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Magnesium in PDB 4rkd: Psychrophilic Aromatic Amino Acids Aminotransferase From Psychrobacter Sp. B6 Cocrystalized with Aspartic Acid

Enzymatic activity of Psychrophilic Aromatic Amino Acids Aminotransferase From Psychrobacter Sp. B6 Cocrystalized with Aspartic Acid

All present enzymatic activity of Psychrophilic Aromatic Amino Acids Aminotransferase From Psychrobacter Sp. B6 Cocrystalized with Aspartic Acid:
2.6.1.57;

Protein crystallography data

The structure of Psychrophilic Aromatic Amino Acids Aminotransferase From Psychrobacter Sp. B6 Cocrystalized with Aspartic Acid, PDB code: 4rkd was solved by A.Bujacz, M.Rutkiewicz-Krotewicz, G.Bujacz, K.Nowakowska-Sapota, M.Turkiewicz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.74 / 2.76
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.250, 103.230, 165.780, 90.00, 98.58, 90.00
R / Rfree (%) 17.3 / 22.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Psychrophilic Aromatic Amino Acids Aminotransferase From Psychrobacter Sp. B6 Cocrystalized with Aspartic Acid (pdb code 4rkd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Psychrophilic Aromatic Amino Acids Aminotransferase From Psychrobacter Sp. B6 Cocrystalized with Aspartic Acid, PDB code: 4rkd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4rkd

Go back to Magnesium Binding Sites List in 4rkd
Magnesium binding site 1 out of 4 in the Psychrophilic Aromatic Amino Acids Aminotransferase From Psychrobacter Sp. B6 Cocrystalized with Aspartic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Psychrophilic Aromatic Amino Acids Aminotransferase From Psychrobacter Sp. B6 Cocrystalized with Aspartic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:15.5
occ:1.00
 O A:HOH594 2.1 15.0 1.0
O A:HOH530 2.2 13.8 1.0
O A:HOH528 2.2 14.2 1.0
O B:HOH552 2.2 13.4 1.0
O B:HOH551 2.2 14.6 1.0
O A:HOH533 2.2 16.2 1.0
O B:HOH634 3.7 22.0 1.0
OD2 A:ASP141 3.8 40.8 1.0
O B:CYS140 4.1 33.9 1.0
OE2 B:GLU112 4.1 34.9 1.0
OE2 A:GLU112 4.2 37.2 1.0
C B:CYS140 4.5 34.9 1.0
O A:CYS140 4.5 35.6 1.0
OD2 B:ASP141 4.5 57.3 1.0
CA B:CYS140 4.5 30.3 1.0
OE1 B:GLU112 4.5 34.3 1.0
O B:GLY139 4.6 25.8 1.0
CG A:ASP141 4.6 38.5 1.0
O A:GLY139 4.6 28.6 1.0
C A:CYS140 4.6 35.6 1.0
CA A:CYS140 4.6 35.3 1.0
CD B:GLU112 4.8 34.9 1.0
OE1 A:GLU112 4.9 45.5 1.0
CD A:GLU112 5.0 38.1 1.0

Magnesium binding site 2 out of 4 in 4rkd

Go back to Magnesium Binding Sites List in 4rkd
Magnesium binding site 2 out of 4 in the Psychrophilic Aromatic Amino Acids Aminotransferase From Psychrobacter Sp. B6 Cocrystalized with Aspartic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Psychrophilic Aromatic Amino Acids Aminotransferase From Psychrobacter Sp. B6 Cocrystalized with Aspartic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:25.9
occ:1.00
 O C:HOH523 2.1 21.1 1.0
O C:HOH575 2.1 38.6 1.0
O D:HOH569 2.1 28.4 1.0
O D:HOH542 2.2 17.2 1.0
O C:HOH569 2.2 25.1 1.0
OD2 D:ASP141 4.1 53.3 1.0
OD2 C:ASP141 4.3 58.9 1.0
O C:CYS140 4.4 36.8 1.0
CA C:CYS140 4.4 34.8 1.0
C C:CYS140 4.4 36.5 1.0
OE2 C:GLU112 4.5 37.5 1.0
O C:GLY139 4.6 32.7 1.0
O D:GLY139 4.7 29.5 1.0
OE2 D:GLU112 4.7 29.1 1.0
O D:CYS140 4.7 32.7 1.0
OE1 C:GLU112 4.8 42.1 1.0
CD2 C:HIS115 4.8 36.4 1.0
C D:CYS140 4.8 31.4 1.0
NE2 C:HIS115 4.9 36.8 1.0
CG D:ASP141 5.0 56.1 1.0
CA D:CYS140 5.0 30.4 1.0
N C:ASP141 5.0 37.3 1.0
CG C:ASP141 5.0 57.0 1.0

