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Sodium in PDB 4c3y: Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 in Complex with 1,4- Androstadiene-3,17-Dione

Enzymatic activity of Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 in Complex with 1,4- Androstadiene-3,17-Dione

All present enzymatic activity of Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 in Complex with 1,4- Androstadiene-3,17-Dione:
1.3.99.4;

Protein crystallography data

The structure of Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 in Complex with 1,4- Androstadiene-3,17-Dione, PDB code: 4c3y was solved by A.Rohman, N.Van Oosterwijk, A.M.W.H.Thunnissen, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.42 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 107.747, 132.142, 363.597, 90.00, 90.00, 90.00
R / Rfree (%) 21.045 / 24.882

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 in Complex with 1,4- Androstadiene-3,17-Dione (pdb code 4c3y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 in Complex with 1,4- Androstadiene-3,17-Dione, PDB code: 4c3y:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4c3y

Go back to Sodium Binding Sites List in 4c3y
Sodium binding site 1 out of 4 in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 in Complex with 1,4- Androstadiene-3,17-Dione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 in Complex with 1,4- Androstadiene-3,17-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na561

b:33.9
occ:1.00
 OE1 A:GLN155 2.2 28.1 1.0
O A:ASP154 2.3 23.9 1.0
OE1 A:GLN160 2.4 31.8 1.0
O B:ASP154 2.4 26.6 1.0
OE1 B:GLN155 2.4 25.3 1.0
OE1 B:GLN160 2.6 34.4 1.0
CD A:GLN160 3.2 30.5 1.0
CD A:GLN155 3.3 27.8 1.0
C A:ASP154 3.4 26.3 1.0
C B:ASP154 3.5 22.6 1.0
NE2 A:GLN160 3.5 30.3 1.0
CD B:GLN160 3.5 32.4 1.0
CD B:GLN155 3.5 27.7 1.0
NE2 B:GLN160 3.7 33.1 1.0
OG1 A:THR158 3.8 30.3 1.0
OG1 B:THR158 3.9 28.4 1.0
O A:HOH2087 3.9 37.7 1.0
CA A:GLN155 4.0 25.3 1.0
N A:GLN155 4.1 25.6 1.0
NE2 A:GLN155 4.1 27.4 1.0
N B:GLN155 4.2 24.0 1.0
CA B:GLN155 4.2 26.6 1.0
CG A:GLN155 4.3 27.4 1.0
NE2 B:GLN155 4.4 26.2 1.0
CB B:ASP154 4.4 27.5 1.0
CA B:ASP154 4.5 25.0 1.0
CB A:ASP154 4.5 29.3 1.0
CA A:ASP154 4.5 28.1 1.0
CG B:GLN155 4.5 25.8 1.0
CG A:GLN160 4.6 28.0 1.0
CB A:GLN155 4.7 27.0 1.0
CG B:GLN160 4.9 28.7 1.0
CB A:THR158 4.9 30.2 1.0
CB B:GLN155 5.0 25.2 1.0
O A:HOH2088 5.0 30.4 1.0
O A:HOH2097 5.0 30.4 1.0
CB B:THR158 5.0 27.1 1.0

Sodium binding site 2 out of 4 in 4c3y

Go back to Sodium Binding Sites List in 4c3y
Sodium binding site 2 out of 4 in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 in Complex with 1,4- Androstadiene-3,17-Dione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 in Complex with 1,4- Androstadiene-3,17-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na561

b:33.1
occ:1.00
 O C:ASP154 2.2 24.3 1.0
OE1 D:GLN155 2.3 27.4 1.0
OE1 C:GLN155 2.3 34.0 1.0
OE1 D:GLN160 2.4 24.4 1.0
OE1 C:GLN160 2.5 28.6 1.0
O D:ASP154 2.5 24.9 1.0
CD D:GLN160 3.3 25.6 1.0
C C:ASP154 3.3 27.8 1.0
CD D:GLN155 3.4 28.7 1.0
CD C:GLN155 3.4 32.2 1.0
CD C:GLN160 3.4 31.2 1.0
NE2 D:GLN160 3.5 25.5 1.0
C D:ASP154 3.6 26.0 1.0
NE2 C:GLN160 3.7 36.3 1.0
OG1 C:THR158 3.8 30.8 1.0
OG1 D:THR158 3.9 34.1 1.0
CA C:GLN155 4.0 29.3 1.0
N C:GLN155 4.0 27.6 1.0
O C:HOH2053 4.1 41.0 1.0
NE2 D:GLN155 4.2 29.2 1.0
CA D:GLN155 4.2 31.0 1.0
NE2 C:GLN155 4.2 34.3 1.0
N D:GLN155 4.3 27.9 1.0
CG C:GLN155 4.3 32.1 1.0
CB C:ASP154 4.4 28.1 1.0
CA C:ASP154 4.4 27.1 1.0
CG D:GLN155 4.4 29.6 1.0
CB D:ASP154 4.6 29.8 1.0
CA D:ASP154 4.6 29.1 1.0
CG D:GLN160 4.7 27.0 1.0
CB C:GLN155 4.7 32.1 1.0
O C:HOH2065 4.8 27.3 1.0
CG C:GLN160 4.8 30.4 1.0
CB D:GLN155 4.8 30.0 1.0
CB C:THR158 4.9 30.4 1.0
O C:HOH2055 4.9 28.4 1.0

