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Zinc in PDB 5vsw: X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex

Enzymatic activity of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex

All present enzymatic activity of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex:
2.7.7.6;

Protein crystallography data

The structure of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex, PDB code: 5vsw was solved by K.S.Murakami, V.Molodtsov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.82 / 4.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 187.274, 205.259, 311.313, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 25.9

Other elements in 5vsw:

The structure of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex (pdb code 5vsw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex, PDB code: 5vsw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5vsw

Go back to Zinc Binding Sites List in 5vsw
Zinc binding site 1 out of 5 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:0.8
occ:1.00
 SG D:CYS70 2.3 0.7 1.0
SG D:CYS72 2.3 0.7 1.0
SG D:CYS85 2.4 0.6 1.0
SG D:CYS88 2.5 0.1 1.0
CB D:CYS85 3.0 0.3 1.0
CB D:CYS72 3.1 0.9 1.0
N D:CYS72 3.6 0.8 1.0
N D:CYS88 3.8 0.9 1.0
O D:CYS88 3.9 0.0 1.0
CA D:CYS72 4.0 0.2 1.0
CB D:LYS87 4.0 0.3 1.0
CB D:CYS70 4.1 0.6 1.0
CB D:CYS88 4.1 0.2 1.0
CA D:CYS88 4.4 0.5 1.0
N D:GLY73 4.4 0.2 1.0
CA D:CYS85 4.5 0.6 1.0
N D:LEU71 4.5 0.9 1.0
C D:CYS88 4.6 0.7 1.0
C D:CYS72 4.6 0.1 1.0
C D:LEU71 4.8 0.8 1.0
C D:LYS87 4.8 0.7 1.0
CA D:LYS87 4.8 0.5 1.0
C D:CYS85 4.9 0.8 1.0
N D:LYS74 4.9 0.6 1.0
N D:LYS87 4.9 0.7 1.0
C D:CYS70 5.0 0.6 1.0

Zinc binding site 2 out of 5 in 5vsw

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Zinc binding site 2 out of 5 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2003

b:0.6
occ:1.00
 SG D:CYS888 2.1 0.5 1.0
SG D:CYS898 2.1 0.6 1.0
SG D:CYS895 2.1 0.7 1.0
SG D:CYS814 2.2 1.0 1.0
CB D:CYS888 3.0 0.2 1.0
CB D:CYS898 3.1 0.5 1.0
CB D:CYS895 3.4 0.5 1.0
CB D:CYS814 3.4 0.1 1.0
CA D:CYS888 3.4 0.5 1.0
NH2 D:ARG883 3.5 0.0 1.0
N D:ASP889 3.9 0.1 1.0
C D:CYS888 4.0 0.8 1.0
N D:CYS895 4.1 0.1 1.0
N D:CYS814 4.2 0.2 1.0
N D:CYS898 4.2 0.2 1.0
CA D:CYS898 4.2 0.9 1.0
CA D:CYS895 4.3 0.5 1.0
CA D:CYS814 4.4 0.6 1.0
N D:THR890 4.5 0.6 1.0
CZ D:ARG883 4.6 0.6 1.0
O D:CYS895 4.7 0.5 1.0
CG2 D:THR816 4.7 0.8 1.0
N D:CYS888 4.7 0.2 1.0
CB D:THR890 4.7 0.5 1.0
NE D:ARG883 4.8 0.2 1.0
C D:CYS895 4.8 0.9 1.0
O D:CYS888 5.0 0.2 1.0

Zinc binding site 3 out of 5 in 5vsw

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Zinc binding site 3 out of 5 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2002

