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Magnesium in PDB 7ry4: Multi-Conformer Model of Ketosteroid Isomerase Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog at 250 K

Enzymatic activity of Multi-Conformer Model of Ketosteroid Isomerase Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog at 250 K

All present enzymatic activity of Multi-Conformer Model of Ketosteroid Isomerase Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog at 250 K:
5.3.3.1;

Protein crystallography data

The structure of Multi-Conformer Model of Ketosteroid Isomerase Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog at 250 K, PDB code: 7ry4 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) 29.37 / 1.11
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.243, 74.554, 50.966, 90, 110.7, 90
R / Rfree (%) 14.2 / 15.8

Other elements in 7ry4:

The structure of Multi-Conformer Model of Ketosteroid Isomerase Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog 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 Ketosteroid Isomerase Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog at 250 K (pdb code 7ry4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Multi-Conformer Model of Ketosteroid Isomerase Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog at 250 K, PDB code: 7ry4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7ry4

Go back to Magnesium Binding Sites List in 7ry4
Magnesium binding site 1 out of 6 in the Multi-Conformer Model of Ketosteroid Isomerase Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog 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 Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog at 250 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:15.8
occ:0.62
 O A:HOH411 2.0 34.1 0.9
O A:HOH308 2.0 19.6 0.8
O A:HOH358 2.1 22.4 0.9
O A:HOH417 2.1 23.8 0.7
O A:HOH316 2.3 32.0 0.9
OD1 A:ASP35 4.0 12.5 0.3
OE1 A:GLN114 4.0 19.7 0.3
OD1 A:ASP35 4.0 12.0 0.3
OD2 A:ASP35 4.2 10.6 0.3
OD2 A:ASP35 4.2 13.2 0.3
OD2 A:ASP108 4.2 15.2 0.5
HB1 A:ALA33 4.2 10.4 0.3
O A:HOH302 4.3 24.9 1.0
OD2 A:ASP108 4.3 13.7 0.3
OD2 A:ASP34 4.3 12.9 0.5
OE1 A:GLN114 4.4 15.2 0.5
OD2 A:ASP34 4.4 12.1 0.2
HE22 A:GLN114 4.4 15.6 0.3
OD1 A:ASP35 4.4 12.5 0.4
CG A:ASP35 4.4 11.2 0.3
HB1 A:ALA33 4.4 13.3 0.5
HB1 A:ALA33 4.5 13.1 0.3
CG A:ASP35 4.5 10.5 0.3
OE2 A:GLU109 4.6 23.7 0.2
OD2 A:ASP108 4.6 15.5 0.2
HE1 A:HIS110 4.7 26.6 0.3
HE1 A:HIS110 4.7 29.0 0.5
HB2 A:ASP108 4.7 14.5 0.3
OD2 A:ASP34 4.8 11.8 0.3
HE22 A:GLN114 4.8 15.4 0.5
HB2 A:ASP108 4.8 14.5 0.2
CD A:GLN114 4.9 12.8 0.3
ND1 A:HIS110 4.9 25.6 0.3
OD2 A:ASP35 4.9 14.6 0.4
NE2 A:GLN114 5.0 13.0 0.3
CG A:ASP35 5.0 11.4 0.4

Magnesium binding site 2 out of 6 in 7ry4

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Magnesium binding site 2 out of 6 in the Multi-Conformer Model of Ketosteroid Isomerase Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog 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 Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog at 250 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:14.9
occ:0.27
 OD2 A:ASP21 1.9 14.5 0.4
O A:HOH365 2.0 16.6 0.3
O A:HOH382 2.0 16.3 0.5
O A:HOH351 2.1 26.5 0.6
OD2 A:ASP21 2.1 14.2 0.2
O A:HOH387 2.2 17.1 0.3
OD2 A:ASP21 2.4 15.6 0.4
OE2 A:GLU18 2.9 38.0 0.3
CG A:ASP21 3.0 11.5 0.4
HB3 A:ASP21 3.1 13.5 0.4
HB3 A:ASP21 3.1 13.4 0.2
CG A:ASP21 3.2 11.4 0.2
HH21 A:ARG67 3.3 25.5 0.5
OE1 A:GLU18 3.3 26.0 0.3
OE1 A:GLU18 3.3 30.5 0.4
CD A:GLU18 3.4 18.3 0.3
HB3 A:ASP21 3.5 11.4 0.4
CG A:ASP21 3.5 11.0 0.4
HG13 A:VAL22 3.5 18.1 0.3
CB A:ASP21 3.6 11.2 0.4
CB A:ASP21 3.6 11.2 0.2
O A:HOH434 3.8 26.5 0.6
NH2 A:ARG67 3.9 21.3 0.5
HH22 A:ARG67 4.0 25.5 0.5
CB A:ASP21 4.0 9.5 0.4
HA A:GLU18 4.0 11.6 0.4
HB2 A:ASP21 4.1 13.4 0.2
O A:HOH332 4.1 20.9 1.0
OD1 A:ASP21 4.1 12.6 0.4
O A:HOH425 4.1 31.5 0.8
HB2 A:ASP21 4.1 13.5 0.4
HG12 A:VAL22 4.1 18.1 0.3
HA A:GLU18 4.2 11.5 0.2
O A:HOH398 4.2 28.4 1.0
OD1 A:ASP21 4.2 12.1 0.2
CG1 A:VAL22 4.2 15.1 0.3
HA A:GLU18 4.3 11.0 0.3
HB3 A:GLU18 4.3 13.8 0.4
HB A:VAL22 4.4 11.1 0.3
CD A:GLU18 4.4 23.9 0.4
HB2 A:ASP21 4.5 11.4 0.4
OD1 A:ASP21 4.5 11.7 0.4
O A:GLU18 4.6 10.5 0.4
HG11 A:VAL22 4.6 18.1 0.3
O A:GLU18 4.6 10.0 0.2
O A:GLU18 4.6 10.0 0.3
C A:ASP21 4.6 9.9 0.4
HB A:VAL22 4.6 12.0 0.4
N A:VAL22 4.7 9.0 0.3
HE A:ARG67 4.7 22.2 0.5
H A:VAL22 4.7 10.8 0.4
HG2 A:GLU18 4.7 15.4 0.2
CA A:ASP21 4.7 10.2 0.4
CG A:GLU18 4.8 18.5 0.3
CA A:GLU18 4.8 9.6 0.4
CZ A:ARG67 4.9 15.5 0.5
H A:VAL22 4.9 12.5 0.2
MG A:MG204 4.9 22.1 0.4
CA A:ASP21 4.9 8.5 0.2
N A:VAL22 4.9 10.4 0.3
C A:ASP21 4.9 10.5 0.2
HG3 A:GLU18 5.0 22.2 0.3
CB A:GLU18 5.0 11.5 0.4
HA A:VAL22 5.0 9.1 0.3
O A:ASP21 5.0 11.0 0.4

Magnesium binding site 3 out of 6 in 7ry4

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Magnesium binding site 3 out of 6 in the Multi-Conformer Model of Ketosteroid Isomerase Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog at 250 K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Multi-Conformer Model of Ketosteroid Isomerase Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog at 250 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:22.1
occ:0.44
 O A:HOH402 1.9 22.5 0.4
O A:HOH384 2.0 17.1 0.6
O A:HOH425 2.2 31.5 0.8
HH21 A:ARG67 2.4 25.5 0.5
O A:HOH402 2.5 23.7 0.6
NH2 A:ARG67 2.5 21.3 0.5
HH22 A:ARG67 2.6 25.5 0.5
CZ A:ARG67 3.3 15.5 0.5
O A:HOH351 3.4 26.5 0.6
HE A:ARG67 3.8 22.2 0.5
OD2 A:ASP21 3.9 14.5 0.4
NE A:ARG67 3.9 18.5 0.5
HB3 A:CYS69 4.0 14.4 0.1
OD1 A:ASP21 4.1 12.6 0.4
O A:HOH307 4.1 34.6 1.0
HB3 A:CYS69 4.1 15.0 0.4
NH1 A:ARG67 4.1 26.7 0.5
HB3 A:ARG67 4.1 18.9 0.5
HB2 A:CYS69 4.1 14.8 0.2
HH12 A:ARG67 4.1 32.0 0.5
OD2 A:ASP21 4.2 14.2 0.2
HB2 A:CYS69 4.2 11.4 0.2
OD1 A:ASP21 4.2 12.1 0.2
OD1 A:ASP21 4.4 11.7 0.4
CG A:ASP21 4.4 11.5 0.4
OD2 A:ASP21 4.4 15.6 0.4
HD3 A:ARG67 4.5 22.1 0.3
CG A:ASP21 4.5 11.4 0.2
O A:HOH332 4.6 20.9 1.0
O A:ALA68 4.6 11.2 0.4
CG A:ASP21 4.7 11.0 0.4
HB3 A:ARG67 4.7 10.8 0.3
HB2 A:CYS69 4.7 14.4 0.1
HB3 A:ARG67 4.7 14.8 0.3
CB A:CYS69 4.8 12.0 0.1
HH11 A:ARG67 4.8 32.0 0.5
MG A:MG203 4.9 14.9 0.3
CB A:CYS69 5.0 9.5 0.2
CB A:CYS69 5.0 12.3 0.2

Magnesium binding site 4 out of 6 in 7ry4

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Magnesium binding site 4 out of 6 in the Multi-Conformer Model of Ketosteroid Isomerase Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog at 250 K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Multi-Conformer Model of Ketosteroid Isomerase Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog at 250 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:17.8
occ:0.57
 O B:HOH313 2.0 19.2 0.7
O B:HOH391 2.0 32.8 0.7
O B:HOH302 2.1 22.1 0.8
O B:HOH354 2.3 39.4 0.8
O B:HOH326 2.5 24.2 0.6
HE1 B:HIS110 3.8 42.2 0.4
OE2 B:GLU109 3.9 36.0 0.3
OD1 B:ASP35 4.0 12.3 0.3
OD1 B:ASP35 4.0 13.3 0.2
OD2 B:ASP108 4.1 16.8 0.3
OD2 B:ASP35 4.1 14.4 0.2
OE1 B:GLN114 4.1 21.9 0.3
O B:HOH326 4.2 28.0 0.4
O B:HOH335 4.2 22.0 1.0
HB1 B:ALA33 4.2 11.9 0.4
OD2 B:ASP34 4.2 13.6 0.4
O B:HOH356 4.2 44.6 1.0
OE1 B:GLN114 4.3 20.6 0.3
HB1 B:ALA33 4.3 11.3 0.4
HD2 B:HIS110 4.3 29.7 0.3
CE1 B:HIS110 4.4 35.1 0.4
OE1 B:GLN114 4.4 19.4 0.4
HE22 B:GLN114 4.4 16.0 0.3
OD2 B:ASP108 4.4 15.4 0.2
OD2 B:ASP35 4.4 12.9 0.3
HB1 B:ALA33 4.4 10.9 0.2
CG B:ASP35 4.5 9.7 0.2
OD1 B:ASP35 4.5 12.6 0.4
OD2 B:ASP34 4.5 11.8 0.4
ND1 B:HIS110 4.5 23.7 0.4
CG B:ASP35 4.6 10.9 0.3
OD2 B:ASP108 4.7 19.4 0.4
OD2 B:ASP34 4.7 14.1 0.3
HB2 B:ASP108 4.8 18.3 0.3
HE22 B:GLN114 4.9 19.8 0.3
HE22 B:GLN114 4.9 19.9 0.4
O B:HOH331 4.9 18.7 1.0
HB2 B:ASP108 4.9 16.6 0.2
CD B:GLN114 4.9 14.8 0.3
NE2 B:GLN114 5.0 13.3 0.3

