Atomistry » Zinc » PDB 5w0r-5w9q » 5w1t
Atomistry »
  Zinc »
    PDB 5w0r-5w9q »
      5w1t »

Zinc in PDB 5w1t: X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa Complex

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

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

Protein crystallography data

The structure of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa Complex, PDB code: 5w1t 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) 47.08 / 4.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 184.000, 204.894, 314.312, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 27.6

Other elements in 5w1t:

The structure of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa 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 Complex (pdb code 5w1t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa Complex, PDB code: 5w1t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5w1t

Go back to Zinc Binding Sites List in 5w1t
Zinc binding site 1 out of 6 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa 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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:0.2
occ:1.00
 SG D:CYS72 2.1 0.4 1.0
SG D:CYS85 2.3 0.8 1.0
SG D:CYS70 2.3 0.1 1.0
SG D:CYS88 2.4 1.0 1.0
CB D:CYS85 2.8 0.5 1.0
CB D:CYS72 2.8 0.6 1.0
N D:CYS72 3.4 0.4 1.0
O D:CYS88 3.6 0.1 1.0
N D:CYS88 3.7 0.9 1.0
CA D:CYS72 3.7 0.6 1.0
CB D:CYS88 4.0 0.2 1.0
CB D:CYS70 4.1 0.8 1.0
CB D:LYS87 4.2 0.6 1.0
CA D:CYS88 4.2 0.6 1.0
CA D:CYS85 4.3 0.6 1.0
N D:GLY73 4.3 0.7 1.0
C D:CYS88 4.4 0.2 1.0
N D:LEU71 4.4 0.2 1.0
C D:CYS72 4.5 1.0 1.0
C D:LEU71 4.6 0.8 1.0
C D:CYS85 4.7 0.2 1.0
N D:LYS74 4.8 0.5 1.0
C D:LYS87 4.8 0.4 1.0
CA D:LYS87 4.9 0.8 1.0
C D:CYS70 4.9 0.1 1.0
CA D:LEU71 4.9 0.2 1.0
CB D:LYS74 4.9 0.3 1.0
CB D:VAL90 4.9 0.4 1.0
N D:LYS87 4.9 1.0 1.0
O D:CYS85 4.9 0.7 1.0
CG2 D:VAL90 5.0 0.6 1.0

Zinc binding site 2 out of 6 in 5w1t

Go back to Zinc Binding Sites List in 5w1t
Zinc binding site 2 out of 6 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa 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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2003

b:0.1
occ:1.00
 SG D:CYS898 2.0 0.5 1.0
SG D:CYS888 2.1 0.4 1.0
SG D:CYS895 2.3 0.6 1.0
SG D:CYS814 2.3 0.5 1.0
CB D:CYS888 2.6 0.1 1.0
CB D:CYS898 2.9 0.1 1.0
CA D:CYS888 3.1 0.3 1.0
CB D:CYS895 3.6 0.2 1.0
CB D:CYS814 3.6 0.0 1.0
C D:CYS888 3.9 0.0 1.0
N D:ASP889 4.0 0.9 1.0
CA D:CYS898 4.1 0.6 1.0
NH2 D:ARG883 4.1 0.6 1.0
N D:CYS898 4.1 0.9 1.0
N D:CYS895 4.3 0.8 1.0
N D:CYS888 4.3 0.8 1.0
CA D:CYS895 4.4 0.7 1.0
N D:CYS814 4.5 0.6 1.0
O D:CYS895 4.6 0.2 1.0
CA D:CYS814 4.7 0.0 1.0
O D:CYS888 4.8 0.8 1.0
CG2 D:THR816 4.8 0.7 1.0
N D:THR890 4.9 0.9 1.0
C D:CYS895 4.9 0.8 1.0
NE D:ARG883 5.0 0.3 1.0

Zinc binding site 3 out of 6 in 5w1t

Go back to Zinc Binding Sites List in 5w1t
Zinc binding site 3 out of 6 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa 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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2002

b:0.8
occ:1.00
 SG J:CYS70 2.0 0.3 1.0
SG J:CYS72 2.3 0.1 1.0
SG J:CYS85 2.3 0.1 1.0
SG J:CYS88 2.6 0.4 1.0
CB J:CYS85 2.8 0.8 1.0
CB J:CYS72 3.2 0.5 1.0
CB J:CYS70 3.7 0.0 1.0
O J:CYS88 3.7 0.5 1.0
N J:CYS72 3.8 1.0 1.0
N J:CYS88 4.0 0.1 1.0
CA J:CYS72 4.1 0.2 1.0
CB J:CYS88 4.3 0.7 1.0
CA J:CYS85 4.3 0.5 1.0
N J:GLY73 4.3 0.4 1.0
CB J:LYS87 4.4 0.4 1.0
N J:LEU71 4.5 0.3 1.0
CA J:CYS88 4.5 0.9 1.0
C J:CYS88 4.6 0.8 1.0
C J:CYS72 4.6 0.3 1.0
N J:LYS74 4.6 0.4 1.0
CA J:CYS70 4.7 0.3 1.0
CB J:LYS74 4.7 0.9 1.0
C J:CYS70 4.8 0.8 1.0
C J:CYS85 4.8 0.4 1.0
C J:LEU71 4.9 0.5 1.0
CB J:VAL90 5.0 1.0 1.0

