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Magnesium 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:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the X-Ray Crystal Structur of Escherichia Coli Rna Polymerase SIGMA70 Holoenzyme, PDB code: 4yg2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4yg2

Go back to Magnesium Binding Sites List in 4yg2
Magnesium 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 Magnesium with other atoms in the Mg 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
C:Mg1401

b:94.5
occ:1.00
 OD2 D:ASP460 1.8 0.1 1.0
O D:ALA459 2.8 67.4 1.0
CG D:ASP460 2.9 0.7 1.0
OE1 C:GLU813 2.9 0.3 1.0
CD C:GLU813 3.4 0.1 1.0
C D:ALA459 3.5 66.8 1.0
OD1 D:ASP460 3.5 0.7 1.0
OE2 C:GLU813 3.6 0.0 1.0
N D:ASP460 3.8 78.3 1.0
CA D:ASP460 3.8 0.0 1.0
CB D:ASP460 3.9 0.7 1.0
OD1 D:ASN458 4.4 87.0 1.0
CG C:GLU813 4.5 0.3 1.0
N D:ALA459 4.5 91.8 1.0
C D:ASN458 4.6 67.5 1.0
CA D:ALA459 4.6 68.1 1.0
O D:CYS454 4.9 71.8 1.0
O D:ASN458 5.0 67.2 1.0
CA D:ASN458 5.0 68.4 1.0

Magnesium binding site 2 out of 4 in 4yg2

Go back to Magnesium Binding Sites List in 4yg2
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2001

b:94.5
occ:1.00
 OD2 D:ASP462 2.4 98.3 1.0
OD1 D:ASP462 2.9 0.8 1.0
CG D:ASP462 2.9 0.4 1.0
OD1 D:ASP464 3.0 0.5 1.0
CG D:ASP464 4.0 98.4 1.0
OD2 D:ASP464 4.2 0.0 1.0
CB D:ASP462 4.4 0.9 1.0
CE C:LYS1073 4.9 63.1 1.0

Magnesium binding site 3 out of 4 in 4yg2

Go back to Magnesium Binding Sites List in 4yg2
Magnesium 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 Magnesium with other atoms in the Mg 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
I:Mg1401

b:94.5
occ:1.00
 OD2 J:ASP460 2.4 97.4 1.0
OE2 I:GLU813 2.9 0.7 1.0
O J:ALA459 3.1 0.3 1.0
OE1 I:GLU813 3.2 0.4 1.0
CD I:GLU813 3.3 0.1 1.0
CG J:ASP460 3.4 0.6 1.0
C J:ALA459 3.8 0.6 1.0
OD1 J:ASN458 4.1 96.3 1.0
O J:CYS454 4.1 95.5 1.0
OD1 J:ASP460 4.1 0.9 1.0
CA J:ASP460 4.2 0.6 1.0
N J:ASP460 4.2 0.3 1.0
CB J:ASP460 4.3 0.2 1.0
CG I:GLU813 4.4 0.3 1.0
N J:ALA459 4.6 94.1 1.0
C J:ASN458 4.6 0.0 1.0
CA J:ASN458 4.7 0.6 1.0
C J:CYS454 4.9 95.7 1.0
CA J:ALA459 4.9 94.0 1.0

Magnesium binding site 4 out of 4 in 4yg2

Go back to Magnesium Binding Sites List in 4yg2
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2001

b:94.5
occ:1.00
 OD1 J:ASP464 2.4 1.0 1.0
OD2 J:ASP462 2.7 0.5 1.0
OD1 J:ASP462 2.7 0.9 1.0
OD2 J:ASP464 3.1 94.4 1.0
CG J:ASP462 3.1 0.1 1.0
CG J:ASP464 3.1 0.7 1.0
NH2 J:ARG425 4.2 0.5 1.0
CB J:ASP464 4.6 0.2 1.0
CB J:ASP462 4.7 1.0 1.0
OD1 J:ASP460 4.8 0.9 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: Mon Dec 14 19:54:04 2020

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