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Sodium in PDB 4c3x: Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1

Enzymatic activity of Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1

All present enzymatic activity of Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1:
1.3.99.4;

Protein crystallography data

The structure of Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1, PDB code: 4c3x 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) 49.26 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 107.385, 131.625, 363.161, 90.00, 90.00, 90.00
R / Rfree (%) 17.733 / 20.805

Other elements in 4c3x:

The structure of Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 (pdb code 4c3x). 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, PDB code: 4c3x:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4c3x

Go back to Sodium Binding Sites List in 4c3x
Sodium binding site 1 out of 4 in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na561

b:23.1
occ:1.00
 O A:ASP154 2.3 23.5 1.0
OE1 A:GLN155 2.3 20.0 1.0
OE1 B:GLN155 2.4 17.1 1.0
OE1 B:GLN160 2.4 25.6 1.0
O B:ASP154 2.4 19.8 1.0
OE1 A:GLN160 2.5 24.2 1.0
CD B:GLN160 3.3 21.9 1.0
C A:ASP154 3.4 22.2 1.0
CD A:GLN160 3.4 25.6 1.0
CD B:GLN155 3.4 19.1 1.0
CD A:GLN155 3.5 19.7 1.0
C B:ASP154 3.5 19.1 1.0
NE2 B:GLN160 3.6 25.2 1.0
NE2 A:GLN160 3.7 24.8 1.0
OG1 B:THR158 3.8 22.3 1.0
OG1 A:THR158 3.8 20.9 1.0
CA B:GLN155 4.1 19.3 1.0
CA A:GLN155 4.1 19.9 1.0
N A:GLN155 4.1 19.8 1.0
N B:GLN155 4.2 19.5 1.0
O A:HOH2189 4.2 34.8 1.0
NE2 B:GLN155 4.2 20.1 1.0
NE2 A:GLN155 4.3 19.7 1.0
CG A:GLN155 4.4 20.3 1.0
CA A:ASP154 4.4 21.0 1.0
CG B:GLN155 4.4 20.2 1.0
CB A:ASP154 4.5 20.3 1.0
CA B:ASP154 4.5 19.2 1.0
CB B:ASP154 4.6 20.3 1.0
CG B:GLN160 4.7 22.1 1.0
CG A:GLN160 4.8 26.6 1.0
CB B:THR158 4.8 23.7 1.0
CB B:GLN155 4.8 19.9 1.0
CB A:GLN155 4.8 19.3 1.0
CB A:THR158 4.9 22.0 1.0

Sodium binding site 2 out of 4 in 4c3x

Go back to Sodium Binding Sites List in 4c3x
Sodium binding site 2 out of 4 in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na561

b:22.2
occ:1.00
 O C:ASP154 2.3 22.2 1.0
OE1 C:GLN160 2.3 23.3 1.0
OE1 D:GLN160 2.4 22.6 1.0
O D:ASP154 2.4 24.1 1.0
OE1 D:GLN155 2.4 28.3 1.0
OE1 C:GLN155 2.4 23.8 1.0
CD D:GLN160 3.3 20.4 1.0
CD C:GLN160 3.3 24.3 1.0
C C:ASP154 3.4 23.2 1.0
CD C:GLN155 3.5 24.4 1.0
C D:ASP154 3.5 24.5 1.0
CD D:GLN155 3.5 26.8 1.0
NE2 D:GLN160 3.6 20.2 1.0
NE2 C:GLN160 3.7 24.0 1.0
OG1 C:THR158 3.7 25.8 1.0
OG1 D:THR158 3.7 30.7 1.0
CA C:GLN155 4.0 23.6 1.0
CA D:GLN155 4.1 26.3 1.0
N C:GLN155 4.1 21.8 1.0
O C:HOH2116 4.1 32.5 1.0
N D:GLN155 4.2 25.2 1.0
NE2 D:GLN155 4.2 24.2 1.0
NE2 C:GLN155 4.2 25.9 1.0
CG C:GLN155 4.4 22.3 1.0
CG D:GLN155 4.4 26.4 1.0
CA C:ASP154 4.5 23.4 1.0
CA D:ASP154 4.6 26.4 1.0
CB C:ASP154 4.6 24.6 1.0
CB D:ASP154 4.6 26.7 1.0
CG D:GLN160 4.7 22.2 1.0
CG C:GLN160 4.7 28.6 1.0
CB C:THR158 4.7 26.6 1.0
CB D:THR158 4.8 27.0 1.0
CB C:GLN155 4.8 23.2 1.0
CB D:GLN155 4.8 26.1 1.0
O C:HOH2118 4.9 24.6 1.0

