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Zinc in PDB 6byu: X-Ray Crystal Structure of Escherichia Coli Rna Polymerase (Rpob- H526Y) and Ppapp Complex

Enzymatic activity of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase (Rpob- H526Y) and Ppapp Complex

All present enzymatic activity of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase (Rpob- H526Y) and Ppapp Complex:
2.7.7.6;

Protein crystallography data

The structure of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase (Rpob- H526Y) and Ppapp Complex, PDB code: 6byu 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) 30.00 / 3.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 186.254, 203.656, 308.322, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 31.1

Other elements in 6byu:

The structure of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase (Rpob- H526Y) and Ppapp 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 (Rpob- H526Y) and Ppapp Complex (pdb code 6byu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase (Rpob- H526Y) and Ppapp Complex, PDB code: 6byu:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6byu

Go back to Zinc Binding Sites List in 6byu
Zinc binding site 1 out of 4 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase (Rpob- H526Y) and Ppapp 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 (Rpob- H526Y) and Ppapp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:0.0
occ:1.00
 SG D:CYS72 2.2 0.3 1.0
SG D:CYS70 2.3 0.5 1.0
SG D:CYS85 2.3 0.9 1.0
SG D:CYS88 2.4 0.3 1.0
CB D:CYS72 2.7 0.7 1.0
CB D:CYS85 3.0 0.4 1.0
N D:CYS72 3.2 0.8 1.0
CA D:CYS72 3.5 0.7 1.0
N D:CYS88 3.9 0.8 1.0
CB D:CYS88 4.0 0.5 1.0
CB D:CYS70 4.0 0.5 1.0
N D:GLY73 4.2 0.1 1.0
C D:CYS72 4.3 1.0 1.0
O D:CYS88 4.3 0.8 1.0
N D:LEU71 4.3 0.3 1.0
CB D:LYS87 4.4 0.9 1.0
C D:LEU71 4.4 0.9 1.0
CA D:CYS85 4.5 0.0 1.0
CA D:CYS88 4.5 0.5 1.0
C D:CYS70 4.8 0.8 1.0
N D:LYS87 4.8 0.6 1.0
N D:LYS74 4.8 0.7 1.0
CA D:LEU71 4.9 0.3 1.0
C D:CYS85 4.9 0.1 1.0
C D:CYS88 4.9 0.3 1.0
C D:LYS87 4.9 0.8 1.0
CA D:LYS87 5.0 0.6 1.0
CA D:CYS70 5.0 0.5 1.0

Zinc binding site 2 out of 4 in 6byu

Go back to Zinc Binding Sites List in 6byu
Zinc binding site 2 out of 4 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase (Rpob- H526Y) and Ppapp 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 (Rpob- H526Y) and Ppapp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2003

b:0.6
occ:1.00
 SG D:CYS888 2.3 0.8 1.0
SG D:CYS814 2.3 0.6 1.0
SG D:CYS898 2.3 0.7 1.0
CB D:CYS888 2.3 0.0 1.0
SG D:CYS895 2.3 0.9 1.0
CA D:CYS888 2.5 0.3 1.0
CB D:CYS898 2.6 0.6 1.0
C D:CYS888 3.4 0.7 1.0
N D:ASP889 3.6 0.3 1.0
N D:CYS888 3.7 0.9 1.0
CB D:CYS895 3.7 0.4 1.0
CB D:CYS814 3.7 0.0 1.0
CA D:CYS898 4.0 0.6 1.0
NH2 D:ARG883 4.3 0.8 1.0
N D:CYS898 4.3 0.8 1.0
N D:CYS895 4.3 0.4 1.0
O D:CYS888 4.4 0.4 1.0
C D:SER887 4.5 0.2 1.0
CA D:CYS895 4.6 0.4 1.0
O D:SER887 4.6 0.3 1.0
CG2 D:THR816 4.7 0.9 1.0
OG1 D:THR890 4.8 0.3 1.0
N D:CYS814 4.8 0.1 1.0
N D:THR890 4.9 0.4 1.0
CA D:CYS814 4.9 0.3 1.0
O D:CYS895 4.9 0.5 1.0
O D:SER884 4.9 0.8 1.0
CA D:ASP889 4.9 0.9 1.0
C D:CYS898 5.0 0.4 1.0