Magnesium binding site 5 out of 6 in 7ry4

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Magnesium binding site 5 out of 6 in the Multi-Conformer Model of Ketosteroid Isomerase Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog at 250 K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Multi-Conformer Model of Ketosteroid Isomerase Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog at 250 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:12.8
occ:0.27
 OD2 B:ASP21 1.8 10.9 0.3
O B:HOH364 1.9 17.1 0.7
O B:HOH361 2.0 16.5 0.3
O B:HOH365 2.1 19.9 0.6
O B:HOH324 2.1 25.1 0.5
O B:HOH345 2.1 21.3 0.4
OD2 B:ASP21 2.5 14.0 0.3
OD2 B:ASP21 2.5 11.1 0.3
OE1 B:GLU18 2.9 23.4 0.3
CG B:ASP21 2.9 8.9 0.3
HB3 B:ASP21 3.1 13.9 0.3
HB3 B:ASP21 3.1 10.8 0.3
HH21 B:ARG67 3.3 19.6 0.4
CG B:ASP21 3.4 10.5 0.3
O B:HOH324 3.5 26.2 0.5
HB3 B:ASP21 3.5 8.7 0.3
CG B:ASP21 3.5 10.1 0.3
CB B:ASP21 3.6 9.0 0.3
HG12 B:VAL22 3.6 19.5 0.3
CB B:ASP21 3.7 11.6 0.3
NH2 B:ARG67 3.9 16.3 0.4
HG3 B:GLU18 3.9 19.1 0.3
OD1 B:ASP21 4.0 9.5 0.3
HA B:GLU18 4.0 10.6 0.3
CB B:ASP21 4.0 7.2 0.3
HG13 B:VAL22 4.0 19.5 0.3
HB2 B:ASP21 4.1 10.8 0.3
O B:HOH332 4.1 19.6 1.0
HH22 B:ARG67 4.1 19.6 0.4
HA B:GLU18 4.1 12.7 0.3
CD B:GLU18 4.1 22.2 0.3
HA B:GLU18 4.2 12.5 0.3
O B:HOH404 4.2 25.0 0.6
HB2 B:ASP21 4.2 13.9 0.3
CG1 B:VAL22 4.2 16.2 0.3
O B:HOH361 4.3 23.0 0.7
HB3 B:GLU18 4.4 14.4 0.3
HB B:VAL22 4.4 11.2 0.3
O B:GLU18 4.5 10.9 0.3
HB2 B:ASP21 4.5 8.7 0.3
HB B:VAL22 4.5 9.4 0.4
OD1 B:ASP21 4.5 9.7 0.3
O B:GLU18 4.5 9.4 0.3
H B:VAL22 4.5 9.3 0.3
OD1 B:ASP21 4.6 10.4 0.3
HG2 B:GLU18 4.6 17.9 0.3
HG11 B:VAL22 4.6 19.5 0.3
O B:GLU18 4.7 9.7 0.3
N B:VAL22 4.7 7.8 0.4
C B:ASP21 4.7 9.8 0.3
HE B:ARG67 4.8 20.2 0.4
CA B:ASP21 4.8 8.0 0.3
CA B:GLU18 4.8 8.8 0.3
C B:ASP21 4.8 9.2 0.3
OE2 B:GLU18 4.8 19.5 0.3
CG B:GLU18 4.9 15.9 0.3
CA B:ASP21 4.9 9.0 0.3
CB B:GLU18 4.9 12.0 0.3
CA B:GLU18 5.0 10.6 0.3
O B:ASP21 5.0 9.7 0.3
CZ B:ARG67 5.0 17.4 0.4
HA B:VAL22 5.0 9.5 0.4
CA B:GLU18 5.0 10.4 0.3

Magnesium binding site 6 out of 6 in 7ry4

Go back to Magnesium Binding Sites List in 7ry4
Magnesium binding site 6 out of 6 in the Multi-Conformer Model of Ketosteroid Isomerase Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog at 250 K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Multi-Conformer Model of Ketosteroid Isomerase Y57F/D40N Mutant From Pseudomonas Putida (Pksi) Bound to A Transition State Analog at 250 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:26.7
occ:0.43
 O B:HOH324 1.9 26.2 0.5
O B:HOH368 2.1 23.4 1.0
O B:HOH392 2.1 33.1 0.6
O B:HOH404 2.2 25.0 0.6
HH21 B:ARG67 2.6 19.6 0.4
NH2 B:ARG67 2.7 16.3 0.4
HH22 B:ARG67 2.8 19.6 0.4
O B:HOH324 3.4 25.1 0.5
CZ B:ARG67 3.4 17.4 0.4
OD2 B:ASP21 3.8 14.0 0.3
HE B:ARG67 3.8 20.2 0.4
O B:HOH405 3.8 21.2 0.4
NE B:ARG67 3.9 16.8 0.4
OD1 B:ASP21 4.1 9.5 0.3
HB2 B:CYS69 4.1 13.7 0.2
HB3 B:ARG67 4.1 16.6 0.4
HB3 B:CYS69 4.2 13.4 0.3
HB3 B:CYS69 4.2 12.2 0.2
OD1 B:ASP21 4.2 9.7 0.3
NH1 B:ARG67 4.2 26.2 0.4
HB2 B:CYS69 4.2 15.9 0.3
OD2 B:ASP21 4.2 10.9 0.3
HD3 B:ARG67 4.3 24.5 0.4
HH12 B:ARG67 4.3 31.4 0.4
OD2 B:ASP21 4.5 11.1 0.3
CG B:ASP21 4.5 10.5 0.3
OD1 B:ASP21 4.5 10.4 0.3
CG B:ASP21 4.6 8.9 0.3
HB3 B:ARG67 4.7 15.9 0.2
CG B:ASP21 4.7 10.1 0.3
O B:HOH332 4.7 19.6 1.0
HB3 B:ARG67 4.7 16.1 0.4
HG3 B:ARG67 4.8 19.5 0.4
O B:ALA68 4.9 11.8 0.4
HH11 B:ARG67 4.9 31.4 0.4
CB B:CYS69 5.0 11.4 0.2
O B:ALA68 5.0 9.1 0.2
H B:ALA68 5.0 9.3 0.4
CB B:ARG67 5.0 13.9 0.4

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 08:09:09 2024

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