Zinc in PDB 5w1s: X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Trar Complex

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

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

Protein crystallography data

The structure of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Trar Complex, PDB code: 5w1s 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) 49.84 / 3.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 186.484, 206.039, 310.300, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 26.2

Other elements in 5w1s:

The structure of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Trar 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 Trar Complex (pdb code 5w1s). 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 Trar Complex, PDB code: 5w1s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5w1s

Go back to Zinc Binding Sites List in 5w1s
Zinc binding site 1 out of 6 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Trar 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 Trar Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:0.1
occ:1.00
SG D:CYS70 2.3 0.8 1.0
SG D:CYS72 2.4 0.3 1.0
SG D:CYS85 2.4 0.2 1.0
SG D:CYS88 2.6 0.2 1.0
CB D:CYS72 3.0 0.3 1.0
CB D:CYS85 3.1 0.1 1.0
N D:CYS72 3.4 0.0 1.0
CA D:CYS72 3.8 0.3 1.0
N D:CYS88 3.9 1.0 1.0
CB D:LYS87 3.9 0.1 1.0
CB D:CYS70 4.0 0.1 1.0
O D:CYS88 4.1 0.7 1.0
CB D:CYS88 4.2 1.0 1.0
N D:LEU71 4.3 0.7 1.0
N D:GLY73 4.4 0.4 1.0
CA D:CYS88 4.5 0.6 1.0
CA D:CYS85 4.5 1.0 1.0
C D:LEU71 4.5 0.7 1.0
C D:CYS72 4.5 0.2 1.0
CA D:LYS87 4.8 0.8 1.0
C D:CYS88 4.8 0.2 1.0
C D:CYS70 4.8 0.7 1.0
C D:LYS87 4.8 0.4 1.0
N D:LYS74 4.8 0.9 1.0
CA D:LEU71 4.8 0.4 1.0
N D:LYS87 4.9 0.6 1.0
CB D:LYS74 4.9 0.1 1.0
C D:CYS85 4.9 0.8 1.0
CG D:LYS87 4.9 0.0 1.0
CA D:CYS70 4.9 0.0 1.0

Zinc binding site 2 out of 6 in 5w1s

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Zinc binding site 2 out of 6 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Trar 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 Trar Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2003

b:0.4
occ:1.00
SG D:CYS895 2.2 0.5 1.0
SG D:CYS888 2.3 0.9 1.0
SG D:CYS898 2.4 1.0 1.0
SG D:CYS814 2.5 0.9 1.0
CB D:CYS888 2.9 0.9 1.0
CB D:CYS898 3.1 0.9 1.0
CB D:CYS895 3.4 0.7 1.0
CA D:CYS888 3.5 0.8 1.0
CB D:CYS814 3.6 0.1 1.0
NH2 D:ARG883 3.9 0.7 1.0
N D:CYS895 4.0 0.5 1.0
CA D:CYS895 4.2 0.0 1.0
C D:CYS888 4.2 0.1 1.0
N D:CYS898 4.2 0.8 1.0
N D:ASP889 4.2 0.1 1.0
CA D:CYS898 4.3 0.1 1.0
N D:CYS814 4.3 0.9 1.0
O D:CYS895 4.4 0.7 1.0
CA D:CYS814 4.6 0.5 1.0
C D:CYS895 4.7 0.8 1.0
N D:CYS888 4.7 0.2 1.0
N D:THR890 4.8 0.2 1.0
CG2 D:THR816 4.8 0.6 1.0
CB D:THR890 4.9 0.7 1.0
CZ D:ARG883 5.0 0.5 1.0

Zinc binding site 3 out of 6 in 5w1s

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Zinc binding site 3 out of 6 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Trar 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 Trar Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2002

b:0.4
occ:1.00
SG J:CYS70 2.3 0.7 1.0
SG J:CYS72 2.3 0.3 1.0
SG J:CYS85 2.4 0.2 1.0
SG J:CYS88 2.5 0.4 1.0
CB J:CYS85 2.9 0.9 1.0
CB J:CYS72 3.2 0.2 1.0
N J:CYS72 3.6 0.8 1.0
CB J:CYS70 3.7 0.6 1.0
O J:CYS88 3.7 0.1 1.0
CA J:CYS72 3.9 0.0 1.0
N J:CYS88 3.9 0.0 1.0
CB J:CYS88 4.2 0.2 1.0
CB J:LYS87 4.3 0.7 1.0
N J:GLY73 4.3 0.4 1.0
CA J:CYS85 4.3 0.6 1.0
N J:LEU71 4.4 0.2 1.0
CA J:CYS88 4.5 0.9 1.0
C J:CYS88 4.5 0.4 1.0
C J:CYS72 4.5 0.9 1.0
C J:CYS70 4.7 0.3 1.0
C J:LEU71 4.7 0.2 1.0
N J:LYS74 4.7 0.2 1.0
CA J:CYS70 4.7 0.8 1.0
C J:CYS85 4.9 0.3 1.0
CB J:LYS74 4.9 0.2 1.0
CB J:VAL90 4.9 1.0 1.0
C J:LYS87 5.0 0.1 1.0

