Zinc in PDB 8yfq: Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex

Enzymatic activity of Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex

All present enzymatic activity of Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex:
2.7.7.6;

Other elements in 8yfq:

The structure of Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex (pdb code 8yfq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex, PDB code: 8yfq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8yfq

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Zinc binding site 1 out of 8 in the Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:134.4
occ:1.00
 NE2 A:HIS80 2.1 64.2 1.0
SG A:CYS70 2.3 84.8 1.0
SG A:CYS77 2.3 69.2 1.0
SG A:CYS67 2.3 89.5 1.0
CB A:CYS70 2.9 84.8 1.0
CB A:CYS67 3.0 89.5 1.0
CE1 A:HIS80 3.0 64.2 1.0
CD2 A:HIS80 3.1 64.2 1.0
CB A:CYS77 3.2 69.2 1.0
N A:CYS70 3.5 84.8 1.0
CA A:CYS70 3.8 84.8 1.0
ND1 A:HIS80 4.1 64.2 1.0
CA A:CYS77 4.1 69.2 1.0
CG A:HIS80 4.2 64.2 1.0
CA A:CYS67 4.5 89.5 1.0
N A:GLY71 4.6 86.0 1.0
C A:CYS70 4.6 84.8 1.0
C A:THR69 4.7 77.8 1.0
CB A:THR69 4.8 77.8 1.0
CA A:GLY59 4.8 73.3 1.0
C A:CYS77 4.9 69.2 1.0
CD A:PRO78 4.9 59.9 1.0
N A:THR69 5.0 77.8 1.0
C A:CYS67 5.0 89.5 1.0
N A:GLY79 5.0 62.5 1.0

Zinc binding site 2 out of 8 in 8yfq

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Zinc binding site 2 out of 8 in the Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:168.1
occ:1.00
 SG A:CYS107 2.3 107.1 1.0
SG A:CYS168 2.3 120.1 1.0
SG A:CYS110 2.3 110.1 1.0
SG A:CYS148 2.3 117.0 1.0
CB A:CYS107 3.2 107.1 1.0
CB A:CYS148 3.3 117.0 1.0
N A:CYS168 3.6 120.1 1.0
CB A:CYS168 3.7 120.1 1.0
CB A:CYS110 3.7 110.1 1.0
N A:CYS110 3.8 110.1 1.0
CA A:CYS168 4.2 120.1 1.0
NE2 A:GLN172 4.2 111.3 1.0
CA A:CYS110 4.4 110.1 1.0
CA A:GLY167 4.5 117.4 1.0
CB A:ASN109 4.5 112.0 1.0
C A:GLY167 4.6 117.4 1.0
CA A:CYS107 4.6 107.1 1.0
N A:GLY169 4.7 115.1 1.0
CA A:CYS148 4.8 117.0 1.0
N A:ASN109 4.8 112.0 1.0
C A:CYS168 4.8 120.1 1.0
C A:ASN109 4.8 112.0 1.0
CA A:ASN109 5.0 112.0 1.0

Zinc binding site 3 out of 8 in 8yfq

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Zinc binding site 3 out of 8 in the Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination 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 Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:118.8
occ:1.00
 SG B:CYS1166 2.3 64.0 1.0
SG B:CYS1185 2.3 80.3 1.0
SG B:CYS1163 2.3 61.6 1.0
SG B:CYS1182 2.3 78.4 1.0
CB B:CYS1163 3.2 61.6 1.0
CB B:CYS1185 3.3 80.3 1.0
CB B:CYS1166 3.3 64.0 1.0
CB B:CYS1182 3.5 78.4 1.0
N B:CYS1166 3.7 64.0 1.0
N B:CYS1185 3.9 80.3 1.0
CA B:CYS1166 4.2 64.0 1.0
CA B:CYS1185 4.2 80.3 1.0
CB B:ILE1165 4.6 66.3 1.0
CA B:CYS1163 4.7 61.6 1.0
CB B:SER1184 4.8 78.3 1.0
CA B:CYS1182 4.8 78.4 1.0
C B:ILE1165 4.8 66.3 1.0
OG B:SER1170 4.9 64.2 1.0
N B:ILE1165 5.0 66.3 1.0

Zinc binding site 4 out of 8 in 8yfq

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Zinc binding site 4 out of 8 in the Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:161.2
occ:1.00
 SG C:CYS91 2.3 70.7 1.0
SG C:CYS87 2.3 97.2 1.0
SG C:CYS85 2.3 71.2 1.0
SG C:CYS94 2.3 58.6 1.0
CB C:CYS91 3.1 70.7 1.0
CB C:CYS94 3.1 58.6 1.0
N C:CYS91 3.2 70.7 1.0
CB C:CYS87 3.3 97.2 1.0
CB C:CYS85 3.5 71.2 1.0
CA C:CYS91 3.6 70.7 1.0
C C:TYR90 4.1 74.2 1.0
N C:CYS94 4.2 58.6 1.0
CA C:CYS94 4.3 58.6 1.0
C C:CYS91 4.3 70.7 1.0
CA C:TYR90 4.4 74.2 1.0
CA C:CYS87 4.5 97.2 1.0
N C:CYS87 4.5 97.2 1.0
O C:CYS91 4.5 70.7 1.0
CG C:GLU93 4.8 62.3 1.0
CA C:CYS85 4.9 71.2 1.0

