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Chlorine 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:

Sodium (Na) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1, PDB code: 4c3x:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4c3x

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Chlorine binding site 1 out of 8 in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl571

b:30.5
occ:1.00
 OH A:TYR487 2.8 22.2 1.0
OH A:TYR318 2.9 29.6 1.0
N A:GLY491 3.2 20.7 1.0
C4 A:FAD551 3.4 24.2 1.0
N3 A:FAD551 3.5 23.4 1.0
CZ A:TYR487 3.6 21.9 1.0
C4X A:FAD551 3.6 22.9 1.0
C2 A:FAD551 3.6 24.4 1.0
CE1 A:TYR487 3.6 21.9 1.0
CA A:PRO490 3.7 22.9 1.0
C10 A:FAD551 3.8 21.3 1.0
N1 A:FAD551 3.8 21.4 1.0
O4 A:FAD551 3.9 23.6 1.0
C A:PRO490 3.9 23.5 1.0
O4 A:PG4581 4.0 62.8 1.0
CZ A:TYR318 4.1 24.3 1.0
OH A:TYR119 4.1 22.4 1.0
CA A:GLY491 4.2 21.4 1.0
N5 A:FAD551 4.3 22.1 1.0
O2 A:FAD551 4.3 21.9 1.0
CB A:PRO490 4.4 23.5 1.0
CE2 A:TYR318 4.5 23.0 1.0
C7 A:PG4581 4.6 60.2 1.0
O A:GLY489 4.6 25.9 1.0
CD A:PRO493 4.6 20.5 1.0
N10 A:FAD551 4.7 23.3 1.0
CE2 A:TYR487 4.8 20.7 1.0
N A:PRO490 4.8 22.8 1.0
C6 A:PG4581 4.9 61.2 1.0
CD1 A:TYR487 4.9 20.3 1.0
CE2 A:TYR119 5.0 20.8 1.0

Chlorine binding site 2 out of 8 in 4c3x

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Chlorine binding site 2 out of 8 in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
B:Cl571

b:33.4
occ:1.00
 OH B:TYR487 2.9 22.9 1.0
OH B:TYR318 2.9 26.5 1.0
N B:GLY491 3.2 25.6 1.0
C4 B:FAD551 3.4 25.5 1.0
N3 B:FAD551 3.5 25.0 1.0
C4X B:FAD551 3.6 24.4 1.0
CZ B:TYR487 3.6 19.8 1.0
C2 B:FAD551 3.7 25.8 1.0
CA B:PRO490 3.7 27.8 1.0
CE1 B:TYR487 3.7 20.9 1.0
C10 B:FAD551 3.8 23.2 1.0
N1 B:FAD551 3.9 23.0 1.0
O4 B:FAD551 3.9 22.0 1.0
C B:PRO490 3.9 29.1 1.0
CZ B:TYR318 4.1 22.3 1.0
OH B:TYR119 4.1 24.7 1.0
CA B:GLY491 4.2 24.2 1.0
N5 B:FAD551 4.3 24.3 1.0
O2 B:FAD551 4.3 21.1 1.0
C4 B:PG4581 4.3 68.2 1.0
CB B:PRO490 4.4 28.4 1.0
C3 B:PG4581 4.5 68.6 1.0
CE2 B:TYR318 4.5 22.6 1.0
O B:GLY489 4.7 26.0 1.0
O2 B:PG4581 4.7 67.7 1.0
CD B:PRO493 4.7 24.6 1.0
N10 B:FAD551 4.8 23.4 1.0
N B:PRO490 4.8 26.6 1.0
CE2 B:TYR487 4.9 21.9 1.0

Chlorine binding site 3 out of 8 in 4c3x

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Chlorine binding site 3 out of 8 in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
C:Cl571

b:34.2
occ:1.00
 OH C:TYR487 2.9 24.8 1.0
OH C:TYR318 2.9 31.1 1.0
N C:GLY491 3.1 27.7 1.0
C4 C:FAD551 3.4 26.6 1.0
N3 C:FAD551 3.4 25.4 1.0
C4X C:FAD551 3.6 25.2 1.0
CZ C:TYR487 3.6 24.2 1.0
CA C:PRO490 3.6 27.0 1.0
C2 C:FAD551 3.7 27.1 1.0
CE1 C:TYR487 3.7 23.4 1.0
N1 C:FAD551 3.8 23.1 1.0
C10 C:FAD551 3.8 25.2 1.0
C C:PRO490 3.9 29.6 1.0
O4 C:FAD551 3.9 25.8 1.0
OH C:TYR119 4.1 28.3 1.0
CZ C:TYR318 4.1 31.5 1.0
CA C:GLY491 4.1 27.8 1.0
N5 C:FAD551 4.2 24.4 1.0
O2 C:FAD551 4.3 25.1 1.0
CB C:PRO490 4.4 29.0 1.0
C8 C:PG4581 4.5 77.8 1.0
O4 C:PG4581 4.5 77.1 1.0
CE2 C:TYR318 4.6 29.6 1.0
O C:GLY489 4.6 26.5 1.0
CD C:PRO493 4.7 28.7 1.0
C6 C:PG4581 4.7 76.3 1.0
N10 C:FAD551 4.7 26.7 1.0
N C:PRO490 4.8 26.0 1.0
CE2 C:TYR487 4.9 24.5 1.0
C7 C:PG4581 4.9 79.3 1.0
CE2 C:TYR119 5.0 23.4 1.0
CD1 C:TYR487 5.0 24.8 1.0
CZ C:TYR119 5.0 23.9 1.0
N C:VAL492 5.0 26.3 1.0

Chlorine binding site 4 out of 8 in 4c3x

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Chlorine binding site 4 out of 8 in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
D:Cl571

b:33.8
occ:1.00
 OH D:TYR487 2.9 28.7 1.0
OH D:TYR318 3.0 26.4 1.0
N D:GLY491 3.1 23.7 1.0
N3 D:FAD551 3.3 24.6 1.0
C4 D:FAD551 3.3 26.4 1.0
C2 D:FAD551 3.5 24.1 1.0
C4X D:FAD551 3.6 25.6 1.0
CA D:PRO490 3.7 25.3 1.0
CZ D:TYR487 3.7 26.7 1.0
CE1 D:TYR487 3.8 25.6 1.0
N1 D:FAD551 3.8 24.6 1.0
C10 D:FAD551 3.8 25.5 1.0
O4 D:PG4581 3.9 56.9 1.0
C D:PRO490 3.9 27.4 1.0
O4 D:FAD551 3.9 26.4 1.0
CA D:GLY491 4.1 22.6 1.0
O2 D:FAD551 4.2 22.3 1.0
OH D:TYR119 4.2 24.7 1.0
C7 D:PG4581 4.2 51.4 1.0
CZ D:TYR318 4.2 26.7 1.0
N5 D:FAD551 4.3 25.2 1.0
CB D:PRO490 4.4 26.0 1.0
O D:GLY489 4.6 29.4 1.0
CD D:PRO493 4.6 27.6 1.0
CE2 D:TYR318 4.7 25.4 1.0
N10 D:FAD551 4.7 24.2 1.0
N D:PRO490 4.9 26.3 1.0
CE2 D:TYR487 4.9 25.8 1.0
C6 D:PG4581 5.0 55.6 1.0
N D:VAL492 5.0 21.9 1.0
C D:GLY491 5.0 21.8 1.0

Chlorine binding site 5 out of 8 in 4c3x

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Chlorine binding site 5 out of 8 in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl571

b:28.5
occ:1.00
 OH E:TYR487 2.9 27.1 1.0
OH E:TYR318 3.0 25.3 1.0
N E:GLY491 3.1 18.8 1.0
C4 E:FAD551 3.4 22.2 1.0
N3 E:FAD551 3.4 20.9 1.0
C4X E:FAD551 3.6 21.4 1.0
C2 E:FAD551 3.6 21.6 1.0
CA E:PRO490 3.7 20.6 1.0
CZ E:TYR487 3.7 22.8 1.0
CE1 E:TYR487 3.8 25.0 1.0
C10 E:FAD551 3.8 21.6 1.0
N1 E:FAD551 3.8 20.8 1.0
C E:PRO490 3.9 21.4 1.0
O4 E:FAD551 3.9 24.9 1.0
O4 E:PG4581 4.0 58.3 1.0
OH E:TYR119 4.1 24.6 1.0
CA E:GLY491 4.1 19.3 1.0
CZ E:TYR318 4.2 28.2 1.0
N5 E:FAD551 4.2 21.5 1.0
O2 E:FAD551 4.2 19.7 1.0
CB E:PRO490 4.3 22.2 1.0
C7 E:PG4581 4.4 55.0 1.0
C6 E:PG4581 4.5 62.9 1.0
CE2 E:TYR318 4.6 24.5 1.0
O E:GLY489 4.7 20.7 1.0
CD E:PRO493 4.7 21.3 1.0
N10 E:FAD551 4.7 20.9 1.0
N E:PRO490 4.8 21.8 1.0
CE2 E:TYR487 5.0 23.8 1.0

Chlorine binding site 6 out of 8 in 4c3x

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Chlorine binding site 6 out of 8 in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl571

b:33.2
occ:1.00
 OH F:TYR487 2.9 32.8 1.0
OH F:TYR318 2.9 26.2 1.0
N F:GLY491 3.2 26.4 1.0
C4 F:FAD551 3.4 22.8 1.0
N3 F:FAD551 3.4 20.6 1.0
C4X F:FAD551 3.5 22.1 1.0
C2 F:FAD551 3.6 21.3 1.0
CA F:PRO490 3.7 27.9 1.0
CZ F:TYR487 3.7 30.1 1.0
CE1 F:TYR487 3.8 30.8 1.0
C10 F:FAD551 3.8 22.9 1.0
N1 F:FAD551 3.8 21.1 1.0
O4 F:FAD551 3.9 23.1 1.0
C F:PRO490 3.9 28.3 1.0
C5 F:PG4581 4.0 63.3 1.0
OH F:TYR119 4.1 29.0 1.0
CZ F:TYR318 4.1 26.6 1.0
N5 F:FAD551 4.1 22.4 1.0
CA F:GLY491 4.2 25.1 1.0
O2 F:FAD551 4.3 20.9 1.0
CB F:PRO490 4.4 28.0 1.0
C6 F:PG4581 4.4 61.2 1.0
CE2 F:TYR318 4.6 26.1 1.0
O F:GLY489 4.7 30.7 1.0
N10 F:FAD551 4.7 22.6 1.0
CD F:PRO493 4.7 25.9 1.0
N F:PRO490 4.9 28.4 1.0
CE2 F:TYR487 4.9 30.9 1.0

Chlorine binding site 7 out of 8 in 4c3x

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Chlorine binding site 7 out of 8 in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl571

b:27.2
occ:1.00
 OH G:TYR487 2.9 20.4 1.0
OH G:TYR318 3.0 28.2 1.0
N G:GLY491 3.1 21.3 1.0
C4 G:FAD551 3.4 22.1 1.0
N3 G:FAD551 3.4 19.7 1.0
C2 G:FAD551 3.6 21.6 1.0
C7 G:PG4581 3.6 69.5 1.0
CA G:PRO490 3.6 20.3 1.0
C4X G:FAD551 3.7 22.3 1.0
CZ G:TYR487 3.7 20.1 1.0
CE1 G:TYR487 3.8 19.1 1.0
N1 G:FAD551 3.9 19.2 1.0
C G:PRO490 3.9 20.8 1.0
C10 G:FAD551 3.9 19.8 1.0
O4 G:FAD551 3.9 22.5 1.0
OH G:TYR119 4.1 21.2 1.0
CA G:GLY491 4.1 22.1 1.0
CZ G:TYR318 4.2 27.9 1.0
O2 G:FAD551 4.2 19.5 1.0
CB G:PRO490 4.3 20.9 1.0
N5 G:FAD551 4.3 21.6 1.0
O4 G:PG4581 4.6 69.4 1.0
CE2 G:TYR318 4.6 27.5 1.0
O G:GLY489 4.6 18.5 1.0
C8 G:PG4581 4.7 69.9 1.0
CD G:PRO493 4.7 23.6 1.0
N G:PRO490 4.8 20.0 1.0
N10 G:FAD551 4.8 21.4 1.0
C6 G:PG4581 4.9 68.0 1.0
CE2 G:TYR487 5.0 19.9 1.0

Chlorine binding site 8 out of 8 in 4c3x

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Chlorine binding site 8 out of 8 in the Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of 3-Ketosteroid DELTA1-Dehydrogenase From Rhodococcus Erythropolis SQ1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl571

b:34.2
occ:1.00
 OH H:TYR487 2.9 25.9 1.0
OH H:TYR318 3.0 28.7 1.0
N H:GLY491 3.1 20.9 1.0
C4 H:FAD551 3.3 24.9 1.0
N3 H:FAD551 3.3 24.9 1.0
C2 H:FAD551 3.5 23.4 1.0
C4X H:FAD551 3.5 24.1 1.0
CA H:PRO490 3.7 23.2 1.0
N1 H:FAD551 3.7 22.5 1.0
CZ H:TYR487 3.7 24.2 1.0
O4 H:FAD551 3.8 25.8 1.0
C10 H:FAD551 3.8 23.5 1.0
CE1 H:TYR487 3.8 23.9 1.0
C7 H:PG4581 3.9 62.9 1.0
C H:PRO490 3.9 21.3 1.0
CA H:GLY491 4.1 21.9 1.0
O2 H:FAD551 4.1 22.1 1.0
OH H:TYR119 4.2 25.9 1.0
N5 H:FAD551 4.2 24.2 1.0
CZ H:TYR318 4.2 25.7 1.0
CB H:PRO490 4.4 24.6 1.0
C8 H:PG4581 4.4 59.7 1.0
CD H:PRO493 4.7 20.0 1.0
O H:GLY489 4.7 25.9 1.0
CE2 H:TYR318 4.7 25.6 1.0
N10 H:FAD551 4.7 23.8 1.0
N H:PRO490 4.8 22.9 1.0
O5 H:PG4581 4.9 55.7 1.0
N H:VAL492 5.0 19.9 1.0
CE2 H:TYR487 5.0 22.4 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: Sun Jul 21 10:48:15 2024

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