Atomistry » Zinc » PDB 7esi-7f9c » 7eu1
Atomistry »
  Zinc »
    PDB 7esi-7f9c »
      7eu1 »

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

Go back to Zinc Binding Sites List in 7eu1
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

Go back to Zinc Binding Sites List in 7eu1
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

Go back to Zinc Binding Sites List in 7eu1
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

Go back to Zinc Binding Sites List in 7eu1
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

Go back to Zinc Binding Sites List in 7eu1
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

Go back to Zinc Binding Sites List in 7eu1
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

Go back to Zinc Binding Sites List in 7eu1
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

Go back to Zinc Binding Sites List in 7eu1
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy