Zinc in PDB 7obb: Cryo-Em Structure of Human Rna Polymerase I Open Complex

Enzymatic activity of Cryo-Em Structure of Human Rna Polymerase I Open Complex

All present enzymatic activity of Cryo-Em Structure of Human Rna Polymerase I Open Complex:
2.7.7.6;

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Human Rna Polymerase I Open Complex (pdb code 7obb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Cryo-Em Structure of Human Rna Polymerase I Open Complex, PDB code: 7obb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 7obb

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Zinc binding site 1 out of 7 in the Cryo-Em Structure of Human Rna Polymerase I Open 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 Cryo-Em Structure of Human Rna Polymerase I Open Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:132.2
occ:1.00
 NE2 A:HIS77 2.2 105.2 1.0
SG A:CYS64 2.5 113.7 1.0
CB A:CYS67 2.6 113.7 1.0
SG A:CYS67 2.9 113.7 1.0
CE1 A:HIS77 3.1 105.2 1.0
CD2 A:HIS77 3.1 105.2 1.0
SG A:CYS74 3.3 112.3 1.0
N A:CYS67 3.6 113.7 1.0
CA A:CYS67 3.6 113.7 1.0
CB A:CYS64 4.1 113.7 1.0
ND1 A:HIS77 4.2 105.2 1.0
CG A:HIS77 4.3 105.2 1.0
C A:CYS67 4.3 113.7 1.0
CB A:CYS74 4.4 112.3 1.0
O A:CYS67 4.5 113.7 1.0
C A:THR66 4.8 111.1 1.0
CB A:THR66 4.9 111.1 1.0
CA A:CYS74 5.0 112.3 1.0

Zinc binding site 2 out of 7 in 7obb

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Zinc binding site 2 out of 7 in the Cryo-Em Structure of Human Rna Polymerase I Open 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 Cryo-Em Structure of Human Rna Polymerase I Open Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:175.7
occ:1.00
 SG A:CYS107 2.5 127.0 1.0
SG A:CYS205 2.5 121.2 1.0
SG A:CYS104 2.5 125.7 1.0
CB A:CYS104 2.9 125.7 1.0
CB A:CYS205 2.9 121.2 1.0
SG A:CYS208 4.1 117.5 1.0
CB A:CYS107 4.3 127.0 1.0
OD1 A:ASN106 4.3 128.0 1.0
CA A:CYS205 4.4 121.2 1.0
CA A:CYS104 4.4 125.7 1.0
CB A:THR210 4.5 116.3 1.0
O A:THR210 4.7 116.3 1.0
O A:CYS107 4.7 127.0 1.0
CE1 A:HIS207 4.9 117.2 1.0

Zinc binding site 3 out of 7 in 7obb

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Zinc binding site 3 out of 7 in the Cryo-Em Structure of Human Rna Polymerase I Open Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Human Rna Polymerase I Open Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:143.2
occ:1.00
 SG B:CYS1101 2.5 110.3 1.0
SG B:CYS1098 2.6 108.0 1.0
CB B:CYS1070 2.8 104.2 1.0
SG B:CYS1070 2.9 104.2 1.0
CB B:CYS1073 3.2 103.0 1.0
SG B:CYS1073 3.4 103.0 1.0
N B:CYS1073 3.8 103.0 1.0
CB B:CYS1101 3.8 110.3 1.0
OG B:SER1078 4.0 100.4 1.0
CB B:CYS1098 4.0 108.0 1.0
CA B:CYS1073 4.1 103.0 1.0
CA B:CYS1070 4.3 104.2 1.0
N B:CYS1101 4.4 110.3 1.0
O B:CYS1070 4.5 104.2 1.0
N B:GLY1074 4.6 97.6 1.0
C B:CYS1070 4.7 104.2 1.0
CB B:SER1078 4.7 100.4 1.0
CA B:CYS1101 4.7 110.3 1.0
CB B:LEU1100 4.8 107.8 1.0
CB B:LYS1072 4.8 103.3 1.0
N B:CYS1070 4.9 104.2 1.0
C B:CYS1073 4.9 103.0 1.0
C B:LYS1072 5.0 103.3 1.0

Zinc binding site 4 out of 7 in 7obb

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Zinc binding site 4 out of 7 in the Cryo-Em Structure of Human Rna Polymerase I Open 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 Cryo-Em Structure of Human Rna Polymerase I Open Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:98.1
occ:1.00
 SG I:CYS20 2.4 66.7 1.0
SG I:CYS38 2.4 76.8 1.0
SG I:CYS41 2.5 75.8 1.0
SG I:CYS23 2.5 71.7 1.0
CB I:CYS38 2.5 76.8 1.0
CB I:CYS20 2.7 66.7 1.0
CB I:CYS41 4.0 75.8 1.0
CA I:CYS38 4.1 76.8 1.0
CB I:CYS23 4.1 71.7 1.0
CA I:CYS20 4.2 66.7 1.0
N I:CYS23 4.2 71.7 1.0
CB I:PHE43 4.5 81.3 1.0
N I:CYS41 4.6 75.8 1.0
CA I:CYS23 4.6 71.7 1.0
CB I:SER25 4.8 57.9 1.0
C I:CYS38 4.8 76.8 1.0
N I:CYS38 4.8 76.8 1.0
C I:CYS23 4.9 71.7 1.0
CA I:CYS41 4.9 75.8 1.0
CG I:ARG40 4.9 75.6 1.0
O I:CYS23 4.9 71.7 1.0
C I:CYS20 5.0 66.7 1.0

