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Zinc in PDB 7eu0: The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex

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

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

Other elements in 7eu0:

The structure of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex 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 Backtracked Complex (pdb code 7eu0). 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 Backtracked Complex, PDB code: 7eu0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7eu0

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


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 Backtracked Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1601

b:61.2
occ:1.00
 SG A:CYS67 2.3 37.0 1.0
NE2 A:HIS70 2.3 35.0 1.0
SG A:CYS56 2.3 44.1 1.0
CB A:CYS59 2.9 45.5 1.0
CD2 A:HIS70 3.1 35.0 1.0
CB A:CYS56 3.1 44.1 1.0
SG A:CYS59 3.2 45.5 1.0
N A:CYS59 3.3 45.5 1.0
CE1 A:HIS70 3.5 35.0 1.0
CA A:CYS59 3.7 45.5 1.0
CB A:CYS67 4.0 37.0 1.0
O A:GLU68 4.0 35.3 1.0
CB A:THR58 4.0 40.7 1.0
CG A:HIS70 4.3 35.0 1.0
C A:THR58 4.3 40.7 1.0
ND1 A:HIS70 4.5 35.0 1.0
CG2 A:THR58 4.6 40.7 1.0
CA A:THR58 4.6 40.7 1.0
CA A:CYS56 4.6 44.1 1.0
N A:THR58 4.7 40.7 1.0
CA A:CYS67 4.8 37.0 1.0
O A:ARG46 4.9 51.1 1.0
C A:CYS59 4.9 45.5 1.0
C A:CYS56 5.0 44.1 1.0
N A:GLU68 5.0 35.3 1.0

Zinc binding site 2 out of 8 in 7eu0

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


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 Backtracked Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1603

b:69.7
occ:1.00
 NE2 A:HIS985 2.0 17.0 1.0
ND1 A:HIS983 2.0 23.6 1.0
SG A:CYS1044 2.3 21.4 1.0
SG A:CYS1031 2.3 43.2 1.0
CE1 A:HIS983 2.8 23.6 1.0
CD2 A:HIS985 2.9 17.0 1.0
CE1 A:HIS985 3.1 17.0 1.0
CB A:CYS1031 3.1 43.2 1.0
CG A:HIS983 3.2 23.6 1.0
CB A:CYS1044 3.6 21.4 1.0
CB A:HIS983 3.7 23.6 1.0
NE2 A:HIS983 4.0 23.6 1.0
CG A:HIS985 4.1 17.0 1.0
ND1 A:HIS985 4.2 17.0 1.0
CD2 A:HIS983 4.2 23.6 1.0
CB A:SER1033 4.3 44.2 1.0
CA A:CYS1031 4.6 43.2 1.0
CA A:HIS983 4.7 23.6 1.0
CA A:CYS1044 4.8 21.4 1.0

Zinc binding site 3 out of 8 in 7eu0

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


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 Backtracked Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:97.5
occ:1.00
 CB B:CYS1111 1.4 49.3 1.0
SG B:CYS1133 2.3 51.2 1.0
SG B:CYS1136 2.3 50.6 1.0
SG B:CYS1108 2.4 42.5 1.0
SG B:CYS1111 2.4 49.3 1.0
CA B:CYS1111 2.8 49.3 1.0
CB B:CYS1108 3.1 42.5 1.0
N B:CYS1111 3.3 49.3 1.0
C B:CYS1111 3.7 49.3 1.0
CB B:CYS1133 3.7 51.2 1.0
CB B:CYS1136 3.9 50.6 1.0
N B:LYS1112 4.2 42.7 1.0
N B:CYS1136 4.2 50.6 1.0
O B:CYS1111 4.4 49.3 1.0
OG1 B:THR1113 4.4 41.8 1.0
CA B:CYS1108 4.6 42.5 1.0
C B:LYS1110 4.6 43.1 1.0
CB B:VAL1135 4.6 46.5 1.0
CA B:CYS1136 4.7 50.6 1.0
N B:THR1113 4.9 41.8 1.0

Zinc binding site 4 out of 8 in 7eu0

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


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 Backtracked Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:84.1
occ:1.00
 SG C:CYS102 2.3 30.8 1.0
CB C:CYS93 2.3 48.8 1.0
SG C:CYS93 2.7 48.8 1.0
CB C:CYS99 2.8 38.1 1.0
SG C:CYS90 2.9 33.6 1.0
CB C:CYS102 3.2 30.8 1.0
SG C:CYS99 3.4 38.1 1.0
N C:CYS102 3.5 30.8 1.0
CA C:CYS93 3.7 48.8 1.0
CA C:CYS102 3.9 30.8 1.0
CA C:CYS99 4.1 38.1 1.0
O C:CYS93 4.2 48.8 1.0
N C:SER103 4.2 21.6 1.0
N C:GLU100 4.2 41.9 1.0
CB C:CYS90 4.3 33.6 1.0
N C:PHE101 4.3 39.7 1.0
C C:CYS93 4.3 48.8 1.0
N C:CYS93 4.4 48.8 1.0
C C:CYS99 4.4 38.1 1.0
C C:CYS102 4.5 30.8 1.0
C C:PHE101 4.7 39.7 1.0
OG C:SER103 4.7 21.6 1.0

Zinc binding site 5 out of 8 in 7eu0

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


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 Backtracked Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:43.8
occ:1.00
 SG I:CYS79 2.3 24.9 1.0
SG I:CYS103 2.3 12.0 1.0
SG I:CYS76 2.3 21.6 1.0
SG I:CYS108 2.4 13.5 1.0
CB I:CYS76 2.5 21.6 1.0
CB I:CYS103 3.2 12.0 1.0
CB I:CYS108 3.3 13.5 1.0
CB I:CYS79 3.9 24.9 1.0
N I:CYS79 3.9 24.9 1.0
O I:CYS79 4.0 24.9 1.0
CA I:CYS76 4.0 21.6 1.0
CA I:CYS79 4.3 24.9 1.0
C I:CYS79 4.5 24.9 1.0
CA I:CYS103 4.6 12.0 1.0
CB I:ASN105 4.7 13.4 1.0
C I:CYS76 4.7 21.6 1.0
CB I:HIS110 4.7 13.1 1.0
CA I:CYS108 4.7 13.5 1.0
CB I:HIS81 4.7 21.7 1.0
N I:CYS76 4.8 21.6 1.0
N I:SER77 4.8 24.4 1.0
N I:LYS78 4.9 22.0 1.0
CZ3 I:TRP112 5.0 21.5 1.0

Zinc binding site 6 out of 8 in 7eu0

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


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 Backtracked Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:73.4
occ:1.00
 CB I:CYS10 1.5 46.9 1.0
SG I:CYS32 2.3 48.3 1.0
SG I:CYS29 2.4 42.8 1.0
SG I:CYS7 2.4 36.8 1.0
SG I:CYS10 2.4 46.9 1.0
CA I:CYS10 2.9 46.9 1.0
CB I:CYS7 3.0 36.8 1.0
N I:CYS10 3.4 46.9 1.0
CB I:CYS29 3.6 42.8 1.0
C I:CYS10 3.6 46.9 1.0
CB I:CYS32 3.7 48.3 1.0
N I:ASN11 4.0 35.3 1.0
CB I:ASN12 4.2 33.2 1.0
N I:CYS32 4.2 48.3 1.0
N I:ASN12 4.2 33.2 1.0
O I:CYS10 4.3 46.9 1.0
CA I:CYS32 4.5 48.3 1.0
CA I:CYS7 4.5 36.8 1.0
CG I:ASN12 4.7 33.2 1.0
C I:GLU9 4.7 48.5 1.0
CA I:ASN12 4.8 33.2 1.0
CB I:ASN31 5.0 54.3 1.0
CA I:CYS29 5.0 42.8 1.0

Zinc binding site 7 out of 8 in 7eu0

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


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 Backtracked Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn200

b:20.4
occ:1.00
 CB J:CYS10 1.3 8.9 1.0
SG J:CYS45 2.3 7.4 1.0
SG J:CYS44 2.4 10.4 1.0
SG J:CYS10 2.4 8.9 1.0
SG J:CYS7 2.4 12.1 1.0
CA J:CYS10 2.7 8.9 1.0
N J:CYS10 3.2 8.9 1.0
CB J:CYS7 3.3 12.1 1.0
N J:CYS45 3.5 7.4 1.0
CB J:CYS45 3.7 7.4 1.0
C J:CYS10 3.7 8.9 1.0
CB J:CYS44 3.7 10.4 1.0
C J:CYS44 3.8 10.4 1.0
CA J:CYS45 3.8 7.4 1.0
N J:GLY11 3.9 9.6 1.0
O J:CYS44 4.1 10.4 1.0
CA J:CYS44 4.4 10.4 1.0
C J:THR9 4.4 11.7 1.0
N J:LYS12 4.6 8.3 1.0
NE J:ARG42 4.7 12.9 1.0
CA J:CYS7 4.7 12.1 1.0
O J:CYS10 4.7 8.9 1.0
NH2 J:ARG42 4.7 12.9 1.0
CB J:LYS12 4.9 8.3 1.0
CG2 J:THR9 5.0 11.7 1.0

Zinc binding site 8 out of 8 in 7eu0

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


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 Backtracked Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:56.0
occ:1.00
 SG L:CYS32 2.3 35.0 1.0
SG L:CYS15 2.3 33.0 1.0
SG L:CYS29 2.3 32.1 1.0
CB L:CYS32 2.6 35.0 1.0
SG L:CYS12 2.9 25.0 1.0
CB L:CYS29 3.3 32.1 1.0
CB L:CYS12 3.4 25.0 1.0
O L:GLY13 3.6 27.9 1.0
CB L:CYS15 4.1 33.0 1.0
CA L:CYS32 4.1 35.0 1.0
C L:CYS32 4.7 35.0 1.0
CA L:CYS12 4.7 25.0 1.0
CA L:CYS29 4.8 32.1 1.0
O L:CYS32 4.8 35.0 1.0
O L:CYS15 4.8 33.0 1.0
C L:GLY13 4.8 27.9 1.0
C L:CYS12 4.9 25.0 1.0
N L:CYS32 4.9 35.0 1.0
N L:CYS15 4.9 33.0 1.0
N L:GLY13 5.0 27.9 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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