Sodium binding site 3 out of 4 in 4c3x

Go back to Sodium Binding Sites List in 4c3x
Sodium binding site 3 out of 4 in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na561

b:23.3
occ:1.00
 O F:ASP154 2.3 18.0 1.0
OE1 E:GLN155 2.3 23.6 1.0
OE1 F:GLN155 2.3 20.4 1.0
O E:ASP154 2.4 20.8 1.0
OE1 F:GLN160 2.4 21.1 1.0
OE1 E:GLN160 2.5 21.0 1.0
C F:ASP154 3.4 20.6 1.0
CD F:GLN160 3.4 21.6 1.0
CD E:GLN155 3.4 25.0 1.0
CD F:GLN155 3.4 20.8 1.0
CD E:GLN160 3.4 21.4 1.0
C E:ASP154 3.5 22.5 1.0
NE2 E:GLN160 3.7 18.1 1.0
NE2 F:GLN160 3.7 20.2 1.0
OG1 F:THR158 3.7 22.3 1.0
OG1 E:THR158 3.9 22.9 1.0
O E:HOH2145 4.0 26.2 1.0
CA F:GLN155 4.0 21.2 1.0
N F:GLN155 4.1 19.9 1.0
CA E:GLN155 4.1 24.8 1.0
N E:GLN155 4.2 22.4 1.0
NE2 E:GLN155 4.2 25.7 1.0
NE2 F:GLN155 4.2 23.2 1.0
CG F:GLN155 4.4 19.8 1.0
CG E:GLN155 4.4 25.1 1.0
CB E:ASP154 4.5 23.0 1.0
CA F:ASP154 4.5 18.5 1.0
CB F:ASP154 4.5 18.3 1.0
CA E:ASP154 4.5 22.5 1.0
CG F:GLN160 4.8 22.6 1.0
CB F:GLN155 4.8 21.7 1.0
CG E:GLN160 4.8 22.0 1.0
CB F:THR158 4.8 21.8 1.0
CB E:GLN155 4.8 25.0 1.0
CB E:THR158 5.0 23.4 1.0

Sodium binding site 4 out of 4 in 4c3x

Go back to Sodium Binding Sites List in 4c3x
Sodium binding site 4 out of 4 in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na561

b:26.4
occ:1.00
 OE1 H:GLN155 2.3 21.7 1.0
O H:ASP154 2.3 25.1 1.0
OE1 G:GLN155 2.3 24.0 1.0
O G:ASP154 2.4 22.9 1.0
OE1 H:GLN160 2.4 23.9 1.0
OE1 G:GLN160 2.5 29.0 1.0
CD H:GLN160 3.3 24.5 1.0
C H:ASP154 3.4 26.6 1.0
CD H:GLN155 3.4 22.0 1.0
CD G:GLN155 3.4 20.5 1.0
CD G:GLN160 3.5 27.4 1.0
C G:ASP154 3.5 19.8 1.0
NE2 H:GLN160 3.7 25.8 1.0
NE2 G:GLN160 3.7 28.7 1.0
OG1 H:THR158 3.7 25.0 1.0
OG1 G:THR158 3.9 24.2 1.0
CA H:GLN155 4.0 24.2 1.0
N H:GLN155 4.0 24.9 1.0
CA G:GLN155 4.1 19.9 1.0
N G:GLN155 4.2 19.6 1.0
O G:HOH2162 4.2 34.2 1.0
NE2 H:GLN155 4.2 21.0 1.0
NE2 G:GLN155 4.2 21.4 1.0
CG H:GLN155 4.4 25.0 1.0
CG G:GLN155 4.4 21.0 1.0
CA H:ASP154 4.4 23.9 1.0
CB G:ASP154 4.5 24.5 1.0
CA G:ASP154 4.5 22.6 1.0
CB H:ASP154 4.5 23.7 1.0
CG H:GLN160 4.7 26.0 1.0
CB H:GLN155 4.7 23.9 1.0
CG G:GLN160 4.8 26.2 1.0
CB G:GLN155 4.8 21.1 1.0
CB H:THR158 4.8 23.6 1.0
CB G:THR158 4.9 24.4 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 14:37:46 2024

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