Zinc binding site 4 out of 6 in 5w1s

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Zinc binding site 4 out of 6 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Trar 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 Trar Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2003

b:0.5
occ:1.00
SG J:CYS895 2.2 0.5 1.0
SG J:CYS888 2.4 0.8 1.0
SG J:CYS814 2.5 0.3 1.0
CB J:CYS898 2.6 0.5 1.0
CB J:CYS888 2.8 0.3 1.0
SG J:CYS898 2.8 0.3 1.0
CA J:CYS888 3.4 0.7 1.0
CB J:CYS895 3.6 0.2 1.0
CA J:CYS898 3.8 0.3 1.0
N J:CYS898 3.8 0.0 1.0
NH2 J:ARG883 3.9 0.4 1.0
CB J:CYS814 3.9 0.3 1.0
C J:CYS888 4.2 0.2 1.0
N J:ASP889 4.3 0.2 1.0
N J:CYS895 4.3 0.9 1.0
O J:CYS895 4.4 0.6 1.0
CA J:CYS895 4.4 0.8 1.0
CG2 J:THR816 4.4 0.2 1.0
OG1 J:THR890 4.4 0.8 1.0
N J:CYS814 4.4 0.6 1.0
N J:CYS888 4.5 0.7 1.0
C J:CYS895 4.7 0.1 1.0
CA J:CYS814 4.8 0.3 1.0
CZ J:ARG883 4.9 0.4 1.0
NE J:ARG883 4.9 0.7 1.0
C J:CYS898 5.0 0.2 1.0
OD1 J:ASP813 5.0 0.7 1.0

Zinc binding site 5 out of 6 in 5w1s

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Zinc binding site 5 out of 6 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Trar 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 Trar Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn101

b:0.3
occ:1.00
SG M:CYS40 2.3 0.1 1.0
SG M:CYS58 2.3 0.9 1.0
SG M:CYS61 2.4 0.6 1.0
SG M:CYS37 2.4 0.2 1.0
CB M:CYS37 3.3 0.1 1.0
CB M:CYS58 3.6 1.0 1.0
CB M:CYS61 3.8 0.5 1.0
CB M:CYS40 3.9 0.2 1.0
CB M:ASN42 4.1 1.0 1.0
ND2 M:ASN42 4.1 0.5 1.0
N M:CYS40 4.2 0.6 1.0
N M:CYS58 4.2 0.5 1.0
N M:ASN42 4.3 0.4 1.0
CG M:ASN42 4.3 0.4 1.0
CA M:CYS40 4.4 0.8 1.0
CA M:CYS58 4.5 0.7 1.0
CB M:ALA39 4.6 0.5 1.0
N M:CYS61 4.6 0.6 1.0
C M:CYS40 4.6 0.2 1.0
N M:GLY41 4.7 0.2 1.0
CA M:ASN42 4.8 0.1 1.0
CA M:CYS37 4.8 0.5 1.0
CA M:CYS61 4.8 0.1 1.0

Zinc binding site 6 out of 6 in 5w1s

Go back to Zinc Binding Sites List in 5w1s
Zinc binding site 6 out of 6 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Trar 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 Trar Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn101

b:0.7
occ:1.00
SG N:CYS40 2.3 0.1 1.0
SG N:CYS61 2.3 0.8 1.0
SG N:CYS58 2.3 0.0 1.0
SG N:CYS37 2.3 0.2 1.0
CB N:CYS61 3.4 0.2 1.0
CB N:CYS37 3.6 0.7 1.0
CB N:CYS58 3.6 0.4 1.0
CB N:ALA39 3.7 0.3 1.0
N N:CYS58 4.0 0.8 1.0
CB N:CYS40 4.1 0.1 1.0
N N:CYS40 4.1 1.0 1.0
N N:CYS61 4.4 0.3 1.0
CA N:CYS58 4.4 0.4 1.0
CA N:CYS61 4.5 0.2 1.0
CA N:ALA39 4.6 0.0 1.0
N N:ALA39 4.6 0.3 1.0
CA N:CYS40 4.7 0.5 1.0
C N:ALA39 4.7 0.8 1.0
O N:CYS58 4.8 0.0 1.0
ND2 N:ASN42 4.9 0.3 1.0
CB N:ASN42 5.0 0.4 1.0
C N:CYS58 5.0 0.2 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: Wed Dec 16 11:14:12 2020

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