Zinc in PDB 8yfr: Cryo Em Structure of Komagataella Phaffii RAT1-RAI1 Complex Bound Within the Rnapii Cleft

Enzymatic activity of Cryo Em Structure of Komagataella Phaffii RAT1-RAI1 Complex Bound Within the Rnapii Cleft

All present enzymatic activity of Cryo Em Structure of Komagataella Phaffii RAT1-RAI1 Complex Bound Within the Rnapii Cleft:
2.7.7.6;

Other elements in 8yfr:

The structure of Cryo Em Structure of Komagataella Phaffii RAT1-RAI1 Complex Bound Within the Rnapii Cleft 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 RAT1-RAI1 Complex Bound Within the Rnapii Cleft (pdb code 8yfr). 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 RAT1-RAI1 Complex Bound Within the Rnapii Cleft, PDB code: 8yfr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8yfr

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Zinc binding site 1 out of 8 in the Cryo Em Structure of Komagataella Phaffii RAT1-RAI1 Complex Bound Within the Rnapii Cleft


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 RAT1-RAI1 Complex Bound Within the Rnapii Cleft within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:296.3
occ:1.00
 NE2 A:HIS80 2.1 244.7 1.0
SG A:CYS67 2.3 260.6 1.0
SG A:CYS70 2.3 251.9 1.0
SG A:CYS77 2.3 254.4 1.0
CB A:CYS67 2.7 260.6 1.0
CD2 A:HIS80 2.7 244.7 1.0
CE1 A:HIS80 3.2 244.7 1.0
CB A:CYS77 3.5 254.4 1.0
CB A:CYS70 3.8 251.9 1.0
CG A:HIS80 3.9 244.7 1.0
N A:CYS70 4.0 251.9 1.0
ND1 A:HIS80 4.1 244.7 1.0
CA A:CYS67 4.2 260.6 1.0
CA A:CYS77 4.2 254.4 1.0
N A:GLY79 4.3 247.6 1.0
CD A:PRO78 4.5 237.3 1.0
CA A:GLY79 4.5 247.6 1.0
CA A:CYS70 4.5 251.9 1.0
C A:CYS67 4.6 260.6 1.0
C A:GLY79 4.7 247.6 1.0
CA A:GLY59 4.7 255.3 1.0
C A:CYS77 4.7 254.4 1.0
N A:PRO78 4.7 237.3 1.0
O A:CYS67 4.8 260.6 1.0
CB A:THR69 4.8 251.5 1.0
O A:GLY79 5.0 247.6 1.0
N A:CYS67 5.0 260.6 1.0

Zinc binding site 2 out of 8 in 8yfr

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Zinc binding site 2 out of 8 in the Cryo Em Structure of Komagataella Phaffii RAT1-RAI1 Complex Bound Within the Rnapii Cleft


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 RAT1-RAI1 Complex Bound Within the Rnapii Cleft within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:381.6
occ:1.00
 SG A:CYS110 2.3 296.9 1.0
SG A:CYS107 2.3 303.1 1.0
SG A:CYS168 2.3 293.5 1.0
SG A:CYS148 2.3 314.3 1.0
CB A:CYS107 2.8 303.1 1.0
CB A:CYS148 3.2 314.3 1.0
CB A:CYS168 3.4 293.5 1.0
CB A:CYS110 3.8 296.9 1.0
NE2 A:GLN172 4.1 279.8 1.0
N A:CYS110 4.2 296.9 1.0
N A:CYS168 4.2 293.5 1.0
CA A:CYS107 4.3 303.1 1.0
CA A:CYS168 4.5 293.5 1.0
CA A:CYS110 4.5 296.9 1.0
CA A:CYS148 4.6 314.3 1.0
N A:GLU149 4.6 305.8 1.0
CB A:LYS112 4.7 302.2 1.0
O A:LYS112 4.7 302.2 1.0
C A:CYS107 4.8 303.1 1.0
N A:LYS112 4.8 302.2 1.0
CB A:ASN109 4.9 287.4 1.0
O A:CYS107 4.9 303.1 1.0
CD A:GLN172 4.9 279.8 1.0
C A:CYS148 4.9 314.3 1.0
C A:GLU149 5.0 305.8 1.0

Zinc binding site 3 out of 8 in 8yfr

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Zinc binding site 3 out of 8 in the Cryo Em Structure of Komagataella Phaffii RAT1-RAI1 Complex Bound Within the Rnapii Cleft


