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Sodium in PDB 7sh5: Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One

Protein crystallography data

The structure of Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One, PDB code: 7sh5 was solved by D.Z.Doherty, S.G.Bell, J.Bruning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.81 / 1.83
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 112.685, 59.2, 114.937, 90, 91.3, 90
R / Rfree (%) 17 / 20

Other elements in 7sh5:

The structure of Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One (pdb code 7sh5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 13 binding sites of Sodium where determined in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One, PDB code: 7sh5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 13 in 7sh5

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Sodium binding site 1 out of 13 in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One


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 CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:46.7
occ:1.00
 O A:ALA75 3.1 21.6 1.0
O A:HOH892 3.3 34.9 1.0
O A:HOH707 3.6 36.0 1.0
N A:ALA75 3.9 16.6 1.0
O A:HOH658 3.9 39.4 1.0
O B:HOH627 4.0 34.9 1.0
C A:ALA75 4.0 23.2 1.0
CB A:ALA75 4.1 20.9 1.0
O B:ARG41 4.1 27.6 1.0
CB A:ASP74 4.1 24.8 1.0
CA A:ALA75 4.2 17.8 1.0
O A:HOH751 4.4 39.0 1.0
O A:HOH955 4.4 37.4 1.0
C A:ASP74 4.6 18.6 1.0
CG A:ASP74 4.6 27.9 1.0
CA B:ARG41 4.7 25.8 1.0
OD2 A:ASP74 4.7 35.1 1.0
CB B:ARG41 4.7 21.3 1.0
C B:ARG41 4.8 26.2 1.0
CA A:ASP74 4.8 24.7 1.0

Sodium binding site 2 out of 13 in 7sh5

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Sodium binding site 2 out of 13 in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One


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 CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:40.9
occ:1.00
 O A:ACT507 2.3 40.7 1.0
N A:ARG22 2.4 31.0 1.0
CA A:ARG22 2.9 36.1 1.0
O A:PHE18 3.1 21.4 1.0
N A:ALA24 3.1 26.4 1.0
N A:GLN23 3.2 35.4 1.0
N A:SER21 3.2 30.4 1.0
CB A:ALA24 3.2 24.1 1.0
OG A:SER21 3.2 33.3 1.0
C A:SER21 3.3 34.9 1.0
C A:ARG22 3.4 39.7 1.0
C A:ACT507 3.4 27.8 1.0
CA A:SER21 3.7 34.2 1.0
CA A:ALA24 3.8 25.1 1.0
C A:TYR19 3.8 20.6 1.0
O A:HOH905 3.8 25.1 1.0
C A:ALA20 3.9 29.8 1.0
O A:TYR19 3.9 21.5 1.0
N A:ALA20 4.0 20.4 1.0
CB A:SER21 4.0 34.6 1.0
C A:GLN23 4.1 30.2 1.0
CH3 A:ACT507 4.1 22.7 1.0
C A:PHE18 4.2 20.6 1.0
CA A:GLN23 4.2 35.3 1.0
CA A:TYR19 4.3 23.1 1.0
CA A:ALA20 4.3 20.7 1.0
O A:SER21 4.4 38.9 1.0
OXT A:ACT507 4.4 37.7 1.0
CB A:ARG22 4.4 40.8 1.0
O A:ARG22 4.5 31.4 1.0
O A:ALA20 4.6 26.8 1.0
N A:TYR19 4.7 19.2 1.0
CG A:ARG22 4.8 38.8 1.0
C A:ALA24 5.0 23.5 1.0

Sodium binding site 3 out of 13 in 7sh5

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Sodium binding site 3 out of 13 in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One


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 CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:38.9
occ:1.00
 O A:HOH620 2.8 39.8 1.0
N A:LEU370 3.0 29.0 1.0
CG A:GLN373 3.1 59.0 1.0
CA A:ARG369 3.6 31.0 1.0
CB A:LEU370 3.7 31.5 1.0
CG A:ARG369 3.7 44.1 1.0
C A:ARG369 3.8 22.3 1.0
CD A:GLN373 3.8 68.4 1.0
CB A:ARG369 3.8 33.5 1.0
CG A:LEU370 3.8 35.2 1.0
CA A:LEU370 3.9 30.2 1.0
CB A:LEU251 4.0 26.6 1.0
O A:LEU251 4.0 34.0 1.0
NE2 A:GLN373 4.2 59.9 1.0
CD1 A:LEU370 4.2 30.3 1.0
CB A:GLN373 4.4 60.7 1.0
O A:LEU370 4.4 32.7 1.0
C A:LEU251 4.4 31.4 1.0
OE1 A:GLN373 4.5 73.2 1.0
NH1 A:ARG254 4.6 43.0 1.0
CA A:LEU251 4.6 30.9 1.0
C A:LEU370 4.7 33.7 1.0
CD2 A:LEU251 4.7 27.5 1.0
CG A:LEU251 4.7 28.0 1.0
CD1 A:LEU251 4.8 26.6 1.0
CD A:ARG369 4.8 53.3 1.0
N A:ARG369 5.0 28.7 1.0

Sodium binding site 4 out of 13 in 7sh5

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Sodium binding site 4 out of 13 in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One


