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Zinc in PDB 8hil: A Cryo-Em Structure of B. Oleracea Rna Polymerase V at 3.57 Angstrom

Other elements in 8hil:

The structure of A Cryo-Em Structure of B. Oleracea Rna Polymerase V at 3.57 Angstrom also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the A Cryo-Em Structure of B. Oleracea Rna Polymerase V at 3.57 Angstrom (pdb code 8hil). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the A Cryo-Em Structure of B. Oleracea Rna Polymerase V at 3.57 Angstrom, PDB code: 8hil:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8hil

Go back to Zinc Binding Sites List in 8hil
Zinc binding site 1 out of 6 in the A Cryo-Em Structure of B. Oleracea Rna Polymerase V at 3.57 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Cryo-Em Structure of B. Oleracea Rna Polymerase V at 3.57 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2101

b:126.1
occ:1.00
 ND1 A:HIS938 2.2 93.4 1.0
CG A:HIS938 2.6 93.4 1.0
CB A:HIS938 2.6 93.4 1.0
NE2 A:HIS940 2.6 90.3 1.0
CD2 A:HIS940 2.8 90.3 1.0
O A:PRO1003 2.9 106.8 1.0
CB A:PRO1003 3.1 106.8 1.0
CE1 A:HIS938 3.3 93.4 1.0
CA A:HIS938 3.6 93.4 1.0
C A:PRO1003 3.6 106.8 1.0
CD2 A:HIS938 3.7 93.4 1.0
CA A:PRO1003 3.8 106.8 1.0
CE1 A:HIS940 3.9 90.3 1.0
CG A:MET1006 3.9 97.0 1.0
SD A:MET1006 4.0 97.0 1.0
NE2 A:HIS938 4.1 93.4 1.0
CG A:HIS940 4.1 90.3 1.0
SG A:CYS988 4.1 120.2 1.0
CG A:PRO1003 4.2 106.8 1.0
N A:ILE939 4.3 82.6 1.0
C A:HIS938 4.3 93.4 1.0
CB A:CYS988 4.4 120.2 1.0
ND1 A:HIS940 4.6 90.3 1.0
O A:CYS1004 4.6 98.3 1.0
N A:HIS938 4.8 93.4 1.0
N A:CYS1004 4.8 98.3 1.0

Zinc binding site 2 out of 6 in 8hil

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Zinc binding site 2 out of 6 in the A Cryo-Em Structure of B. Oleracea Rna Polymerase V at 3.57 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Cryo-Em Structure of B. Oleracea Rna Polymerase V at 3.57 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:129.9
occ:1.00
 SG C:CYS94 2.4 96.8 1.0
SG C:CYS100 2.5 66.9 1.0
SG C:CYS91 2.5 75.4 1.0
CB C:CYS94 2.5 96.8 1.0
CB C:CYS100 3.3 66.9 1.0
SG C:CYS103 3.5 68.4 1.0
CB C:CYS91 3.7 75.4 1.0
CA C:CYS94 3.7 96.8 1.0
C C:ALA93 3.8 88.6 1.0
N C:CYS94 3.8 96.8 1.0
CB C:ALA93 4.1 88.6 1.0
O C:ALA93 4.1 88.6 1.0
CA C:ALA93 4.4 88.6 1.0
N C:ALA93 4.6 88.6 1.0
N C:CYS103 4.7 68.4 1.0
CA C:CYS100 4.8 66.9 1.0
C C:CYS94 4.8 96.8 1.0
CB C:CYS103 4.9 68.4 1.0

Zinc binding site 3 out of 6 in 8hil

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Zinc binding site 3 out of 6 in the A Cryo-Em Structure of B. Oleracea Rna Polymerase V at 3.57 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A Cryo-Em Structure of B. Oleracea Rna Polymerase V at 3.57 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:131.1
occ:1.00
 SG I:CYS29 2.6 90.5 1.0
SG I:CYS32 2.6 97.4 1.0
SG I:CYS7 2.8 87.4 1.0
SG I:CYS10 3.2 95.8 1.0
CB I:CYS29 3.3 90.5 1.0
CB I:CYS10 3.4 95.8 1.0
N I:CYS32 3.5 97.4 1.0
CB I:CYS7 3.7 87.4 1.0
CB I:CYS32 3.8 97.4 1.0
N I:CYS10 3.9 95.8 1.0
CB I:ASN31 4.0 90.5 1.0
CB I:HIS34 4.1 89.4 1.0
CA I:CYS10 4.3 95.8 1.0
CA I:CYS32 4.3 97.4 1.0
N I:ASN31 4.5 90.5 1.0
N I:HIS34 4.5 89.4 1.0
CB I:GLU9 4.5 97.6 1.0
C I:ASN31 4.5 90.5 1.0
CA I:ASN31 4.6 90.5 1.0
CA I:CYS29 4.7 90.5 1.0
N I:ASP33 4.8 92.6 1.0
C I:GLU9 4.9 97.6 1.0
CA I:HIS34 4.9 89.4 1.0
OE1 I:GLU9 4.9 97.6 1.0

