Magnesium in PDB 6c1x: Crystal Structure of Ketosteroid Isomerase D40N/D103N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol

Enzymatic activity of Crystal Structure of Ketosteroid Isomerase D40N/D103N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol

All present enzymatic activity of Crystal Structure of Ketosteroid Isomerase D40N/D103N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol:
5.3.3.1;

Protein crystallography data

The structure of Crystal Structure of Ketosteroid Isomerase D40N/D103N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol, PDB code: 6c1x was solved by F.Yabukarski, M.M.Pinney, D.Herschlag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.50 / 1.05
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 36.386, 95.339, 72.999, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 17.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Ketosteroid Isomerase D40N/D103N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol (pdb code 6c1x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Ketosteroid Isomerase D40N/D103N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol, PDB code: 6c1x:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6c1x

Go back to Magnesium Binding Sites List in 6c1x
Magnesium binding site 1 out of 2 in the Crystal Structure of Ketosteroid Isomerase D40N/D103N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Ketosteroid Isomerase D40N/D103N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:19.6
occ:0.60
O A:HOH308 2.0 18.4 0.6
O A:HOH431 2.0 24.2 0.6
O A:HOH426 2.1 28.5 0.6
O A:HOH309 2.1 17.8 0.6
O A:HOH326 2.1 22.1 0.6
OD1 A:ASP35 4.1 12.6 0.5
OD2 A:ASP35 4.1 16.2 0.5
O A:HOH315 4.2 23.5 1.0
HB1 A:ALA33 4.2 14.5 1.0
OE1 A:GLN114 4.3 20.0 1.0
OD2 A:ASP108 4.3 19.9 1.0
OD1 A:ASP35 4.4 15.4 0.5
HE1 A:HIS110 4.5 34.3 1.0
OD2 A:ASP34 4.5 17.4 1.0
CG A:ASP35 4.5 13.6 0.5
HE22 A:GLN114 4.7 20.1 1.0
O A:HOH350 4.8 19.1 1.0
OD2 A:ASP35 4.9 17.6 0.5
HB2 A:ASP108 4.9 19.7 1.0
CG A:ASP35 4.9 15.7 0.5
ND1 A:HIS110 4.9 27.9 1.0

Magnesium binding site 2 out of 2 in 6c1x

Go back to Magnesium Binding Sites List in 6c1x
Magnesium binding site 2 out of 2 in the Crystal Structure of Ketosteroid Isomerase D40N/D103N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Ketosteroid Isomerase D40N/D103N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:18.6
occ:0.51
O A:HOH384 1.9 33.6 1.0
OD2 A:ASP21 1.9 16.4 1.0
O A:HOH311 2.0 18.1 0.5
O A:HOH325 2.0 19.2 0.5
O A:HOH408 2.1 24.3 0.5
O A:HOH302 2.1 28.1 0.5
CG A:ASP21 3.1 12.9 1.0
HB3 A:ASP21 3.2 13.8 1.0
HH21 A:ARG67 3.4 20.0 0.7
OE1 A:GLU18 3.5 20.7 0.6
CB A:ASP21 3.6 11.5 1.0
O A:HOH472 3.8 39.3 1.0
NH2 A:ARG67 3.9 16.6 0.7
HG13 A:VAL22 4.0 21.5 0.3
O A:HOH442 4.1 23.8 1.0
HH22 A:ARG67 4.1 20.0 0.7
O A:HOH341 4.1 15.7 1.0
HG12 A:VAL22 4.1 21.5 0.3
OD1 A:ASP21 4.1 13.8 1.0
O A:HOH414 4.1 25.6 1.0
HB2 A:ASP21 4.1 13.8 1.0
HA A:GLU18 4.1 13.0 0.6
HA A:GLU18 4.2 13.2 0.4
CD A:GLU18 4.3 19.2 0.6
CG1 A:VAL22 4.5 17.9 0.3
HG3 A:GLU18 4.5 19.8 0.4
OE2 A:GLU18 4.5 19.9 0.6
HB A:VAL22 4.6 18.8 0.7
O A:GLU18 4.6 11.4 0.4
O A:GLU18 4.7 11.0 0.6
HE A:ARG67 4.8 20.9 0.7
C A:ASP21 4.9 13.0 1.0
CA A:ASP21 4.9 10.9 1.0
HG11 A:VAL22 5.0 21.5 0.3
N A:VAL22 5.0 13.6 0.3
CZ A:ARG67 5.0 16.1 0.7
N A:VAL22 5.0 13.2 0.7
HB3 A:GLU18 5.0 14.6 0.6

Reference:

M.M.Pinney, A.Natarajan, F.Yabukarski, D.M.Sanchez, F.Liu, R.Liang, T.Doukov, J.P.Schwans, T.J.Martinez, D.Herschlag. Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein. J. Am. Chem. Soc. V. 140 9827 2018.
ISSN: ESSN 1520-5126
PubMed: 29990421
DOI: 10.1021/JACS.8B01596
Page generated: Mon Dec 14 22:25:56 2020

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