Zinc binding site 5 out of 8 in 8yfq

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Zinc binding site 5 out of 8 in the Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:180.8
occ:1.00
 SG I:CYS75 2.3 122.7 1.0
SG I:CYS78 2.3 123.1 1.0
SG I:CYS106 2.3 106.7 1.0
SG I:CYS103 2.3 100.2 1.0
CB I:CYS103 3.0 100.2 1.0
CB I:CYS75 3.3 122.7 1.0
CB I:CYS78 3.9 123.1 1.0
CB I:CYS106 3.9 106.7 1.0
OG I:SER80 3.9 118.9 1.0
N I:CYS106 4.0 106.7 1.0
OE2 I:GLU77 4.1 120.9 1.0
CB I:SER80 4.2 118.9 1.0
CA I:CYS103 4.5 100.2 1.0
CA I:CYS106 4.6 106.7 1.0
N I:CYS78 4.6 123.1 1.0
CA I:CYS78 4.7 123.1 1.0
N I:SER80 4.8 118.9 1.0
CA I:CYS75 4.8 122.7 1.0
CB I:ASN105 4.8 107.1 1.0
N I:ASN105 4.8 107.1 1.0
N I:LEU104 4.9 101.5 1.0
CD I:GLU77 4.9 120.9 1.0

Zinc binding site 6 out of 8 in 8yfq

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Zinc binding site 6 out of 8 in the Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination 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 Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:187.9
occ:1.00
 SG I:CYS10 2.3 119.7 1.0
SG I:CYS7 2.3 117.4 1.0
SG I:CYS32 2.3 119.3 1.0
SG I:CYS29 2.3 118.1 1.0
CB I:CYS7 3.2 117.4 1.0
CB I:CYS29 3.3 118.1 1.0
CB I:CYS32 3.7 119.3 1.0
N I:CYS32 4.0 119.3 1.0
CB I:CYS10 4.0 119.7 1.0
CA I:CYS32 4.4 119.3 1.0
CB I:ASN31 4.4 111.7 1.0
N I:CYS10 4.5 119.7 1.0
OE2 I:GLU9 4.5 122.9 1.0
CB I:TYR34 4.5 113.4 1.0
CA I:CYS7 4.6 117.4 1.0
CG I:GLU9 4.7 122.9 1.0
CA I:CYS29 4.7 118.1 1.0
CD I:GLU9 4.7 122.9 1.0
C I:ASN31 4.8 111.7 1.0
CA I:CYS10 4.8 119.7 1.0
C I:CYS32 4.9 119.3 1.0
CB I:ASN12 4.9 108.3 1.0

Zinc binding site 7 out of 8 in 8yfq

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Zinc binding site 7 out of 8 in the Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination 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 Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:71.2
occ:1.00
 SG J:CYS10 2.3 17.5 1.0
SG J:CYS45 2.3 18.6 1.0
SG J:CYS44 2.3 20.1 1.0
SG J:CYS7 2.3 15.7 1.0
CB J:CYS7 3.2 15.7 1.0
N J:CYS45 3.2 18.6 1.0
CB J:CYS44 3.4 20.1 1.0
CB J:CYS45 3.6 18.6 1.0
CB J:CYS10 3.7 17.5 1.0
CA J:CYS45 3.8 18.6 1.0
C J:CYS44 3.8 20.1 1.0
N J:CYS10 4.0 17.5 1.0
CA J:CYS44 4.2 20.1 1.0
NE J:ARG42 4.3 19.4 1.0
CA J:CYS10 4.4 17.5 1.0
NH2 J:ARG42 4.6 19.4 1.0
O J:CYS44 4.6 20.1 1.0
CA J:CYS7 4.6 15.7 1.0
CB J:LYS12 4.6 14.4 1.0
N J:GLY11 4.7 15.6 1.0
CB J:SER9 4.8 16.9 1.0
N J:CYS44 4.8 20.1 1.0
N J:LYS12 4.9 14.4 1.0
CB J:ARG42 4.9 19.4 1.0
CZ J:ARG42 4.9 19.4 1.0

Zinc binding site 8 out of 8 in 8yfq

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Zinc binding site 8 out of 8 in the Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo Em Structure of Komagataella Phaffii Rnapii-RAT1-RAI1 Pre- Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:127.3
occ:1.00
 SG L:CYS50 2.3 87.4 1.0
SG L:CYS33 2.3 73.6 1.0
SG L:CYS53 2.3 90.8 1.0
SG L:CYS36 2.3 82.6 1.0
CB L:CYS33 3.0 73.6 1.0
CB L:CYS50 3.1 87.4 1.0
CB L:CYS53 3.6 90.8 1.0
CB L:CYS36 3.8 82.6 1.0
N L:CYS36 3.9 82.6 1.0
CB L:HIS55 4.3 71.8 1.0
N L:CYS53 4.3 90.8 1.0
CA L:CYS36 4.4 82.6 1.0
CA L:CYS53 4.5 90.8 1.0
CA L:CYS33 4.5 73.6 1.0
CB L:ALA35 4.5 74.9 1.0
CA L:CYS50 4.6 87.4 1.0
N L:HIS55 4.8 71.8 1.0
N L:ALA35 4.8 74.9 1.0
C L:ALA35 4.9 74.9 1.0
C L:CYS53 4.9 90.8 1.0
CB L:HIS38 5.0 79.8 1.0
N L:GLY54 5.0 83.6 1.0
OE2 L:GLU52 5.0 90.0 1.0

Reference:

T.Yanagisawa, Y.Murayama, H.Ehara, M.Goto, M.Aoki, S.I.Sekine. Structural Basis of Eukaryotic Transcription Termination By the RAT1 Exonuclease Complex. Nat Commun V. 15 7854 2024.
ISSN: ESSN 2041-1723
PubMed: 39245712
DOI: 10.1038/S41467-024-52157-0
Page generated: Thu Oct 31 14:00:13 2024

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