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 RAT1-RAI1 Complex Bound Within the Rnapii Cleft within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:260.2
occ:1.00
 SG B:CYS1166 2.3 212.8 1.0
SG B:CYS1182 2.3 206.1 1.0
SG B:CYS1163 2.3 201.8 1.0
SG B:CYS1185 2.3 210.4 1.0
CB B:CYS1166 2.7 212.8 1.0
CB B:CYS1163 2.8 201.8 1.0
N B:CYS1166 3.3 212.8 1.0
CB B:CYS1185 3.4 210.4 1.0
CA B:CYS1166 3.5 212.8 1.0
CB B:CYS1182 3.7 206.1 1.0
N B:CYS1185 3.9 210.4 1.0
OG B:SER1170 4.1 206.0 1.0
CB B:SER1184 4.2 216.5 1.0
CA B:CYS1185 4.3 210.4 1.0
N B:GLY1167 4.3 212.8 1.0
CA B:CYS1163 4.3 201.8 1.0
C B:CYS1166 4.4 212.8 1.0
C B:ILE1165 4.5 204.3 1.0
OG B:SER1184 4.6 216.5 1.0
C B:SER1184 4.7 216.5 1.0
CB B:ILE1165 4.8 204.3 1.0
N B:ILE1165 4.9 204.3 1.0
C B:CYS1163 4.9 201.8 1.0
CA B:SER1184 4.9 216.5 1.0
CA B:ILE1165 5.0 204.3 1.0

Zinc binding site 4 out of 8 in 8yfr

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Zinc binding site 4 out of 8 in the Cryo Em Structure of Komagataella Phaffii RAT1-RAI1 Complex Bound Within the Rnapii Cleft


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 RAT1-RAI1 Complex Bound Within the Rnapii Cleft within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:180.8
occ:1.00
 SG C:CYS91 2.3 123.5 1.0
SG C:CYS85 2.3 139.6 1.0
SG C:CYS87 2.3 156.2 1.0
SG C:CYS94 2.3 106.6 1.0
CB C:CYS91 3.0 123.5 1.0
N C:CYS91 3.3 123.5 1.0
CB C:CYS85 3.3 139.6 1.0
CB C:CYS87 3.4 156.2 1.0
CB C:CYS94 3.5 106.6 1.0
CA C:CYS91 3.6 123.5 1.0
N C:CYS94 4.1 106.6 1.0
C C:CYS91 4.2 123.5 1.0
C C:TYR90 4.2 122.3 1.0
CA C:CYS94 4.4 106.6 1.0
CA C:CYS87 4.5 156.2 1.0
O C:CYS91 4.5 123.5 1.0
N C:CYS87 4.5 156.2 1.0
CA C:TYR90 4.6 122.3 1.0
CA C:CYS85 4.7 139.6 1.0
C C:GLU93 4.7 111.3 1.0
N C:GLU93 4.7 111.3 1.0
CB C:GLU93 4.9 111.3 1.0
N C:ASP92 4.9 107.3 1.0

Zinc binding site 5 out of 8 in 8yfr

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Zinc binding site 5 out of 8 in the Cryo Em Structure of Komagataella Phaffii RAT1-RAI1 Complex Bound Within the Rnapii Cleft


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 RAT1-RAI1 Complex Bound Within the Rnapii Cleft within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:247.8
occ:1.00
 SG I:CYS75 2.3 183.1 1.0
SG I:CYS78 2.3 184.6 1.0
SG I:CYS106 2.3 171.9 1.0
SG I:CYS103 2.3 164.3 1.0
CB I:CYS103 2.8 164.3 1.0
CB I:CYS75 3.2 183.1 1.0
CB I:CYS106 3.4 171.9 1.0
N I:CYS106 3.7 171.9 1.0
CB I:CYS78 3.7 184.6 1.0
CA I:CYS106 4.1 171.9 1.0
OG I:SER80 4.3 175.2 1.0
CA I:CYS103 4.3 164.3 1.0
CB I:ASN105 4.5 168.9 1.0
CB I:SER80 4.5 175.2 1.0
OE2 I:GLU77 4.6 181.0 1.0
CA I:CYS75 4.6 183.1 1.0
N I:CYS78 4.7 184.6 1.0
CA I:CYS78 4.7 184.6 1.0
C I:ASN105 4.7 168.9 1.0
N I:ASN105 4.8 168.9 1.0
C I:CYS103 4.9 164.3 1.0
CD I:GLU77 4.9 181.0 1.0
CA I:ASN105 4.9 168.9 1.0
C I:CYS106 4.9 171.9 1.0

Zinc binding site 6 out of 8 in 8yfr

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Zinc binding site 6 out of 8 in the Cryo Em Structure of Komagataella Phaffii RAT1-RAI1 Complex Bound Within the Rnapii Cleft


