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Magnesium in PDB 6ucy: Multi-Conformer Model of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to 4-Androstenedione at 250 K

Enzymatic activity of Multi-Conformer Model of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to 4-Androstenedione at 250 K

All present enzymatic activity of Multi-Conformer Model of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to 4-Androstenedione at 250 K:
5.3.3.1;

Protein crystallography data

The structure of Multi-Conformer Model of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to 4-Androstenedione at 250 K, PDB code: 6ucy was solved by F.Yabukarski, D.Herschlag, J.T.Biel, J.S.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.40 / 1.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 36.061, 73.852, 95.610, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 16.4

Other elements in 6ucy:

The structure of Multi-Conformer Model of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to 4-Androstenedione at 250 K also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Multi-Conformer Model of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to 4-Androstenedione at 250 K (pdb code 6ucy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Multi-Conformer Model of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to 4-Androstenedione at 250 K, PDB code: 6ucy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6ucy

Go back to Magnesium Binding Sites List in 6ucy
Magnesium binding site 1 out of 2 in the Multi-Conformer Model of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to 4-Androstenedione at 250 K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Multi-Conformer Model of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to 4-Androstenedione at 250 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:13.9
occ:0.29
 O A:HOH448 1.9 25.2 0.5
O A:HOH415 1.9 17.3 0.5
OD2 A:ASP21 2.0 12.5 0.5
O A:HOH407 2.0 22.4 0.6
O A:HOH383 2.1 35.6 1.0
OD2 A:ASP21 2.4 13.1 0.5
O A:HOH415 2.9 23.6 0.5
OE1 A:GLU18 3.1 22.2 0.4
HB3 A:ASP21 3.1 9.8 0.5
CG A:ASP21 3.1 10.6 0.5
HH21 A:ARG67 3.4 22.1 0.6
HB3 A:ASP21 3.5 10.7 0.5
CG A:ASP21 3.5 9.0 0.5
CB A:ASP21 3.6 8.2 0.5
HH21 A:ARG67 3.8 23.4 0.4
HG3 A:GLU18 3.8 15.4 0.3
CD A:GLU18 4.0 19.0 0.4
CB A:ASP21 4.0 8.9 0.5
HA A:GLU18 4.1 12.2 0.4
NH2 A:ARG67 4.1 18.4 0.6
HB2 A:ASP21 4.1 9.8 0.5
HA A:GLU18 4.2 12.3 0.3
OD1 A:ASP21 4.2 10.3 0.5
O A:HOH324 4.2 18.3 1.0
O A:HOH445 4.2 29.1 1.0
HH22 A:ARG67 4.2 22.1 0.6
HA A:GLU18 4.3 8.9 0.3
OE2 A:GLU18 4.3 21.2 0.4
HB2 A:ASP21 4.4 10.7 0.5
HB3 A:GLU18 4.5 11.1 0.4
HB A:VAL22 4.5 10.8 0.5
NH2 A:ARG67 4.5 19.5 0.4
O A:GLU18 4.5 8.0 0.3
OD1 A:ASP21 4.6 10.5 0.5
HH22 A:ARG67 4.7 23.4 0.4
O A:GLU18 4.7 9.4 0.3
HG2 A:GLU18 4.7 17.0 0.3
C A:ASP21 4.8 8.0 0.5
CG A:GLU18 4.8 12.8 0.3
CA A:ASP21 4.8 7.5 0.5
O A:GLU18 4.8 9.0 0.4
N A:VAL22 4.9 9.3 0.5
HE A:ARG67 4.9 17.0 0.6
H A:VAL22 4.9 11.2 0.5
CA A:GLU18 4.9 10.2 0.4
HB A:VAL22 4.9 12.1 0.5
CB A:GLU18 5.0 9.3 0.4
CA A:GLU18 5.0 10.2 0.3

Magnesium binding site 2 out of 2 in 6ucy

Go back to Magnesium Binding Sites List in 6ucy
Magnesium binding site 2 out of 2 in the Multi-Conformer Model of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to 4-Androstenedione at 250 K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Multi-Conformer Model of Ketosteroid Isomerase From Pseudomonas Putida (Pksi) Bound to 4-Androstenedione at 250 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:16.8
occ:0.45
 O A:HOH355 1.9 32.4 0.7
O A:HOH426 2.0 26.2 0.6
O A:HOH303 2.0 25.2 1.0
O A:HOH348 2.0 17.2 0.7
O A:HOH379 2.2 25.1 0.6
OD2 A:ASP108 4.0 14.1 0.5
O A:HOH369 4.1 25.9 0.5
OD1 A:ASP35 4.1 13.2 0.6
OE1 A:GLN114 4.2 21.9 0.1
OE2 A:GLU109 4.3 36.8 0.3
HB1 A:ALA33 4.3 11.9 0.4
HB1 A:ALA33 4.3 12.9 0.6
OE1 A:GLN114 4.3 15.9 0.5
O A:HOH321 4.3 20.4 1.0
HE1 A:HIS110 4.3 27.6 0.4
OD2 A:ASP108 4.4 13.4 0.5
OD2 A:ASP35 4.4 22.2 0.6
OD2 A:ASP34 4.6 13.8 0.6
CG A:ASP35 4.6 14.4 0.6
ND1 A:HIS110 4.6 22.6 0.4
HE22 A:GLN114 4.7 18.0 0.5
CE1 A:HIS110 4.8 23.0 0.4
HB2 A:ASP108 4.8 14.6 0.5
HE1 A:HIS110 4.8 29.2 0.3
HD2 A:HIS110 4.8 27.7 0.2
HB2 A:ASP108 4.9 12.2 0.5
O A:ASP34 4.9 12.3 0.4
OE2 A:GLU109 4.9 29.4 0.4
CG A:ASP108 5.0 10.4 0.5

Reference:

F.Yabukarski, D.Herschlag. Assessing Active Site Positioning and Testing Catalytic Proposals Via Ketosteroid Isomerase Conformational Ensembles To Be Published.
Page generated: Wed Aug 13 18:30:07 2025

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