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Magnesium in PDB 7rxk: Multi-Conformer Model of Apo Ketosteroid Isomerase Y32F/Y57F Mutant From Pseudomonas Putida (Pksi) at 250 K

Enzymatic activity of Multi-Conformer Model of Apo Ketosteroid Isomerase Y32F/Y57F Mutant From Pseudomonas Putida (Pksi) at 250 K

All present enzymatic activity of Multi-Conformer Model of Apo Ketosteroid Isomerase Y32F/Y57F Mutant From Pseudomonas Putida (Pksi) at 250 K:
5.3.3.1;

Protein crystallography data

The structure of Multi-Conformer Model of Apo Ketosteroid Isomerase Y32F/Y57F Mutant From Pseudomonas Putida (Pksi) at 250 K, PDB code: 7rxk was solved by F.Yabukarski, T.Doukov, D.Herschlag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.56 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 36.266, 74.059, 96.229, 90, 90, 90
R / Rfree (%) 15.3 / 16.6

Other elements in 7rxk:

The structure of Multi-Conformer Model of Apo Ketosteroid Isomerase Y32F/Y57F Mutant From Pseudomonas Putida (Pksi) at 250 K also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Multi-Conformer Model of Apo Ketosteroid Isomerase Y32F/Y57F Mutant From Pseudomonas Putida (Pksi) at 250 K (pdb code 7rxk). 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 Apo Ketosteroid Isomerase Y32F/Y57F Mutant From Pseudomonas Putida (Pksi) at 250 K, PDB code: 7rxk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7rxk

Go back to Magnesium Binding Sites List in 7rxk
Magnesium binding site 1 out of 2 in the Multi-Conformer Model of Apo Ketosteroid Isomerase Y32F/Y57F Mutant From Pseudomonas Putida (Pksi) 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 Apo Ketosteroid Isomerase Y32F/Y57F Mutant From Pseudomonas Putida (Pksi) at 250 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:14.5
occ:0.39
 OD2 A:ASP21 1.9 12.7 0.5
O A:HOH372 2.0 17.1 0.5
O A:HOH382 2.1 18.4 0.5
O A:HOH374 2.1 15.6 0.6
O A:HOH386 2.1 19.0 0.5
O A:HOH440 2.2 21.8 0.5
OD2 A:ASP21 2.4 9.3 0.2
OD2 A:ASP21 2.6 10.8 0.3
OE1 A:GLU18 3.0 23.7 0.4
CG A:ASP21 3.0 10.1 0.5
HH21 A:ARG67 3.1 17.4 0.4
HB3 A:ASP21 3.1 12.4 0.2
HB3 A:ASP21 3.2 11.9 0.5
HH21 A:ARG67 3.4 21.7 0.3
CG A:ASP21 3.4 10.4 0.2
HB3 A:ASP21 3.5 9.4 0.3
CG A:ASP21 3.6 8.8 0.3
CB A:ASP21 3.7 10.0 0.5
HH21 A:ARG67 3.7 15.8 0.3
CB A:ASP21 3.7 10.3 0.2
NH2 A:ARG67 3.8 14.5 0.4
HH22 A:ARG67 3.9 17.4 0.4
CD A:GLU18 4.0 19.2 0.4
HA A:GLU18 4.0 11.6 0.4
HA A:GLU18 4.0 12.8 0.3
HG3 A:GLU18 4.0 22.1 0.3
NH2 A:ARG67 4.1 18.1 0.3
CB A:ASP21 4.1 7.8 0.3
OD1 A:ASP21 4.1 10.5 0.5
O A:HOH399 4.1 27.7 1.0
HB2 A:ASP21 4.2 12.4 0.2
O A:HOH317 4.2 17.9 1.0
HA A:GLU18 4.2 11.3 0.3
HB2 A:ASP21 4.2 11.9 0.5
HH22 A:ARG67 4.2 21.7 0.3
O A:HOH435 4.3 28.6 1.0
NH2 A:ARG67 4.3 13.2 0.3
HH22 A:ARG67 4.4 15.8 0.3
O A:GLU18 4.5 9.8 0.3
HB3 A:GLU18 4.5 14.3 0.4
HB2 A:ASP21 4.5 9.4 0.3
OE2 A:GLU18 4.5 19.7 0.4
HG2 A:GLU18 4.6 19.8 0.3
OD1 A:ASP21 4.6 11.3 0.2
O A:GLU18 4.6 7.4 0.3
HB A:VAL22 4.6 11.6 0.1
OD1 A:ASP21 4.6 11.6 0.3
HB A:VAL22 4.6 11.4 0.5
HE A:ARG67 4.6 19.4 0.4
O A:GLU18 4.7 10.2 0.4
HB A:VAL22 4.7 11.1 0.4
C A:ASP21 4.7 9.3 0.5
HE A:ARG67 4.8 18.6 0.3
CA A:GLU18 4.8 9.7 0.4
CA A:ASP21 4.8 10.6 0.5
HB3 A:GLU18 4.9 13.7 0.3
CA A:GLU18 4.9 10.7 0.3
CZ A:ARG67 4.9 11.2 0.4
CG A:GLU18 4.9 18.4 0.3
N A:VAL22 4.9 9.0 0.5
O A:ASP21 5.0 11.5 0.5
CB A:GLU18 5.0 11.9 0.4
H A:VAL22 5.0 10.8 0.5