Zinc binding site 3 out of 4 in 6byu

Go back to Zinc Binding Sites List in 6byu
Zinc binding site 3 out of 4 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase (Rpob- H526Y) and Ppapp 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 (Rpob- H526Y) and Ppapp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2002

b:0.3
occ:1.00
 SG J:CYS85 2.3 0.2 1.0
SG J:CYS70 2.3 0.2 1.0
SG J:CYS72 2.3 0.8 1.0
SG J:CYS88 2.3 0.1 1.0
CB J:CYS72 2.8 0.3 1.0
CB J:CYS85 2.9 0.4 1.0
N J:CYS72 3.2 0.6 1.0
N J:CYS88 3.5 0.9 1.0
CA J:CYS72 3.5 0.4 1.0
CB J:CYS88 3.8 0.2 1.0
CB J:CYS70 3.9 0.1 1.0
CB J:LYS87 3.9 0.7 1.0
O J:CYS88 3.9 0.2 1.0
CA J:CYS88 4.1 0.1 1.0
N J:GLY73 4.2 0.5 1.0
N J:LEU71 4.2 0.4 1.0
C J:CYS72 4.3 0.2 1.0
CA J:CYS85 4.4 0.7 1.0
C J:LEU71 4.4 0.4 1.0
N J:LYS87 4.5 0.5 1.0
C J:LYS87 4.5 0.9 1.0
C J:CYS88 4.5 0.0 1.0
CA J:LYS87 4.5 0.5 1.0
C J:CYS85 4.7 0.7 1.0
C J:CYS70 4.7 0.8 1.0
CA J:LEU71 4.8 0.5 1.0
N J:LYS74 4.8 0.6 1.0
CA J:CYS70 4.9 0.7 1.0
O J:CYS85 4.9 0.3 1.0

Zinc binding site 4 out of 4 in 6byu

Go back to Zinc Binding Sites List in 6byu
Zinc binding site 4 out of 4 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase (Rpob- H526Y) and Ppapp 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 (Rpob- H526Y) and Ppapp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2003

b:0.8
occ:1.00
 SG J:CYS898 2.2 0.4 1.0
SG J:CYS895 2.2 0.1 1.0
SG J:CYS814 2.3 0.3 1.0
SG J:CYS888 2.3 0.8 1.0
CB J:CYS898 2.5 0.2 1.0
CB J:CYS888 2.8 0.2 1.0
CA J:CYS888 3.2 0.6 1.0
CB J:CYS895 3.7 0.4 1.0
NH2 J:ARG883 3.7 0.7 1.0
CA J:CYS898 3.8 0.4 1.0
CB J:CYS814 3.9 0.0 1.0
N J:ASP889 4.0 0.0 1.0
C J:CYS888 4.0 0.0 1.0
N J:CYS898 4.0 0.6 1.0
N J:CYS895 4.3 0.8 1.0
N J:CYS888 4.4 0.3 1.0
CA J:CYS895 4.5 0.4 1.0
N J:CYS814 4.6 0.9 1.0
OG1 J:THR890 4.6 0.7 1.0
O J:CYS895 4.8 0.2 1.0
CZ J:ARG883 4.8 0.3 1.0
CA J:CYS814 4.8 0.9 1.0
CG2 J:THR816 4.9 0.3 1.0
N J:THR890 4.9 0.1 1.0
C J:CYS898 4.9 0.0 1.0

Reference:

B.Bruhn-Olszewska, V.Molodtsov, M.Sobala, M.Dylewski, K.S.Murakami, M.Cashel, K.Potrykus. Structure-Function Comparisons of (P)Ppapp Vs (P)Ppgpp For Escherichia Coli Rna Polymerase Binding Sites and For Rrnb P1 Promoter Regulatory Responses in Vitro. Biochim. Biophys. Acta V.1861 731 2018.
ISSN: ISSN 0006-3002
PubMed: 30012465
DOI: 10.1016/J.BBAGRM.2018.07.005
Page generated: Mon Oct 28 18:23:24 2024

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