Zinc binding site 5 out of 7 in 7obb

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Zinc binding site 5 out of 7 in the Cryo-Em Structure of Human Rna Polymerase I Open 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 Cryo-Em Structure of Human Rna Polymerase I Open Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:152.4
occ:1.00
 SG I:CYS115 2.4 78.4 1.0
SG I:CYS118 2.4 87.8 1.0
SG I:CYS87 2.4 89.4 1.0
SG I:CYS90 2.4 97.1 1.0
CB I:CYS115 2.8 78.4 1.0
CB I:CYS87 3.3 89.4 1.0
CB I:CYS118 3.7 87.8 1.0
N I:CYS118 3.7 87.8 1.0
CB I:CYS90 3.7 97.1 1.0
CA I:CYS118 4.1 87.8 1.0
N I:CYS90 4.2 97.1 1.0
CA I:CYS115 4.3 78.4 1.0
N I:LYS119 4.4 83.8 1.0
C I:CYS118 4.5 87.8 1.0
CA I:CYS90 4.5 97.1 1.0
N I:PHE120 4.6 80.6 1.0
CB I:PHE120 4.7 80.6 1.0
CA I:CYS87 4.7 89.4 1.0
C I:CYS115 4.8 78.4 1.0
N I:ASN117 4.8 83.6 1.0
C I:ASN117 4.8 83.6 1.0
CB I:HIS92 4.8 85.3 1.0
N I:THR116 4.9 79.8 1.0
CB I:ASN117 5.0 83.6 1.0

Zinc binding site 6 out of 7 in 7obb

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Zinc binding site 6 out of 7 in the Cryo-Em Structure of Human Rna Polymerase I Open Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Human Rna Polymerase I Open Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:52.7
occ:1.00
 SG J:CYS45 2.4 44.0 1.0
SG J:CYS7 2.5 29.8 1.0
SG J:CYS10 2.5 32.8 1.0
O J:CYS10 2.6 32.8 1.0
SG J:CYS44 2.8 40.4 1.0
CB J:CYS7 3.3 29.8 1.0
N J:CYS10 3.4 32.8 1.0
C J:CYS10 3.5 32.8 1.0
CB J:CYS10 3.7 32.8 1.0
CA J:CYS10 3.7 32.8 1.0
CB J:CYS45 3.9 44.0 1.0
N J:CYS45 3.9 44.0 1.0
CA J:CYS45 4.1 44.0 1.0
C J:CYS44 4.1 40.4 1.0
CB J:CYS44 4.2 40.4 1.0
O J:CYS44 4.2 40.4 1.0
NH2 J:ARG42 4.2 38.6 1.0
CB J:THR9 4.5 34.8 1.0
C J:THR9 4.5 34.8 1.0
N J:LYS12 4.6 30.9 1.0
CA J:CYS7 4.7 29.8 1.0
CB J:LYS12 4.7 30.9 1.0
NE J:ARG42 4.7 38.6 1.0
N J:GLY11 4.8 28.7 1.0
CA J:CYS44 4.8 40.4 1.0
N J:THR9 4.8 34.8 1.0
C J:CYS7 4.8 29.8 1.0
CA J:THR9 4.9 34.8 1.0
CZ J:ARG42 5.0 38.6 1.0

Zinc binding site 7 out of 7 in 7obb

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Zinc binding site 7 out of 7 in the Cryo-Em Structure of Human Rna Polymerase I Open Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Human Rna Polymerase I Open Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:82.3
occ:1.00
 SG L:CYS36 2.4 64.3 1.0
SG L:CYS19 2.4 54.7 1.0
SG L:CYS22 2.4 61.1 1.0
SG L:CYS39 2.5 68.6 1.0
CB L:CYS36 2.9 64.3 1.0
CB L:CYS19 3.0 54.7 1.0
CB L:CYS22 3.8 61.1 1.0
CB L:CYS39 3.9 68.6 1.0
N L:CYS22 4.0 61.1 1.0
N L:CYS39 4.1 68.6 1.0
CB L:TYR41 4.2 56.3 1.0
CA L:CYS36 4.4 64.3 1.0
OG1 L:THR24 4.4 56.3 1.0
CA L:CYS39 4.4 68.6 1.0
CA L:CYS22 4.4 61.1 1.0
CA L:CYS19 4.5 54.7 1.0
N L:TYR41 4.6 56.3 1.0
C L:CYS39 4.7 68.6 1.0
N L:GLY40 4.8 62.0 1.0
N L:HIS23 4.8 58.0 1.0
C L:CYS36 4.9 64.3 1.0
C L:CYS22 4.9 61.1 1.0
CB L:GLU38 5.0 68.9 1.0

Reference:

A.D.Misiaszek, M.Girbig, C.W.Mueller. Cryo-Em Structures of Human Rna Polymerase I. To Be Published.
DOI: 10.1038/S41594-021-00693-4
Page generated: Fri Dec 17 11:51:39 2021

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