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 RAT1-RAI1 Complex Bound Within the Rnapii Cleft within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:254.4
occ:1.00
 SG I:CYS32 2.3 208.3 1.0
SG I:CYS7 2.3 188.3 1.0
SG I:CYS10 2.3 185.4 1.0
SG I:CYS29 2.3 212.4 1.0
CB I:CYS10 2.6 185.4 1.0
CB I:CYS32 2.6 208.3 1.0
CB I:CYS29 3.0 212.4 1.0
CB I:CYS7 3.4 188.3 1.0
N I:CYS32 3.6 208.3 1.0
CA I:CYS32 3.7 208.3 1.0
OE2 I:GLU9 3.8 186.1 1.0
CA I:CYS10 3.9 185.4 1.0
C I:ASN31 4.1 192.4 1.0
N I:CYS10 4.1 185.4 1.0
CA I:CYS29 4.4 212.4 1.0
O I:CYS29 4.4 212.4 1.0
CB I:ASN31 4.5 192.4 1.0
O I:ASN31 4.5 192.4 1.0
C I:CYS29 4.6 212.4 1.0
CD I:GLU9 4.6 186.1 1.0
C I:CYS32 4.6 208.3 1.0
CB I:ASN12 4.7 171.2 1.0
CA I:ASN31 4.7 192.4 1.0
N I:ASN31 4.8 192.4 1.0
CA I:CYS7 4.8 188.3 1.0
OD1 I:ASN12 4.9 171.2 1.0
C I:CYS10 4.9 185.4 1.0

Zinc binding site 7 out of 8 in 8yfr

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Zinc binding site 7 out of 8 in the Cryo Em Structure of Komagataella Phaffii RAT1-RAI1 Complex Bound Within the Rnapii Cleft


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 RAT1-RAI1 Complex Bound Within the Rnapii Cleft within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:93.5
occ:1.00
 SG J:CYS10 2.3 53.7 1.0
SG J:CYS44 2.3 50.9 1.0
SG J:CYS7 2.3 48.9 1.0
SG J:CYS45 2.3 49.2 1.0
CB J:CYS7 3.1 48.9 1.0
N J:CYS45 3.2 49.2 1.0
CB J:CYS10 3.4 53.7 1.0
CB J:CYS44 3.4 50.9 1.0
CB J:CYS45 3.6 49.2 1.0
CA J:CYS45 3.7 49.2 1.0
C J:CYS44 3.8 50.9 1.0
N J:CYS10 4.0 53.7 1.0
CA J:CYS44 4.2 50.9 1.0
CA J:CYS10 4.2 53.7 1.0
NE J:ARG42 4.4 44.6 1.0
NH2 J:ARG42 4.4 44.6 1.0
N J:GLY11 4.5 49.1 1.0
O J:CYS44 4.5 50.9 1.0
CA J:CYS7 4.5 48.9 1.0
CB J:LYS12 4.6 44.8 1.0
N J:LYS12 4.7 44.8 1.0
N J:CYS44 4.8 50.9 1.0
CZ J:ARG42 4.8 44.6 1.0
C J:CYS10 4.9 53.7 1.0
CB J:ARG42 5.0 44.6 1.0

Zinc binding site 8 out of 8 in 8yfr

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Zinc binding site 8 out of 8 in the Cryo Em Structure of Komagataella Phaffii RAT1-RAI1 Complex Bound Within the Rnapii Cleft


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 RAT1-RAI1 Complex Bound Within the Rnapii Cleft within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:151.9
occ:1.00
 SG L:CYS33 2.3 115.7 1.0
SG L:CYS50 2.3 110.5 1.0
SG L:CYS36 2.3 117.6 1.0
SG L:CYS53 2.3 121.1 1.0
CB L:CYS33 3.0 115.7 1.0
CB L:CYS50 3.2 110.5 1.0
CB L:CYS36 3.3 117.6 1.0
CB L:CYS53 3.3 121.1 1.0
N L:CYS36 3.7 117.6 1.0
N L:CYS53 3.7 121.1 1.0
CA L:CYS53 4.0 121.1 1.0
CA L:CYS36 4.0 117.6 1.0
CB L:HIS55 4.2 103.1 1.0
C L:CYS53 4.5 121.1 1.0
CA L:CYS33 4.5 115.7 1.0
N L:HIS55 4.5 103.1 1.0
N L:GLY54 4.6 112.2 1.0
C L:CYS36 4.6 117.6 1.0
CA L:CYS50 4.6 110.5 1.0
N L:ALA37 4.7 115.0 1.0
CB L:GLU52 4.7 118.6 1.0
C L:ALA35 4.8 110.0 1.0
C L:GLU52 4.8 118.6 1.0
CB L:ALA35 4.9 110.0 1.0
N L:ALA35 4.9 110.0 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 14:01:04 2024

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