Magnesium binding site 2 out of 2 in 7rxk

Go back to Magnesium Binding Sites List in 7rxk
Magnesium binding site 2 out of 2 in the Multi-Conformer Model of Apo Ketosteroid Isomerase Y32F/Y57F Mutant From Pseudomonas Putida (Pksi) 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 Apo Ketosteroid Isomerase Y32F/Y57F Mutant From Pseudomonas Putida (Pksi) at 250 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:16.8
occ:0.67
 O A:HOH302 2.0 19.1 0.8
O A:HOH336 2.0 18.4 0.8
O A:HOH422 2.0 28.4 0.8
O A:HOH387 2.1 29.8 0.8
O A:HOH354 2.1 25.7 0.8
HE1 A:HIS110 3.9 30.3 0.3
OD1 A:ASP35 4.0 12.2 0.4
OD1 A:ASP35 4.1 12.2 0.3
OD2 A:ASP108 4.1 15.8 0.4
OE1 A:GLN114 4.1 16.1 0.3
OD2 A:ASP35 4.2 14.4 0.3
OE1 A:GLN114 4.2 15.9 0.4
HB1 A:ALA33 4.2 12.6 0.6
OD2 A:ASP35 4.3 12.8 0.4
O A:HOH319 4.3 21.9 1.0
OD2 A:ASP108 4.3 15.5 0.5
OD1 A:ASP34 4.4 12.2 0.6
HD2 A:HIS110 4.4 26.4 0.3
OE1 A:GLN114 4.4 15.5 0.3
OD2 A:ASP108 4.4 15.8 0.1
HB1 A:ALA33 4.4 10.4 0.4
HE22 A:GLN114 4.5 15.6 0.4
CG A:ASP35 4.5 12.4 0.4
ND1 A:HIS110 4.5 27.2 0.3
OD1 A:ASP35 4.5 10.5 0.3
CG A:ASP35 4.5 11.2 0.3
CE1 A:HIS110 4.5 25.3 0.3
HB2 A:ASP108 4.7 18.6 0.4
OE2 A:GLU109 4.7 35.3 0.4
HD2 A:HIS110 4.7 26.3 0.4
HE22 A:GLN114 4.8 18.0 0.3
OD2 A:ASP34 4.8 13.6 0.4
HB2 A:ASP108 4.9 17.2 0.1
HE22 A:GLN114 4.9 18.2 0.3

Reference:

F.Yabukarski, T.Doukov, M.Pinney, J.Biel, J.Fraser, D.Herschlag. Ensemble-Function Relationships to Evaluate Catalysis in the Ketosteroid Isomerase Oxyanion Hole To Be Published.
Page generated: Thu Oct 3 08:08:05 2024

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