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Zinc in PDB 4yg2: X-Ray Crystal Structur of Escherichia Coli Rna Polymerase SIGMA70 Holoenzyme

Enzymatic activity of X-Ray Crystal Structur of Escherichia Coli Rna Polymerase SIGMA70 Holoenzyme

All present enzymatic activity of X-Ray Crystal Structur of Escherichia Coli Rna Polymerase SIGMA70 Holoenzyme:
2.7.7.6;

Protein crystallography data

The structure of X-Ray Crystal Structur of Escherichia Coli Rna Polymerase SIGMA70 Holoenzyme, PDB code: 4yg2 was solved by K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.98 / 3.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 187.308, 205.901, 309.185, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 26

Other elements in 4yg2:

The structure of X-Ray Crystal Structur of Escherichia Coli Rna Polymerase SIGMA70 Holoenzyme also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Crystal Structur of Escherichia Coli Rna Polymerase SIGMA70 Holoenzyme (pdb code 4yg2). 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 Structur of Escherichia Coli Rna Polymerase SIGMA70 Holoenzyme, PDB code: 4yg2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4yg2

Go back to Zinc Binding Sites List in 4yg2
Zinc binding site 1 out of 4 in the X-Ray Crystal Structur of Escherichia Coli Rna Polymerase SIGMA70 Holoenzyme


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 Structur of Escherichia Coli Rna Polymerase SIGMA70 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:0.3
occ:1.00
 SG D:CYS85 2.5 0.7 1.0
SG D:CYS72 2.6 0.8 1.0
SG D:CYS70 2.6 0.8 1.0
SG D:CYS88 2.8 1.0 1.0
CB D:CYS72 3.0 0.2 1.0
CB D:LYS87 3.3 0.5 1.0
CB D:CYS85 3.4 0.9 1.0
N D:CYS72 3.5 0.8 1.0
N D:CYS88 3.6 0.3 1.0
CA D:CYS72 3.8 0.6 1.0
CB D:CYS88 4.2 1.0 1.0
CA D:LYS87 4.2 0.1 1.0
O D:CYS88 4.2 0.5 1.0
CG D:LYS87 4.3 0.5 1.0
N D:GLY73 4.3 0.3 1.0
CB D:CYS70 4.4 1.0 1.0
N D:LEU71 4.4 0.4 1.0
N D:LYS87 4.4 0.3 1.0
CA D:CYS88 4.4 1.0 1.0
C D:LYS87 4.4 0.9 1.0
C D:CYS72 4.6 0.7 1.0
C D:LEU71 4.6 0.8 1.0
CA D:CYS85 4.7 0.9 1.0
N D:LYS74 4.7 0.1 1.0
CB D:LYS74 4.7 0.1 1.0
C D:CYS88 4.8 0.4 1.0
C D:CYS85 4.8 0.9 1.0
CA D:LEU71 4.9 0.7 1.0
CD D:LYS87 4.9 0.5 1.0
O D:CYS85 4.9 0.5 1.0
C D:CYS70 4.9 0.1 1.0

Zinc binding site 2 out of 4 in 4yg2

Go back to Zinc Binding Sites List in 4yg2
Zinc binding site 2 out of 4 in the X-Ray Crystal Structur of Escherichia Coli Rna Polymerase SIGMA70 Holoenzyme


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 Structur of Escherichia Coli Rna Polymerase SIGMA70 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2003

b:94.5
occ:1.00
 SG D:CYS895 2.2 99.0 1.0
SG D:CYS898 2.2 0.6 1.0
SG D:CYS814 2.2 0.4 1.0
SG D:CYS888 2.3 99.2 1.0
CB D:CYS898 2.8 98.9 1.0
CB D:CYS888 2.9 99.5 1.0
CB D:CYS895 3.3 0.6 1.0
CB D:CYS814 3.4 0.3 1.0
CA D:CYS888 3.5 0.9 1.0
N D:CYS895 4.0 94.6 1.0
CA D:CYS898 4.0 98.3 1.0
N D:CYS898 4.0 98.1 1.0
NH2 D:ARG883 4.1 0.9 1.0
CA D:CYS895 4.2 95.2 1.0
N D:ASP889 4.2 0.1 1.0
C D:CYS888 4.2 0.4 1.0
N D:CYS814 4.2 0.6 1.0
O D:CYS895 4.4 94.3 1.0
CA D:CYS814 4.4 0.7 1.0
C D:CYS895 4.7 94.4 1.0
N D:CYS888 4.7 0.2 1.0
N D:THR890 4.8 0.8 1.0

