Zinc in PDB 8him: A Cryo-Em Structure of B. Oleracea Rna Polymerase V Elongation Complex at 2.73 Angstrom

Other elements in 8him:

The structure of A Cryo-Em Structure of B. Oleracea Rna Polymerase V Elongation Complex at 2.73 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 Elongation Complex at 2.73 Angstrom (pdb code 8him). 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 Elongation Complex at 2.73 Angstrom, PDB code: 8him:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8him

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Zinc binding site 1 out of 6 in the A Cryo-Em Structure of B. Oleracea Rna Polymerase V Elongation Complex at 2.73 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 Elongation Complex at 2.73 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3001

b:155.6
occ:1.00
 ND1 A:HIS938 2.2 121.0 1.0
NE2 A:HIS940 2.4 124.4 1.0
SG A:CYS989 2.5 131.7 1.0
SG A:CYS1004 2.6 125.7 1.0
CD2 A:HIS940 2.9 124.4 1.0
CG A:HIS938 2.9 121.0 1.0
CB A:HIS938 3.0 121.0 1.0
CB A:CYS1004 3.2 125.7 1.0
CE1 A:HIS938 3.4 121.0 1.0
CB A:CYS989 3.5 131.7 1.0
CE1 A:HIS940 3.5 124.4 1.0
CA A:HIS938 4.1 121.0 1.0
CG A:HIS940 4.1 124.4 1.0
CD2 A:HIS938 4.2 121.0 1.0
CB A:PHE991 4.4 127.5 1.0
NE2 A:HIS938 4.4 121.0 1.0
ND1 A:HIS940 4.4 124.4 1.0
CA A:CYS1004 4.5 125.7 1.0
C A:HIS938 4.7 121.0 1.0
CA A:CYS989 4.9 131.7 1.0
N A:PHE991 4.9 127.5 1.0
CG A:MET1006 5.0 120.7 1.0
O A:HIS938 5.0 121.0 1.0

Zinc binding site 2 out of 6 in 8him

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Zinc binding site 2 out of 6 in the A Cryo-Em Structure of B. Oleracea Rna Polymerase V Elongation Complex at 2.73 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 Elongation Complex at 2.73 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn400

b:115.1
occ:1.00
 SG C:CYS102 2.5 60.5 1.0
SG C:CYS99 2.5 65.0 1.0
SG C:CYS93 2.5 97.1 1.0
SG C:CYS90 2.6 74.4 1.0
CB C:CYS93 2.8 97.1 1.0
CB C:CYS99 3.6 65.0 1.0
N C:CYS93 3.7 97.1 1.0
CB C:CYS90 3.7 74.4 1.0
CA C:CYS93 3.8 97.1 1.0
CB C:CYS102 3.8 60.5 1.0
C C:ALA92 3.9 91.5 1.0
O C:ALA92 4.2 91.5 1.0
O C:GLU100 4.2 66.6 1.0
CB C:ALA92 4.4 91.5 1.0
CA C:ALA92 4.4 91.5 1.0
N C:ALA92 4.5 91.5 1.0
C C:CYS93 4.7 97.1 1.0
O C:CYS99 4.9 65.0 1.0
CA C:CYS99 4.9 65.0 1.0
C C:CYS99 4.9 65.0 1.0
N C:CYS102 4.9 60.5 1.0
CA C:CYS102 4.9 60.5 1.0
CA C:CYS90 4.9 74.4 1.0

Zinc binding site 3 out of 6 in 8him

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Zinc binding site 3 out of 6 in the A Cryo-Em Structure of B. Oleracea Rna Polymerase V Elongation Complex at 2.73 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 Elongation Complex at 2.73 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn200

b:30.0
occ:1.00
 SG J:CYS44 2.4 22.8 1.0
SG J:CYS45 2.4 22.2 1.0
SG J:CYS10 2.4 20.1 1.0
SG J:CYS7 2.5 19.0 1.0
CB J:CYS10 3.1 20.1 1.0
CB J:CYS7 3.3 19.0 1.0
N J:CYS45 3.5 22.2 1.0
CB J:CYS45 3.7 22.2 1.0
CB J:CYS44 3.7 22.8 1.0
N J:CYS10 3.7 20.1 1.0
CA J:CYS45 3.8 22.2 1.0
C J:CYS44 3.9 22.8 1.0
CA J:CYS10 4.0 20.1 1.0
NE J:ARG42 4.2 23.0 1.0
O J:CYS44 4.4 22.8 1.0
CA J:CYS44 4.4 22.8 1.0
N J:GLY11 4.6 16.9 1.0
NH2 J:ARG42 4.7 23.0 1.0
C J:CYS10 4.8 20.1 1.0
CA J:CYS7 4.8 19.0 1.0
CB J:THR9 4.8 19.9 1.0
C J:THR9 4.8 19.9 1.0
CB J:ARG42 4.9 23.0 1.0
CB J:LYS12 4.9 17.3 1.0
CZ J:ARG42 4.9 23.0 1.0