Zinc binding site 4 out of 6 in 8hil

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Zinc binding site 4 out of 6 in the A Cryo-Em Structure of B. Oleracea Rna Polymerase V at 3.57 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A Cryo-Em Structure of B. Oleracea Rna Polymerase V at 3.57 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:185.2
occ:1.00
 N I:LYS78 2.2 150.8 1.0
CB I:ALA77 2.7 30.0 1.0
N I:ALA77 2.8 149.6 1.0
CA I:ALA77 2.9 149.6 1.0
C I:ALA77 2.9 149.6 1.0
CA I:LYS78 3.3 150.8 1.0
SG I:CYS108 3.3 137.9 1.0
CB I:LYS78 3.4 150.8 1.0
CD I:LYS78 3.4 150.8 1.0
CA I:CYS108 3.5 137.9 1.0
CB I:CYS108 3.7 137.9 1.0
O I:CYS108 4.0 137.9 1.0
C I:CYS76 4.0 142.5 1.0
CG I:LYS78 4.0 150.8 1.0
N I:CYS79 4.1 151.7 1.0
CB I:CYS76 4.1 142.5 1.0
C I:CYS108 4.1 137.9 1.0
O I:ALA77 4.1 149.6 1.0
C I:LYS78 4.2 150.8 1.0
CZ3 I:TRP112 4.5 134.5 1.0
CA I:CYS76 4.6 142.5 1.0
N I:CYS108 4.6 137.9 1.0
O I:ASN107 4.7 136.8 1.0
CE I:LYS78 4.8 150.8 1.0
CH2 I:TRP112 4.8 134.5 1.0
O I:CYS76 4.9 142.5 1.0
CB I:HIS110 5.0 134.2 1.0

Zinc binding site 5 out of 6 in 8hil

Go back to Zinc Binding Sites List in 8hil
Zinc binding site 5 out of 6 in the A Cryo-Em Structure of B. Oleracea Rna Polymerase V at 3.57 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of A Cryo-Em Structure of B. Oleracea Rna Polymerase V at 3.57 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:100.7
occ:1.00
 NH2 J:ARG42 2.3 31.6 1.0
CZ J:ARG42 2.3 31.6 1.0
SG J:CYS10 2.4 27.1 1.0
CB J:CYS10 2.5 27.1 1.0
NE J:ARG42 2.8 31.6 1.0
SG J:CYS44 2.9 29.4 1.0
NH1 J:ARG42 2.9 31.6 1.0
CD J:ARG42 3.8 31.6 1.0
SG J:CYS45 3.8 30.5 1.0
CA J:CYS10 4.0 27.1 1.0
CB J:ARG42 4.1 31.6 1.0
OG1 C:THR185 4.6 31.6 1.0
CG J:ARG42 4.6 31.6 1.0
O C:ALA184 4.6 29.5 1.0
N J:CYS10 4.6 27.1 1.0
CB J:CYS44 4.6 29.4 1.0
C J:CYS10 4.9 27.1 1.0

Zinc binding site 6 out of 6 in 8hil

Go back to Zinc Binding Sites List in 8hil
Zinc binding site 6 out of 6 in the A Cryo-Em Structure of B. Oleracea Rna Polymerase V at 3.57 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of A Cryo-Em Structure of B. Oleracea Rna Polymerase V at 3.57 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn201

b:109.5
occ:1.00
 SG L:CYS15 2.4 81.6 1.0
SG L:CYS29 2.5 89.7 1.0
SG L:CYS12 2.5 83.1 1.0
SG L:CYS32 2.5 30.0 1.0
CB L:CYS29 2.8 89.7 1.0
CB L:CYS15 3.3 81.6 1.0
CB L:CYS12 3.4 83.1 1.0
OD1 L:ASP14 3.9 77.2 1.0
CB L:CYS32 4.0 30.0 1.0
N L:CYS15 4.1 81.6 1.0
CA L:CYS29 4.2 89.7 1.0
CA L:CYS15 4.3 81.6 1.0
O L:TYR34 4.4 72.1 1.0
O L:ARG30 4.4 94.6 1.0
C L:CYS29 4.5 89.7 1.0
O L:CYS29 4.5 89.7 1.0
CB L:TYR34 4.8 72.1 1.0
CA L:CYS12 4.8 83.1 1.0
N L:CYS29 5.0 89.7 1.0
C L:TYR34 5.0 72.1 1.0

Reference:

G.Xie, X.Du, H.Hu, S.Li, X.Cao, S.E.Jacobsen, J.Du. Structure and Mechanism of the Plant Rna Polymerase V. Science F8231 2023.
ISSN: ESSN 1095-9203
PubMed: 36893216
DOI: 10.1126/SCIENCE.ADF8231
Page generated: Fri Aug 22 10:48:31 2025

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