
 NE2 A:HIS84 2.1 82.2 1.0
SG A:CYS81 2.3 84.5 1.0
SG A:CYS74 2.3 85.0 1.0
SG A:CYS71 2.3 86.9 1.0
CD2 A:HIS84 2.4 82.2 1.0
CB A:CYS71 2.7 86.9 1.0
CE1 A:HIS84 3.3 82.2 1.0
CB A:CYS81 3.7 84.5 1.0
CG A:HIS84 3.7 82.2 1.0
O A:PRO82 3.8 81.5 1.0
CB A:CYS74 4.0 85.0 1.0
ND1 A:HIS84 4.1 82.2 1.0
CA A:CYS71 4.2 86.9 1.0
N A:CYS74 4.2 85.0 1.0
CA A:CYS81 4.4 84.5 1.0
CA A:GLY63 4.4 88.5 1.0
CA A:CYS74 4.7 85.0 1.0
C A:CYS81 4.7 84.5 1.0
C A:CYS71 4.8 86.9 1.0
CB A:THR73 4.8 86.3 1.0
C A:PRO82 4.9 81.5 1.0
C A:GLY63 5.0 88.5 1.0
N A:PRO82 5.0 81.5 1.0
CB A:HIS84 5.0 82.2 1.0
N A:CYS71 5.0 86.9 1.0

Zinc binding site 2 out of 10 in 9fd2

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Zinc binding site 2 out of 10 in the Structure of Pol II-Tc-Ner-STK19 Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Pol II-Tc-Ner-STK19 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:138.0
occ:1.00
 SG A:CYS111 2.3 115.0 1.0
SG A:CYS114 2.3 117.3 1.0
SG A:CYS154 2.3 119.3 1.0
SG A:CYS184 2.3 117.2 1.0
CB A:CYS114 2.9 117.3 1.0
CB A:CYS111 3.1 115.0 1.0
N A:CYS184 3.4 117.2 1.0
N A:CYS114 3.4 117.3 1.0
CB A:CYS154 3.5 119.3 1.0
CA A:CYS114 3.7 117.3 1.0
CB A:CYS184 3.7 117.2 1.0
CA A:CYS184 4.1 117.2 1.0
C A:GLY183 4.1 116.5 1.0
CA A:GLY183 4.2 116.5 1.0
C A:CYS114 4.3 117.3 1.0
NE2 A:GLN188 4.4 115.2 1.0
N A:SER115 4.5 115.4 1.0
CA A:CYS111 4.6 115.0 1.0
C A:PHE113 4.6 115.0 1.0
N A:GLY185 4.7 116.0 1.0
CB A:PHE113 4.7 115.0 1.0
C A:CYS184 4.8 117.2 1.0
N A:PHE113 4.8 115.0 1.0
CA A:CYS154 4.8 119.3 1.0
CA A:PHE113 5.0 115.0 1.0
N A:LYS116 5.0 112.6 1.0

Zinc binding site 3 out of 10 in 9fd2

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Zinc binding site 3 out of 10 in the Structure of Pol II-Tc-Ner-STK19 Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Pol II-Tc-Ner-STK19 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:108.1
occ:1.00
 SG B:CYS1122 2.3 80.7 1.0
SG B:CYS1137 2.3 89.0 1.0
SG B:CYS1140 2.3 90.3 1.0
SG B:CYS1119 2.3 81.3 1.0
CB B:CYS1119 2.8 81.3 1.0
CB B:CYS1122 2.9 80.7 1.0
CB B:CYS1140 3.4 90.3 1.0
CB B:CYS1137 3.6 89.0 1.0
N B:CYS1122 3.7 80.7 1.0
CA B:CYS1122 3.9 80.7 1.0
N B:CYS1140 3.9 90.3 1.0
OD1 B:ASN1142 4.0 87.6 1.0
CA B:CYS1119 4.3 81.3 1.0
CA B:CYS1140 4.3 90.3 1.0
N B:GLY1123 4.8 78.8 1.0
C B:CYS1122 4.8 80.7 1.0
C B:CYS1119 4.8 81.3 1.0
CG B:ASN1142 4.9 87.6 1.0
C B:LEU1121 4.9 80.2 1.0
CA B:CYS1137 4.9 89.0 1.0