Zinc binding site 4 out of 6 in 8him

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Zinc binding site 4 out of 6 in the A Cryo-Em Structure of B. Oleracea Rna Polymerase V Elongation Complex at 2.73 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 Elongation Complex at 2.73 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:101.2
occ:1.00
 SG L:CYS29 2.4 74.0 1.0
SG L:CYS15 2.5 71.9 1.0
SG L:CYS12 2.5 65.8 1.0
SG L:CYS32 2.8 75.7 1.0
CB L:CYS32 2.9 75.7 1.0
CB L:CYS29 3.2 74.0 1.0
CB L:CYS12 3.4 65.8 1.0
N L:CYS32 3.6 75.7 1.0
CA L:CYS32 3.8 75.7 1.0
CB L:CYS15 3.9 71.9 1.0
N L:CYS15 4.1 71.9 1.0
C L:GLU31 4.4 81.8 1.0
CA L:CYS15 4.6 71.9 1.0
CA L:CYS29 4.7 74.0 1.0
CB L:ASP14 4.7 65.9 1.0
CA L:CYS12 4.9 65.8 1.0
N L:GLY33 4.9 66.6 1.0
C L:CYS32 4.9 75.7 1.0
CB L:GLU31 4.9 81.8 1.0
N L:GLU31 4.9 81.8 1.0
CA L:GLU31 4.9 81.8 1.0
N L:GLY16 5.0 72.6 1.0

Zinc binding site 5 out of 6 in 8him

Go back to Zinc Binding Sites List in 8him
Zinc binding site 5 out of 6 in the A Cryo-Em Structure of B. Oleracea Rna Polymerase V Elongation Complex at 2.73 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 Elongation Complex at 2.73 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:164.3
occ:1.00
 N I:GLY82 2.2 147.4 1.0
CA I:GLY82 2.6 147.4 1.0
O I:GLN80 3.1 143.6 1.0
NE I:ARG75 3.1 146.8 1.0
C I:HIS81 3.1 147.1 1.0
NH1 I:ARG75 3.5 146.8 1.0
CZ I:ARG75 3.7 146.8 1.0
CA I:HIS81 3.7 147.1 1.0
C I:GLY82 3.8 147.4 1.0
O I:HIS81 4.0 147.1 1.0
C I:GLN80 4.1 143.6 1.0
CD I:ARG75 4.1 146.8 1.0
O I:GLY82 4.4 147.4 1.0
N I:HIS81 4.4 147.1 1.0
N I:GLU83 4.6 145.2 1.0
CD2 I:HIS81 4.7 147.1 1.0
NH2 I:ARG75 5.0 146.8 1.0

Zinc binding site 6 out of 6 in 8him

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Zinc binding site 6 out of 6 in the A Cryo-Em Structure of B. Oleracea Rna Polymerase V Elongation Complex at 2.73 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 Elongation Complex at 2.73 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:144.7
occ:1.00
 SG I:CYS29 2.5 122.6 1.0
SG I:CYS32 2.5 125.3 1.0
CB I:CYS10 2.6 114.1 1.0
SG I:CYS7 2.7 112.8 1.0
CB I:CYS29 3.2 122.6 1.0
CB I:CYS7 3.2 112.8 1.0
CB I:CYS32 3.6 125.3 1.0
SG I:CYS10 3.6 114.1 1.0
CA I:CYS10 3.9 114.1 1.0
N I:CYS32 4.0 125.3 1.0
N I:CYS10 4.1 114.1 1.0
CA I:CYS32 4.4 125.3 1.0
CB I:ASN12 4.4 104.2 1.0
C I:CYS10 4.4 114.1 1.0
OD1 I:ASN12 4.4 104.2 1.0
CA I:CYS29 4.7 122.6 1.0
N I:ASN11 4.7 104.5 1.0
N I:ASN12 4.7 104.2 1.0
CA I:CYS7 4.8 112.8 1.0
ND2 I:ASN31 4.8 119.0 1.0
CB I:ASN31 4.8 119.0 1.0
CG I:ASN12 4.9 104.2 1.0
C I:ASN31 4.9 119.0 1.0
C I:CYS32 5.0 125.3 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: Thu Oct 31 07:17:33 2024

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