Sodium binding site 3 out of 4 in 4c3y

Go back to Sodium Binding Sites List in 4c3y
Sodium binding site 3 out of 4 in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 in Complex with 1,4- Androstadiene-3,17-Dione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 in Complex with 1,4- Androstadiene-3,17-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na561

b:30.2
occ:1.00
 O E:ASP154 2.2 27.2 1.0
OE1 E:GLN155 2.3 34.3 1.0
OE1 F:GLN160 2.4 25.3 1.0
OE1 F:GLN155 2.4 27.4 1.0
OE1 E:GLN160 2.4 26.8 1.0
O F:ASP154 2.5 24.1 1.0
CD F:GLN160 3.3 27.5 1.0
C E:ASP154 3.3 25.9 1.0
CD E:GLN160 3.4 24.1 1.0
CD E:GLN155 3.4 33.3 1.0
NE2 F:GLN160 3.5 28.7 1.0
CD F:GLN155 3.5 27.5 1.0
C F:ASP154 3.6 24.5 1.0
NE2 E:GLN160 3.7 23.7 1.0
OG1 E:THR158 3.7 27.9 1.0
OG1 F:THR158 3.8 29.4 1.0
CA E:GLN155 4.0 28.3 1.0
N E:GLN155 4.1 26.2 1.0
O E:HOH2069 4.2 33.9 1.0
NE2 E:GLN155 4.2 38.6 1.0
CA F:GLN155 4.3 27.1 1.0
NE2 F:GLN155 4.3 23.3 1.0
N F:GLN155 4.4 23.7 1.0
CG E:GLN155 4.4 30.9 1.0
CB E:ASP154 4.4 26.0 1.0
CA E:ASP154 4.4 25.4 1.0
CG F:GLN155 4.5 25.6 1.0
CB F:ASP154 4.6 24.8 1.0
CA F:ASP154 4.7 24.6 1.0
CG F:GLN160 4.7 27.7 1.0
CG E:GLN160 4.7 25.4 1.0
CB E:GLN155 4.7 28.3 1.0
CB E:THR158 4.8 29.0 1.0
CB F:THR158 4.9 30.9 1.0
CB F:GLN155 4.9 26.5 1.0

Sodium binding site 4 out of 4 in 4c3y

Go back to Sodium Binding Sites List in 4c3y
Sodium binding site 4 out of 4 in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 in Complex with 1,4- Androstadiene-3,17-Dione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 in Complex with 1,4- Androstadiene-3,17-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na561

b:25.7
occ:1.00
 OE1 H:GLN155 2.1 24.3 1.0
OE1 G:GLN155 2.2 24.8 1.0
O G:ASP154 2.3 22.9 1.0
O H:ASP154 2.4 32.3 1.0
OE1 H:GLN160 2.5 38.4 1.0
OE1 G:GLN160 2.7 29.5 1.0
CD H:GLN155 3.2 26.3 1.0
CD G:GLN155 3.4 22.6 1.0
C G:ASP154 3.4 24.1 1.0
CD H:GLN160 3.4 33.8 1.0
C H:ASP154 3.4 25.8 1.0
CD G:GLN160 3.6 31.6 1.0
NE2 H:GLN160 3.6 35.3 1.0
NE2 G:GLN160 3.9 30.8 1.0
OG1 H:THR158 3.9 32.5 1.0
O G:HOH2061 4.0 32.5 1.0
CA H:GLN155 4.0 30.5 1.0
NE2 H:GLN155 4.0 25.8 1.0
OG1 G:THR158 4.1 30.2 1.0
N H:GLN155 4.1 30.7 1.0
N G:GLN155 4.1 23.9 1.0
CA G:GLN155 4.1 24.6 1.0
NE2 G:GLN155 4.2 23.3 1.0
CG H:GLN155 4.2 27.8 1.0
CB G:ASP154 4.3 27.3 1.0
CG G:GLN155 4.3 24.5 1.0
CA G:ASP154 4.4 26.1 1.0
CB H:ASP154 4.4 29.7 1.0
CA H:ASP154 4.5 28.8 1.0
CB H:GLN155 4.7 28.8 1.0
CG H:GLN160 4.7 31.1 1.0
CB G:GLN155 4.8 25.7 1.0
CG G:GLN160 5.0 31.8 1.0

Reference:

A.Rohman, N.Van Oosterwijk, A.M.W.H.Thunnissen, B.W.Dijkstra. Crystal Structure and Site-Directed Mutagenesis of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 Explain Its Catalytic Mechanism J.Biol.Chem. V. 288 35559 2013.
ISSN: ISSN 0021-9258
PubMed: 24165124
DOI: 10.1074/JBC.M113.522771
Page generated: Mon Oct 7 14:38:04 2024

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