Zinc binding site 4 out of 10 in 9fd2

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Zinc binding site 4 out of 10 in the Structure of Pol II-Tc-Ner-STK19 Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Pol II-Tc-Ner-STK19 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:94.6
occ:1.00
 SG C:CYS94 2.3 71.5 1.0
SG C:CYS90 2.3 79.2 1.0
SG C:CYS88 2.3 76.1 1.0
SG C:CYS97 2.3 70.1 1.0
CB C:CYS97 3.0 70.1 1.0
CB C:CYS94 3.0 71.5 1.0
CB C:CYS88 3.5 76.1 1.0
CB C:CYS90 3.5 79.2 1.0
N C:CYS94 3.7 71.5 1.0
CA C:CYS94 3.9 71.5 1.0
N C:CYS97 3.9 70.1 1.0
CA C:CYS97 4.1 70.1 1.0
C C:PHE93 4.2 73.2 1.0
C C:CYS94 4.5 71.5 1.0
CA C:CYS90 4.5 79.2 1.0
O C:CYS94 4.5 71.5 1.0
N C:CYS90 4.5 79.2 1.0
O C:GLU91 4.5 81.9 1.0
C C:GLU96 4.5 71.7 1.0
O C:PHE93 4.8 73.2 1.0
CA C:CYS88 4.8 76.1 1.0
CA C:PHE93 4.8 73.2 1.0
C C:CYS97 4.9 70.1 1.0
N C:GLU96 4.9 71.7 1.0
C C:CYS90 5.0 79.2 1.0

Zinc binding site 5 out of 10 in 9fd2

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Zinc binding site 5 out of 10 in the Structure of Pol II-Tc-Ner-STK19 Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Pol II-Tc-Ner-STK19 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:86.4
occ:1.00
 SG I:CYS42 2.3 81.1 1.0
SG I:CYS17 2.3 80.1 1.0
SG I:CYS20 2.3 81.7 1.0
SG I:CYS39 2.3 81.3 1.0
CB I:CYS17 3.0 80.1 1.0
CB I:CYS39 3.3 81.3 1.0
CB I:CYS42 3.8 81.1 1.0
CB I:CYS20 4.0 81.7 1.0
N I:CYS42 4.0 81.1 1.0
N I:CYS20 4.0 81.7 1.0
CA I:CYS42 4.5 81.1 1.0
CB I:GLU19 4.5 82.4 1.0
CB I:ASN41 4.5 80.8 1.0
CB I:TYR44 4.5 79.6 1.0
CA I:CYS17 4.5 80.1 1.0
CA I:CYS20 4.6 81.7 1.0
CA I:CYS39 4.7 81.3 1.0
ND2 I:ASN41 4.8 80.8 1.0
CB I:ASN22 4.9 80.5 1.0
N I:GLU19 5.0 82.4 1.0
C I:CYS42 5.0 81.1 1.0

Zinc binding site 6 out of 10 in 9fd2

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Zinc binding site 6 out of 10 in the Structure of Pol II-Tc-Ner-STK19 Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Pol II-Tc-Ner-STK19 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:111.2
occ:1.00
 SG I:CYS119 2.3 97.9 1.0
SG I:CYS89 2.3 99.3 1.0
SG I:CYS114 2.3 92.4 1.0
SG I:CYS86 2.3 99.2 1.0
CB I:CYS86 3.0 99.2 1.0
CB I:CYS114 3.2 92.4 1.0
CB I:CYS119 3.5 97.9 1.0
CB I:CYS89 3.5 99.3 1.0
N I:CYS89 3.9 99.3 1.0
CB I:HIS121 4.1 92.8 1.0
CA I:CYS89 4.2 99.3 1.0
CB I:HIS91 4.4 95.9 1.0
CA I:CYS86 4.5 99.2 1.0
CA I:CYS114 4.7 92.4 1.0
CB I:LYS88 4.7 98.9 1.0
N I:HIS121 4.7 92.8 1.0
N I:HIS91 4.7 95.9 1.0
C I:CYS89 4.8 99.3 1.0
CA I:CYS119 4.8 97.9 1.0
N I:GLY90 4.9 98.9 1.0
C I:LYS88 4.9 98.9 1.0
C I:CYS86 5.0 99.2 1.0

Zinc binding site 7 out of 10 in 9fd2

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Zinc binding site 7 out of 10 in the Structure of Pol II-Tc-Ner-STK19 Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Pol II-Tc-Ner-STK19 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:81.1
occ:1.00
 SG J:CYS44 2.3 56.8 1.0
SG J:CYS10 2.3 56.5 1.0
SG J:CYS7 2.3 54.8 1.0
SG J:CYS45 2.3 56.4 1.0
CB J:CYS7 3.0 54.8 1.0
N J:CYS45 3.3 56.4 1.0
CB J:CYS44 3.4 56.8 1.0
CB J:CYS10 3.7 56.5 1.0
CB J:CYS45 3.7 56.4 1.0
CA J:CYS45 3.8 56.4 1.0
C J:CYS44 3.9 56.8 1.0
N J:CYS10 4.0 56.5 1.0
CA J:CYS44 4.2 56.8 1.0
NE J:ARG42 4.3 55.5 1.0
CA J:CYS10 4.4 56.5 1.0
CA J:CYS7 4.5 54.8 1.0
CB J:ARG42 4.6 55.5 1.0
O J:CYS44 4.7 56.8 1.0
CB J:THR9 4.8 53.5 1.0
N J:CYS44 4.8 56.8 1.0
CD J:ARG42 4.8 55.5 1.0
N J:GLY11 4.9 53.5 1.0
CB J:LYS12 4.9 53.7 1.0
C J:CYS10 5.0 56.5 1.0
N J:LYS12 5.0 53.7 1.0
C J:CYS7 5.0 54.8 1.0