b:0.8
occ:1.00
 SG J:CYS70 2.3 0.2 1.0
SG J:CYS72 2.4 0.0 1.0
SG J:CYS85 2.4 0.2 1.0
SG J:CYS88 2.6 0.5 1.0
CB J:CYS85 3.0 0.6 1.0
CB J:CYS72 3.2 0.7 1.0
N J:CYS72 3.6 0.8 1.0
CB J:CYS70 3.7 0.2 1.0
O J:CYS88 3.8 0.6 1.0
N J:CYS88 3.9 0.5 1.0
CA J:CYS72 3.9 0.6 1.0
CB J:LYS87 4.1 0.5 1.0
CB J:CYS88 4.1 0.7 1.0
N J:GLY73 4.3 0.5 1.0
N J:LEU71 4.4 0.4 1.0
CA J:CYS88 4.4 0.2 1.0
CA J:CYS85 4.5 0.9 1.0
C J:CYS72 4.5 0.6 1.0
C J:CYS88 4.6 0.5 1.0
C J:CYS70 4.7 0.1 1.0
C J:LEU71 4.7 0.3 1.0
CA J:CYS70 4.8 0.4 1.0
N J:LYS74 4.8 0.9 1.0
C J:LYS87 4.9 0.5 1.0
CA J:LYS87 4.9 0.3 1.0
C J:CYS85 4.9 0.5 1.0

Zinc binding site 4 out of 5 in 5vsw

Go back to Zinc Binding Sites List in 5vsw
Zinc binding site 4 out of 5 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2003

b:0.3
occ:1.00
 SG J:CYS895 2.3 0.9 1.0
CB J:CYS898 2.5 0.4 1.0
SG J:CYS888 2.6 0.1 1.0
SG J:CYS898 2.7 0.3 1.0
CB J:CYS888 2.9 0.1 1.0
SG J:CYS814 3.0 0.4 1.0
CA J:CYS888 3.6 0.5 1.0
CA J:CYS898 3.6 0.6 1.0
N J:CYS898 3.7 0.9 1.0
CB J:CYS895 3.8 0.8 1.0
NH2 J:ARG883 4.0 0.0 1.0
O J:CYS895 4.3 0.3 1.0
CG2 J:THR816 4.4 0.6 1.0
N J:CYS895 4.4 0.3 1.0
C J:CYS888 4.5 0.5 1.0
CB J:CYS814 4.5 0.7 1.0
N J:ASP889 4.5 0.5 1.0
CA J:CYS895 4.6 0.6 1.0
OG1 J:THR890 4.6 0.7 1.0
N J:CYS888 4.7 0.3 1.0
N J:CYS814 4.7 0.4 1.0
C J:CYS895 4.8 0.4 1.0
C J:CYS898 4.8 0.6 1.0
OD1 J:ASP813 4.9 0.9 1.0
NE J:ARG883 4.9 0.4 1.0
C J:HIS897 5.0 0.2 1.0
CZ J:ARG883 5.0 0.0 1.0

Zinc binding site 5 out of 5 in 5vsw

Go back to Zinc Binding Sites List in 5vsw
Zinc binding site 5 out of 5 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:0.1
occ:1.01
 SG M:CYS114 2.3 0.0 1.0
SG M:CYS117 2.3 0.9 1.0
SG M:CYS138 2.3 0.3 1.0
SG M:CYS135 2.4 0.1 1.0
CB M:CYS138 3.1 0.4 1.0
CB M:CYS114 3.5 0.2 1.0
CB M:CYS135 3.8 0.4 1.0
CB M:CYS117 3.8 0.4 1.0
N M:CYS117 4.0 0.2 1.0
N M:CYS138 4.0 0.1 1.0
CA M:CYS138 4.2 0.4 1.0
N M:CYS135 4.3 0.1 1.0
CB M:SER116 4.4 0.7 1.0
CA M:CYS117 4.4 0.8 1.0
O M:CYS117 4.5 0.2 1.0
CA M:CYS135 4.6 0.3 1.0
C M:CYS117 4.9 0.1 1.0
CA M:CYS114 4.9 0.3 1.0
CB M:VAL119 4.9 0.5 1.0
C M:SER116 4.9 0.1 1.0
O M:CYS135 5.0 0.3 1.0
N M:SER116 5.0 0.6 1.0
OG M:SER116 5.0 0.1 1.0

Reference:

V.Molodtsov, E.Sineva, L.Zhang, X.Huang, M.Cashel, S.E.Ades, K.S.Murakami. Allosteric Effector Ppgpp Potentiates the Inhibition of Transcript Initiation By Dksa. Mol. Cell V. 69 828 2018.
ISSN: ISSN 1097-4164
PubMed: 29478808
DOI: 10.1016/J.MOLCEL.2018.01.035
Page generated: Mon Oct 28 13:23:15 2024

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