Magnesium binding site 3 out of 4 in 4rkd

Go back to Magnesium Binding Sites List in 4rkd
Magnesium binding site 3 out of 4 in the Psychrophilic Aromatic Amino Acids Aminotransferase From Psychrobacter Sp. B6 Cocrystalized with Aspartic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Psychrophilic Aromatic Amino Acids Aminotransferase From Psychrobacter Sp. B6 Cocrystalized with Aspartic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:13.8
occ:1.00
 O F:HOH543 2.1 12.8 1.0
O E:HOH524 2.2 15.7 1.0
O E:HOH523 2.2 15.3 1.0
O F:HOH567 2.2 19.5 1.0
O F:HOH545 2.2 10.5 1.0
OE2 E:GLU112 3.3 35.2 1.0
OE2 F:GLU112 3.4 44.0 1.0
O F:GLY139 4.3 31.5 1.0
CD E:GLU112 4.3 34.1 1.0
O E:GLY139 4.3 28.0 1.0
CD F:GLU112 4.4 38.7 1.0
OE1 F:GLU112 4.5 39.5 1.0
OE1 E:GLU112 4.5 31.9 1.0
CA E:CYS140 4.5 37.4 1.0
O F:CYS140 4.6 34.6 1.0
OD2 F:ASP141 4.6 46.5 1.0
CA F:CYS140 4.6 35.0 1.0
O E:CYS140 4.7 34.7 1.0
C F:CYS140 4.7 36.3 1.0
C E:CYS140 4.8 36.9 1.0

Magnesium binding site 4 out of 4 in 4rkd

Go back to Magnesium Binding Sites List in 4rkd
Magnesium binding site 4 out of 4 in the Psychrophilic Aromatic Amino Acids Aminotransferase From Psychrobacter Sp. B6 Cocrystalized with Aspartic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Psychrophilic Aromatic Amino Acids Aminotransferase From Psychrobacter Sp. B6 Cocrystalized with Aspartic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg401

b:19.1
occ:1.00
 O H:HOH544 2.1 16.9 1.0
O H:HOH570 2.1 19.1 1.0
O G:HOH563 2.2 21.2 1.0
O G:HOH543 2.2 17.5 1.0
O H:HOH543 2.2 18.9 1.0
O H:HOH571 2.2 22.1 1.0
OD2 H:ASP141 3.8 59.8 1.0
O G:HOH509 4.2 8.7 1.0
O H:CYS140 4.3 26.4 1.0
OE2 G:GLU112 4.3 50.0 1.0
OE2 H:GLU112 4.4 29.6 1.0
O G:CYS140 4.4 29.0 1.0
O H:GLY139 4.5 25.1 1.0
OD2 G:ASP141 4.5 48.5 1.0
C H:CYS140 4.5 28.6 1.0
OE1 G:GLU112 4.6 46.5 1.0
C G:CYS140 4.6 31.6 1.0
CG H:ASP141 4.6 59.5 1.0
CA G:CYS140 4.7 28.2 1.0
CA H:CYS140 4.7 26.5 1.0
O G:GLY139 4.8 24.0 1.0
CD G:GLU112 4.9 47.3 1.0
OE1 H:GLU112 5.0 31.7 1.0

Reference:

A.Bujacz, K.Nowakowska-Sapota, M.Rutkiewicz-Krotewicz, M.Turkiewicz. Crystal Structure and Enzymatic Properties of Psychrophilic Aminotransferase From Antarctic Soil Bacterium, Psychrobacter Sp. B6 To Be Published.
Page generated: Mon Aug 11 23:23:30 2025

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