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Magnesium in PDB 6c1j: Crystal Structure of Ketosteroid Isomerase Y32F/Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol

Enzymatic activity of Crystal Structure of Ketosteroid Isomerase Y32F/Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol

All present enzymatic activity of Crystal Structure of Ketosteroid Isomerase Y32F/Y57F/D40N 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 Y32F/Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol, PDB code: 6c1j 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) 36.46 / 1.06
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 35.902, 94.998, 72.910, 90.00, 90.00, 90.00
R / Rfree (%) 12.9 / 15.4

Other elements in 6c1j:

The structure of Crystal Structure of Ketosteroid Isomerase Y32F/Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Ketosteroid Isomerase Y32F/Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol (pdb code 6c1j). 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 Y32F/Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol, PDB code: 6c1j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6c1j

Go back to Magnesium Binding Sites List in 6c1j
Magnesium binding site 1 out of 2 in the Crystal Structure of Ketosteroid Isomerase Y32F/Y57F/D40N 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 Y32F/Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:19.2
occ:0.77
 O A:HOH344 2.0 19.2 0.7
O A:HOH323 2.0 19.0 0.8
O A:HOH453 2.0 29.3 0.8
O A:HOH339 2.1 37.8 0.9
O A:HOH392 2.2 27.4 0.9
O A:HOH435 2.2 37.7 0.8
O A:HOH421 3.8 42.8 1.0
HD2 A:HIS110 4.2 35.2 1.0
OD1 A:ASP35 4.2 15.3 1.0
HB1 A:ALA33 4.2 13.7 1.0
OE1 A:GLN114 4.3 17.9 1.0
OD2 A:ASP108 4.3 17.8 1.0
OE2 A:GLU109 4.3 19.8 0.1
O A:HOH312 4.4 23.3 1.0
OD2 A:ASP34 4.5 17.8 1.0
OD2 A:ASP35 4.5 18.9 1.0
HE2 A:HIS110 4.6 36.8 1.0
O A:HOH380 4.6 25.7 0.6
CG A:ASP35 4.7 15.5 1.0
HE22 A:GLN114 4.7 18.1 1.0
HB2 A:ASP108 4.8 18.0 1.0
O A:HOH372 4.8 19.4 1.0
CD2 A:HIS110 4.9 29.4 1.0

Magnesium binding site 2 out of 2 in 6c1j

Go back to Magnesium Binding Sites List in 6c1j
Magnesium binding site 2 out of 2 in the Crystal Structure of Ketosteroid Isomerase Y32F/Y57F/D40N 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 Y32F/Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to 3,4-Dinitrophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:25.3
occ:0.86
 O A:HOH308 1.9 13.0 0.4
O A:HOH303 2.0 13.5 0.4
O A:HOH363 2.1 11.4 0.3
OD2 A:ASP21 2.1 14.5 1.0
O A:HOH387 2.2 17.6 0.6
OE1 A:GLU18 2.9 13.7 0.6
HB3 A:ASP21 3.2 13.1 1.0
CG A:ASP21 3.2 12.8 1.0
HH21 A:ARG67 3.3 35.3 0.4
HH21 A:ARG67 3.5 19.6 0.6
HG13 A:VAL22 3.6 17.3 0.6
HH22 A:ARG67 3.6 35.3 0.4
O A:HOH363 3.7 10.4 0.4
CB A:ASP21 3.7 10.9 1.0
NH2 A:ARG67 3.7 29.4 0.4
CD A:GLU18 3.8 12.7 0.6
HG3 A:GLU18 3.9 20.6 0.4
OE2 A:GLU18 4.0 13.2 0.6
O A:HOH424 4.0 28.3 0.6
NH2 A:ARG67 4.0 16.3 0.6
HA A:GLU18 4.1 11.8 0.6
HA A:GLU18 4.1 13.2 0.4
HH22 A:ARG67 4.2 19.6 0.6
O A:HOH358 4.2 14.7 1.0
HB2 A:ASP21 4.2 13.1 1.0
HG12 A:VAL22 4.2 17.3 0.6
O A:HOH440 4.2 22.1 1.0
OD1 A:ASP21 4.3 12.6 1.0
CG1 A:VAL22 4.3 14.4 0.6
O A:HOH363 4.4 20.0 0.3
HB A:VAL22 4.5 13.9 0.4
O A:GLU18 4.5 10.5 1.0
HG2 A:GLU18 4.6 20.6 0.4
CG A:GLU18 4.7 17.1 0.4
HG11 A:VAL22 4.7 17.3 0.6
CZ A:ARG67 4.9 28.7 0.4
HE A:ARG67 4.9 18.5 0.6
C A:ASP21 4.9 12.1 1.0
CA A:GLU18 4.9 9.8 0.6
H A:VAL22 4.9 14.3 0.6
CA A:GLU18 4.9 11.0 0.4
N A:VAL22 4.9 11.9 0.6
CA A:ASP21 4.9 10.9 1.0
N A:VAL22 5.0 11.6 0.4

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 Sep 30 20:05:54 2024

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