Zinc binding site 4 out of 6 in 5w1t

Go back to Zinc Binding Sites List in 5w1t
Zinc binding site 4 out of 6 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa 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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2003

b:0.8
occ:1.00
 SG J:CYS888 2.3 0.1 1.0
SG J:CYS895 2.3 0.7 1.0
SG J:CYS814 2.4 0.9 1.0
CB J:CYS888 2.6 0.2 1.0
SG J:CYS898 2.8 0.7 1.0
CB J:CYS898 2.8 0.6 1.0
CA J:CYS888 3.2 1.0 1.0
NH2 J:ARG883 3.6 0.0 1.0
CB J:CYS814 3.7 0.9 1.0
CB J:CYS895 3.8 0.6 1.0
CA J:CYS898 4.0 0.7 1.0
N J:CYS898 4.0 0.0 1.0
C J:CYS888 4.1 0.5 1.0
N J:ASP889 4.2 0.2 1.0
N J:CYS888 4.4 0.8 1.0
N J:CYS814 4.4 0.2 1.0
N J:CYS895 4.5 0.2 1.0
CG2 J:THR816 4.5 0.7 1.0
CZ J:ARG883 4.6 0.8 1.0
O J:CYS895 4.6 0.8 1.0
CA J:CYS895 4.6 0.0 1.0
NE J:ARG883 4.7 0.2 1.0
CA J:CYS814 4.7 0.5 1.0
OG1 J:THR890 4.7 0.6 1.0
C J:CYS895 4.9 0.3 1.0

Zinc binding site 5 out of 6 in 5w1t

Go back to Zinc Binding Sites List in 5w1t
Zinc binding site 5 out of 6 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa 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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn200

b:0.0
occ:1.01
 SG M:CYS138 2.4 0.2 1.0
SG M:CYS114 2.4 0.4 1.0
SG M:CYS135 2.4 0.4 1.0
SG M:CYS117 2.5 0.2 1.0
CB M:CYS138 3.2 0.2 1.0
CB M:CYS114 3.5 0.6 1.0
CB M:CYS135 3.8 0.8 1.0
CB M:CYS117 4.1 0.6 1.0
N M:CYS135 4.1 0.0 1.0
N M:CYS117 4.2 0.1 1.0
N M:CYS138 4.3 0.8 1.0
CA M:CYS138 4.4 0.2 1.0
CA M:CYS135 4.5 1.0 1.0
O M:CYS117 4.6 0.9 1.0
CA M:CYS117 4.7 0.2 1.0
CB M:SER116 4.7 0.8 1.0
CB M:VAL119 4.9 0.7 1.0
CA M:CYS114 5.0 0.4 1.0
O M:CYS135 5.0 0.5 1.0

Zinc binding site 6 out of 6 in 5w1t

Go back to Zinc Binding Sites List in 5w1t
Zinc binding site 6 out of 6 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn200

b:0.5
occ:1.01
 SG N:CYS135 2.3 0.0 1.0
SG N:CYS138 2.4 0.9 1.0
SG N:CYS114 2.4 0.5 1.0
SG N:CYS117 2.5 0.3 1.0
CB N:CYS138 2.8 0.5 1.0
CB N:CYS135 3.5 0.6 1.0
CB N:CYS114 3.7 0.5 1.0
N N:CYS135 3.8 0.9 1.0
CB N:CYS117 3.9 0.5 1.0
N N:CYS117 4.0 0.6 1.0
N N:CYS138 4.0 0.1 1.0
CA N:CYS138 4.0 0.6 1.0
CA N:CYS135 4.2 0.5 1.0
CB N:SER116 4.3 0.6 1.0
CA N:CYS117 4.5 0.7 1.0
O N:CYS117 4.7 0.2 1.0
O N:CYS135 4.7 0.5 1.0
C N:CYS135 4.8 0.8 1.0
OG N:SER116 4.8 0.8 1.0
CB N:LEU134 4.9 0.6 1.0
C N:LEU134 4.9 0.0 1.0
C N:SER116 4.9 0.9 1.0
CA N:SER116 5.0 0.3 1.0
CA N:LEU134 5.0 0.9 1.0
N N:SER116 5.0 0.3 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 13:37:26 2024

Last articles

Na in 7A74
Na in 7A70
Na in 7A56
Na in 7A3K
Na in 7A68
Na in 7A3I
Na in 7A5Z
Na in 7A2N
Na in 7A2K
Na in 7A36
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy