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Zinc in PDB 7eu1: The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme

Enzymatic activity of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme

All present enzymatic activity of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme:
2.7.7.48; 2.7.7.6;

Other elements in 7eu1:

The structure of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme (pdb code 7eu1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme, PDB code: 7eu1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7eu1

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Zinc binding site 1 out of 8 in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1601

b:152.0
occ:1.00
 SG A:CYS67 2.3 82.0 1.0
CE1 A:HIS70 2.4 77.5 1.0
SG A:CYS59 2.4 90.8 1.0
ND1 A:HIS70 2.5 77.5 1.0
SG A:CYS56 2.5 93.1 1.0
CB A:CYS56 2.9 93.1 1.0
CB A:CYS67 3.3 82.0 1.0
NE2 A:HIS70 3.6 77.5 1.0
CB A:CYS59 3.8 90.8 1.0
CG A:HIS70 3.8 77.5 1.0
CA A:CYS56 4.3 93.1 1.0
CD2 A:HIS70 4.4 77.5 1.0
CA A:CYS67 4.4 82.0 1.0
O A:LEU47 4.7 72.9 1.0
C A:LEU47 4.7 72.9 1.0
N A:GLY48 4.8 72.4 1.0
CB A:HIS70 4.8 77.5 1.0
CA A:GLY48 4.9 72.4 1.0
O A:ARG46 5.0 69.7 1.0

Zinc binding site 2 out of 8 in 7eu1

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Zinc binding site 2 out of 8 in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1603

b:43.7
occ:1.00
 SG A:CYS1031 2.3 37.8 1.0
SG A:CYS1044 2.3 15.7 1.0
ND1 A:HIS983 2.3 11.1 1.0
NE2 A:HIS985 2.3 8.5 1.0
CD2 A:HIS985 2.7 8.5 1.0
CB A:CYS1031 2.7 37.8 1.0
CG A:HIS983 2.9 11.1 1.0
CB A:HIS983 3.0 11.1 1.0
CB A:CYS1044 3.4 15.7 1.0
CE1 A:HIS983 3.4 11.1 1.0
CE1 A:HIS985 3.6 8.5 1.0
CG A:HIS985 4.0 8.5 1.0
CD2 A:HIS983 4.1 11.1 1.0
CA A:CYS1031 4.1 37.8 1.0
CA A:HIS983 4.3 11.1 1.0
NE2 A:HIS983 4.3 11.1 1.0
ND1 A:HIS985 4.4 8.5 1.0
N A:PHE984 4.7 7.7 1.0
CA A:CYS1044 4.7 15.7 1.0
C A:HIS983 4.8 11.1 1.0
N A:CYS1031 5.0 37.8 1.0

Zinc binding site 3 out of 8 in 7eu1

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Zinc binding site 3 out of 8 in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:138.8
occ:1.00
 CB B:CYS1136 1.7 95.1 1.0
SG B:CYS1111 2.4 71.2 1.0
SG B:CYS1136 2.4 95.1 1.0
CA B:CYS1136 3.1 95.1 1.0
SG B:CYS1108 3.2 64.0 1.0
CB B:CYS1108 3.5 64.0 1.0
SG B:CYS1133 3.6 82.2 1.0
N B:CYS1136 3.7 95.1 1.0
CB B:CYS1133 3.7 82.2 1.0
C B:CYS1136 3.8 95.1 1.0
CB B:CYS1111 4.0 71.2 1.0
N B:VAL1137 4.2 87.1 1.0
O B:VAL1137 4.3 87.1 1.0
N B:CYS1111 4.5 71.2 1.0
O B:CYS1136 4.5 95.1 1.0
C B:VAL1135 4.8 83.3 1.0
CA B:CYS1111 4.9 71.2 1.0
CA B:CYS1108 4.9 64.0 1.0
CG1 B:VAL1135 4.9 83.3 1.0
C B:VAL1137 4.9 87.1 1.0

Zinc binding site 4 out of 8 in 7eu1

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Zinc binding site 4 out of 8 in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:60.6
occ:1.00
 CB C:CYS102 2.7 18.2 1.0
SG C:CYS99 2.9 26.4 1.0
SG C:CYS90 3.0 26.6 1.0
CB C:CYS99 3.6 26.4 1.0
CA C:CYS102 3.6 18.2 1.0
N C:CYS102 3.7 18.2 1.0
CB C:CYS90 3.7 26.6 1.0
SG C:CYS102 3.8 18.2 1.0
SG C:CYS93 3.9 53.9 1.0
CB C:CYS93 4.0 53.9 1.0
C C:CYS102 4.1 18.2 1.0
O C:ALA92 4.2 50.2 1.0
N C:SER103 4.5 17.8 1.0
O C:CYS102 4.6 18.2 1.0
C C:PHE101 4.7 23.1 1.0
O C:CYS90 4.9 26.6 1.0
C C:ALA92 5.0 50.2 1.0
OG C:SER103 5.0 17.8 1.0