Zinc binding site 3 out of 4 in 4yg2

Go back to Zinc Binding Sites List in 4yg2
Zinc binding site 3 out of 4 in the X-Ray Crystal Structur of Escherichia Coli Rna Polymerase SIGMA70 Holoenzyme


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 Structur of Escherichia Coli Rna Polymerase SIGMA70 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2002

b:0.4
occ:1.00
 SG J:CYS85 2.3 1.0 1.0
SG J:CYS72 2.4 0.6 1.0
SG J:CYS70 2.4 0.2 1.0
CB J:CYS85 2.8 0.5 1.0
CB J:CYS70 3.4 0.1 1.0
SG J:CYS88 3.5 0.4 1.0
CB J:CYS72 3.5 0.4 1.0
N J:CYS72 3.9 0.7 1.0
O J:CYS88 4.1 0.3 1.0
CA J:CYS72 4.1 0.5 1.0
N J:GLY73 4.1 0.1 1.0
CB J:LYS87 4.2 0.1 1.0
N J:CYS88 4.2 0.3 1.0
CA J:CYS85 4.3 0.8 1.0
N J:LYS74 4.4 0.4 1.0
CB J:LYS74 4.4 0.0 1.0
C J:CYS72 4.5 0.5 1.0
N J:LEU71 4.6 0.3 1.0
CA J:CYS70 4.6 0.8 1.0
CD1 J:TYR75 4.7 0.4 1.0
C J:CYS70 4.7 0.0 1.0
C J:CYS85 4.7 0.0 1.0
CB J:CYS88 4.9 0.8 1.0
N J:LYS87 4.9 0.4 1.0
CA J:CYS88 4.9 0.5 1.0
C J:LEU71 5.0 0.1 1.0
CA J:LYS87 5.0 0.9 1.0
C J:CYS88 5.0 0.8 1.0

Zinc binding site 4 out of 4 in 4yg2

Go back to Zinc Binding Sites List in 4yg2
Zinc binding site 4 out of 4 in the X-Ray Crystal Structur of Escherichia Coli Rna Polymerase SIGMA70 Holoenzyme


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 Structur of Escherichia Coli Rna Polymerase SIGMA70 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2003

b:94.5
occ:1.00
 SG J:CYS895 2.2 0.1 1.0
SG J:CYS814 2.3 0.8 1.0
SG J:CYS888 2.5 0.8 1.0
CB J:CYS898 2.6 0.7 1.0
SG J:CYS898 2.8 0.8 1.0
CB J:CYS888 3.0 0.7 1.0
CB J:CYS895 3.6 0.3 1.0
CA J:CYS888 3.6 0.7 1.0
NH2 J:ARG883 3.8 0.5 1.0
CA J:CYS898 3.8 0.1 1.0
CB J:CYS814 3.8 0.4 1.0
N J:CYS898 3.8 0.1 1.0
CG2 J:THR816 4.3 0.7 1.0
N J:ASP889 4.3 0.4 1.0
C J:CYS888 4.3 0.6 1.0
OG1 J:THR890 4.4 0.7 1.0
N J:CYS814 4.5 0.6 1.0
N J:CYS895 4.5 0.8 1.0
O J:CYS895 4.6 0.3 1.0
CA J:CYS895 4.6 0.2 1.0
CZ J:ARG883 4.7 0.3 1.0
CA J:CYS814 4.8 0.0 1.0
NE J:ARG883 4.8 0.2 1.0
N J:CYS888 4.8 0.6 1.0
C J:CYS895 4.9 0.3 1.0
OD1 J:ASP813 4.9 0.1 1.0
N J:THR890 5.0 0.3 1.0

Reference:

K.S.Murakami, K.S.Murakami. N/A N/A.
ISSN: ESSN 1083-351X
PubMed: 23389035
DOI: 10.1074/JBC.M112.430900
Page generated: Sun Oct 27 11:11:42 2024

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