Zinc binding site 8 out of 10 in 9fd2

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Zinc binding site 8 out of 10 in the Structure of Pol II-Tc-Ner-STK19 Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Pol II-Tc-Ner-STK19 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:95.0
occ:1.00
 SG L:CYS22 2.3 79.2 1.0
SG L:CYS39 2.3 79.0 1.0
SG L:CYS19 2.3 77.8 1.0
SG L:CYS36 2.3 79.3 1.0
CB L:CYS19 3.1 77.8 1.0
CB L:CYS36 3.4 79.3 1.0
CB L:CYS39 3.5 79.0 1.0
CB L:CYS22 3.6 79.2 1.0
N L:CYS22 3.8 79.2 1.0
N L:CYS39 3.9 79.0 1.0
CA L:CYS22 4.2 79.2 1.0
CB L:TYR41 4.2 76.3 1.0
CA L:CYS39 4.2 79.0 1.0
OG1 L:THR24 4.2 80.2 1.0
CA L:CYS19 4.6 77.8 1.0
N L:TYR41 4.6 76.3 1.0
CB L:GLU38 4.6 80.0 1.0
C L:CYS22 4.6 79.2 1.0
N L:HIS23 4.7 77.8 1.0
C L:CYS39 4.7 79.0 1.0
CB L:GLU21 4.8 80.2 1.0
CA L:CYS36 4.8 79.3 1.0
N L:GLY40 4.8 77.3 1.0
C L:GLU21 4.9 80.2 1.0
C L:GLU38 4.9 80.0 1.0
N L:GLU21 4.9 80.2 1.0
N L:THR24 4.9 80.2 1.0
CB L:THR24 4.9 80.2 1.0

Zinc binding site 9 out of 10 in 9fd2

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Zinc binding site 9 out of 10 in the Structure of Pol II-Tc-Ner-STK19 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Pol II-Tc-Ner-STK19 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Zn1001

b:137.1
occ:1.00
 SG f:CYS53 2.3 81.5 1.0
SG f:CYS26 2.3 89.5 1.0
SG f:CYS29 2.3 82.4 1.0
SG f:CYS50 2.3 87.2 1.0
CB f:CYS26 2.9 89.5 1.0
CB f:CYS50 3.2 87.2 1.0
CB f:CYS29 3.3 82.4 1.0
CB f:CYS53 3.8 81.5 1.0
N f:CYS53 3.9 81.5 1.0
N f:CYS29 3.9 82.4 1.0
CA f:CYS29 4.2 82.4 1.0
CA f:CYS53 4.3 81.5 1.0
CA f:CYS26 4.4 89.5 1.0
N f:LEU54 4.6 81.7 1.0
CA f:CYS50 4.6 87.2 1.0
CB f:VAL52 4.8 77.6 1.0
C f:CYS53 4.8 81.5 1.0
N f:VAL52 4.8 77.6 1.0
O f:SER34 4.9 85.6 1.0
C f:VAL52 5.0 77.6 1.0
CB f:PHE28 5.0 79.5 1.0

Zinc binding site 10 out of 10 in 9fd2

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Zinc binding site 10 out of 10 in the Structure of Pol II-Tc-Ner-STK19 Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Pol II-Tc-Ner-STK19 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
d:Zn1001

b:170.8
occ:1.00
 ND1 d:HIS588 2.1 161.0 1.0
CE1 d:HIS588 2.3 161.0 1.0
SG d:CYS567 2.3 167.3 1.0
SG d:CYS585 2.3 157.3 1.0
SG d:CYS577 2.3 164.0 1.0
CB d:CYS567 2.9 167.3 1.0
CB d:CYS585 3.2 157.3 1.0
CB d:CYS577 3.3 164.0 1.0
CG d:HIS588 3.3 161.0 1.0
NE2 d:HIS588 3.5 161.0 1.0
CD2 d:HIS588 4.0 161.0 1.0
CB d:HIS588 4.2 161.0 1.0
CB d:ALA569 4.3 170.0 1.0
CB d:ARG579 4.3 145.4 1.0
CA d:CYS567 4.4 167.3 1.0
CA d:CYS585 4.7 157.3 1.0
CA d:CYS577 4.7 164.0 1.0
C d:CYS567 4.9 167.3 1.0
N d:ALA569 4.9 170.0 1.0
N d:HIS588 5.0 161.0 1.0

Reference:

S.-H.Lee, T.K.Sixma. Structure of Pol II-Tc-Ner-STK19 Complex Mol.Cell 2024.
ISSN: ISSN 1097-2765
DOI: 10.1016/J.MOLCEL.2024.10.030
Page generated: Wed Nov 27 21:14:12 2024

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