Zinc binding site 5 out of 8 in 7eu1

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Zinc binding site 5 out of 8 in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:23.8
occ:1.00
 CB I:CYS79 1.7 21.4 1.0
SG I:CYS103 2.3 8.2 1.0
SG I:CYS79 2.4 21.4 1.0
SG I:CYS108 2.4 13.1 1.0
SG I:CYS76 2.4 16.2 1.0
CA I:CYS79 3.1 21.4 1.0
CB I:CYS108 3.4 13.1 1.0
CB I:CYS76 3.5 16.2 1.0
N I:CYS79 3.7 21.4 1.0
CB I:CYS103 3.7 8.2 1.0
C I:CYS79 3.9 21.4 1.0
N I:GLN80 4.2 19.2 1.0
CB I:ASN105 4.3 12.4 1.0
CB I:HIS81 4.4 16.4 1.0
O I:CYS79 4.6 21.4 1.0
N I:HIS81 4.6 16.4 1.0
ND2 I:ASN105 4.6 12.4 1.0
CA I:CYS108 4.8 13.1 1.0
CA I:CYS76 4.9 16.2 1.0
CG I:ASN105 4.9 12.4 1.0
C I:LYS78 5.0 18.1 1.0

Zinc binding site 6 out of 8 in 7eu1

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Zinc binding site 6 out of 8 in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:136.7
occ:1.00
 CB I:CYS32 2.2 69.3 1.0
SG I:CYS10 2.2 55.2 1.0
SG I:CYS7 2.4 57.9 1.0
CB I:CYS10 2.4 55.2 1.0
SG I:CYS29 2.4 70.2 1.0
SG I:CYS32 2.8 69.3 1.0
CA I:CYS32 3.3 69.3 1.0
N I:CYS32 3.5 69.3 1.0
CB I:CYS7 3.7 57.9 1.0
CB I:CYS29 3.8 70.2 1.0
CA I:CYS10 3.9 55.2 1.0
C I:CYS32 4.2 69.3 1.0
CD2 I:HIS34 4.3 70.1 1.0
N I:ASP33 4.5 66.9 1.0
N I:CYS10 4.7 55.2 1.0
C I:CYS10 4.7 55.2 1.0
C I:ASN31 4.8 63.2 1.0
O I:ARG8 4.9 56.8 1.0
N I:HIS34 5.0 70.1 1.0

Zinc binding site 7 out of 8 in 7eu1

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Zinc binding site 7 out of 8 in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn200

b:12.1
occ:1.00
 SG J:CYS45 2.3 3.6 1.0
SG J:CYS7 2.3 4.4 1.0
N J:CYS45 2.7 3.6 1.0
SG J:CYS44 2.8 5.4 1.0
C J:CYS44 2.8 5.4 1.0
SG J:CYS10 2.9 1.9 1.0
CA J:CYS45 3.1 3.6 1.0
CB J:CYS44 3.1 5.4 1.0
O J:CYS44 3.1 5.4 1.0
CB J:CYS45 3.2 3.6 1.0
CB J:CYS10 3.2 1.9 1.0
CB J:CYS7 3.3 4.4 1.0
CA J:CYS44 3.6 5.4 1.0
N J:CYS10 4.0 1.9 1.0
CA J:CYS10 4.3 1.9 1.0
C J:CYS45 4.6 3.6 1.0
N J:CYS44 4.6 5.4 1.0
CA J:CYS7 4.7 4.4 1.0

Zinc binding site 8 out of 8 in 7eu1

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Zinc binding site 8 out of 8 in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:114.8
occ:1.00
 CB L:CYS15 2.0 42.1 1.0
SG L:CYS29 2.1 69.6 1.0
SG L:CYS32 2.1 62.6 1.0
SG L:CYS15 2.1 42.1 1.0
CB L:CYS32 2.2 62.6 1.0
SG L:CYS12 2.6 28.1 1.0
CA L:CYS15 3.5 42.1 1.0
CA L:CYS32 3.7 62.6 1.0
CB L:CYS12 3.8 28.1 1.0
CB L:CYS29 3.8 69.6 1.0
N L:CYS15 4.2 42.1 1.0
C L:CYS15 4.3 42.1 1.0
N L:CYS32 4.4 62.6 1.0
C L:CYS32 4.5 62.6 1.0
N L:GLY33 4.6 49.3 1.0
N L:GLY16 4.8 35.8 1.0
CB L:GLN17 4.9 38.1 1.0
O L:CYS15 4.9 42.1 1.0
CA L:CYS29 4.9 69.6 1.0
C L:GLU31 5.0 83.1 1.0

Reference:

K.Huang, X.X.Wu, C.L.Fang, Y.Zhang. Pol IV and RDR2: A Two-Rna-Polymerase Machine That Produces Double-Stranded Rna. Science 2021.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ABJ9184
Page generated: Tue Oct 29 20:01:12 2024

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