Atomistry » Zinc » PDB 5vmz-5vuq » 5vsw
Atomistry »
  Zinc »
    PDB 5vmz-5vuq »
      5vsw »

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

Go back to Zinc Binding Sites List in 5vsw
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

Go back to Zinc Binding Sites List in 5vsw
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

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