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Magnesium in PDB 4yfk: Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8.

Enzymatic activity of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8.

All present enzymatic activity of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8.:
2.7.7.6;

Protein crystallography data

The structure of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8., PDB code: 4yfk was solved by V.Molodtsov, P.R.Fleming, C.J.Eyermann, A.D.Ferguson, M.A.Foulk, D.C.Mckinney, C.E.Masse, E.T.Buurman, K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.97 / 3.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 186.105, 206.438, 307.993, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 25.2

Other elements in 4yfk:

The structure of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8. also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8. (pdb code 4yfk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8., PDB code: 4yfk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4yfk

Go back to Magnesium Binding Sites List in 4yfk
Magnesium binding site 1 out of 4 in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1401

b:0.1
occ:1.00
OE1 C:GLU813 2.4 0.3 1.0
OD2 D:ASP460 2.6 0.6 1.0
O D:ALA459 2.8 92.4 1.0
CD C:GLU813 3.2 1.0 1.0
CG D:ASP460 3.3 0.9 1.0
C D:ALA459 3.5 99.0 1.0
OE2 C:GLU813 3.6 0.5 1.0
N D:ASP460 3.8 0.7 1.0
OD1 D:ASP460 3.8 0.8 1.0
CA D:ASP460 3.9 0.8 1.0
CB D:ASP460 4.2 0.8 1.0
OD1 D:ASN458 4.3 0.7 1.0
CG C:GLU813 4.3 0.0 1.0
N D:ALA459 4.4 92.4 1.0
O D:CYS454 4.4 0.9 1.0
C D:ASN458 4.5 95.4 1.0
CA D:ALA459 4.5 92.7 1.0
O D:ASN458 4.8 92.2 1.0
CA D:ASN458 5.0 95.8 1.0

Magnesium binding site 2 out of 4 in 4yfk

Go back to Magnesium Binding Sites List in 4yfk
Magnesium binding site 2 out of 4 in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2001

b:0.1
occ:1.00
OD2 D:ASP462 2.2 0.7 1.0
OD1 D:ASP462 2.3 0.3 1.0
CG D:ASP462 2.6 0.1 1.0
OD1 D:ASP464 3.0 0.9 1.0
OD2 D:ASP464 3.5 0.6 1.0
CG D:ASP464 3.7 1.0 1.0
CB D:ASP462 4.1 0.1 1.0
OD1 D:ASP460 4.4 0.8 1.0
CB D:ASP460 4.5 0.8 1.0
CE C:LYS1073 4.6 0.0 1.0
CA D:ASP462 5.0 96.5 1.0
CG D:ASP460 5.0 0.9 1.0

Magnesium binding site 3 out of 4 in 4yfk

Go back to Magnesium Binding Sites List in 4yfk
Magnesium binding site 3 out of 4 in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1401

b:0.1
occ:1.00
OE1 I:GLU813 3.0 0.9 1.0
OE2 I:GLU813 3.1 0.9 1.0
OD2 J:ASP460 3.2 0.8 1.0
O J:ALA459 3.2 0.9 1.0
CD I:GLU813 3.2 0.0 1.0
O J:CYS454 3.7 0.5 1.0
C J:ALA459 3.8 0.8 1.0
CG J:ASP460 3.8 0.9 1.0
OD1 J:ASN458 3.9 0.6 1.0
N J:ASP460 4.2 0.9 1.0
OD1 J:ASP460 4.3 0.2 1.0
CA J:ASP460 4.3 0.7 1.0
C J:ASN458 4.3 0.6 1.0
CG I:GLU813 4.3 0.1 1.0
N J:ALA459 4.3 0.1 1.0
CA J:ASN458 4.5 0.7 1.0
C J:CYS454 4.6 0.1 1.0
O J:ASN458 4.7 0.2 1.0
CB J:ASP460 4.7 0.7 1.0
CA J:ALA459 4.7 0.1 1.0
CG J:ASN458 4.9 0.4 1.0

Magnesium binding site 4 out of 4 in 4yfk

Go back to Magnesium Binding Sites List in 4yfk
Magnesium binding site 4 out of 4 in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg2001

b:0.1
occ:1.00
OD2 J:ASP464 2.4 0.1 1.0
OD1 J:ASP464 2.6 0.0 1.0
OD1 J:ASP462 2.7 0.7 1.0
CG J:ASP464 2.9 0.7 1.0
OD2 J:ASP462 2.9 0.6 1.0
CG J:ASP462 3.2 0.5 1.0
OD1 J:ASP460 3.8 0.2 1.0
CB J:ASP460 4.0 0.7 1.0
NH2 J:ARG425 4.2 0.2 1.0
NH1 J:ARG425 4.4 0.2 1.0
CG J:ASP460 4.4 0.9 1.0
CB J:ASP464 4.4 0.1 1.0
N J:ASP460 4.6 0.9 1.0
CB J:ASP462 4.7 0.8 1.0
CZ J:ARG425 4.8 0.9 1.0
CA J:ASP460 4.8 0.7 1.0

Reference:

V.Molodtsov, P.R.Fleming, C.J.Eyermann, A.D.Ferguson, M.A.Foulk, D.C.Mckinney, C.E.Masse, E.T.Buurman, K.S.Murakami. X-Ray Crystal Structures of Escherichia Coli Rna Polymerase with Switch Region Binding Inhibitors Enable Rational Design of Squaramides with An Improved Fraction Unbound to Human Plasma Protein To Be Published.
Page generated: Mon Dec 14 19:53:53 2020

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