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 CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:30.1
occ:1.00
 O A:VAL178 3.1 17.5 1.0
NA C:NA504 3.1 20.6 1.0
O A:HOH893 3.2 31.9 1.0
N A:ALA182 3.3 16.8 1.0
CB A:ASP181 3.6 20.5 1.0
CA A:ALA182 3.6 19.3 1.0
C A:ASP181 3.7 19.8 1.0
CB A:ALA182 3.8 18.1 1.0
OD2 A:ASP162 3.8 20.3 1.0
O A:HOH608 3.9 26.1 1.0
CG1 A:VAL178 3.9 19.1 1.0
C A:VAL178 4.0 18.8 1.0
O A:HOH668 4.0 20.9 1.0
CA A:VAL178 4.2 16.5 1.0
CA A:ASP181 4.2 17.4 1.0
O A:ASP181 4.2 18.8 1.0
CE C:LYS101 4.5 28.6 1.0
CB A:VAL178 4.6 15.8 1.0
CG A:ASP162 4.6 22.2 1.0
CB A:ASP162 4.8 14.9 1.0
N A:ASP181 4.8 20.5 1.0
CG A:ASP181 4.9 24.6 1.0
O C:HOH648 5.0 21.9 1.0
CG C:LYS101 5.0 39.9 1.0

Sodium binding site 5 out of 13 in 7sh5

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Sodium binding site 5 out of 13 in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:49.2
occ:1.00
 NH2 B:ARG22 2.5 42.7 1.0
O B:HOH977 2.5 29.1 1.0
O B:HOH677 2.6 31.8 1.0
O B:HOH882 2.8 27.8 1.0
O B:HOH966 3.3 19.5 1.0
O B:HOH774 3.5 26.4 1.0
CZ B:ARG22 3.5 44.9 1.0
NH1 B:ARG22 4.1 33.0 1.0
CD1 B:LEU379 4.2 24.8 1.0
O B:HOH726 4.3 18.3 1.0
CD2 B:LEU379 4.3 20.4 1.0
O B:HOH1000 4.4 29.3 1.0
NE B:ARG22 4.4 43.2 1.0
O B:HOH769 4.5 18.2 1.0
CD B:ARG22 4.6 39.9 1.0
O B:HOH641 4.7 24.1 1.0
CG B:LEU379 4.8 20.4 1.0
NH1 B:ARG25 4.8 22.9 1.0
NE1 B:TRP277 4.8 22.6 1.0

Sodium binding site 6 out of 13 in 7sh5

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Sodium binding site 6 out of 13 in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:30.9
occ:1.00
 O C:HOH656 2.4 24.8 1.0
O C:HOH907 2.5 30.9 1.0
OG1 C:THR193 2.8 25.8 1.0
CB C:THR193 3.2 23.8 1.0
CG2 C:THR193 3.4 23.0 1.0
CD1 C:PHE189 3.6 23.0 1.0
OG1 C:THR190 3.6 18.7 1.0
CE1 C:PHE189 3.6 24.6 1.0
CA C:THR190 3.6 20.1 1.0
CB C:THR190 3.9 20.6 1.0
CZ C:PHE156 3.9 17.7 1.0
CG2 C:THR190 4.0 18.2 1.0
N C:THR190 4.3 20.2 1.0
CE2 C:PHE156 4.4 18.6 1.0
O C:PHE189 4.4 21.2 1.0
O C:HOH846 4.4 27.1 1.0
O C:HOH684 4.5 27.9 1.0
C C:PHE189 4.6 21.2 1.0
O C:THR190 4.6 20.3 1.0
C C:THR190 4.6 23.0 1.0
CA C:THR193 4.7 24.9 1.0
CG C:PHE189 4.8 23.9 1.0
O C:HOH733 4.8 32.0 1.0
CG2 C:VAL206 4.9 19.6 1.0
CZ C:PHE189 4.9 28.1 1.0

Sodium binding site 7 out of 13 in 7sh5

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Sodium binding site 7 out of 13 in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na504

b:20.6
occ:1.00
 O A:HOH668 2.9 20.9 1.0
NA A:NA506 3.1 30.1 1.0
O A:HOH608 3.2 26.1 1.0
N C:LYS101 3.4 16.5 1.0
CG C:LYS101 3.5 39.9 1.0
CB C:LYS101 3.6 19.1 1.0
O C:HOH710 3.8 33.6 1.0
N C:ARG100 3.9 15.6 1.0
CB C:ARG100 4.0 15.5 1.0
CB C:THR99 4.0 20.0 1.0
CA C:LYS101 4.1 22.2 1.0
OG1 C:THR99 4.2 18.7 1.0
O C:HOH763 4.2 16.4 1.0
CA C:ARG100 4.3 14.3 1.0
CG2 A:VAL178 4.3 15.9 1.0
C C:ARG100 4.3 18.8 1.0
CD C:LYS101 4.3 38.7 1.0
O A:HOH893 4.6 31.9 1.0
C C:THR99 4.6 15.8 1.0
CG1 A:VAL178 4.6 19.1 1.0
CE C:LYS101 4.7 28.6 1.0
CB A:VAL178 4.8 15.8 1.0
CB A:ASP181 4.8 20.5 1.0
CA C:THR99 4.8 16.6 1.0
OD2 A:ASP181 4.9 26.3 1.0
CG C:ARG100 4.9 19.2 1.0
CA A:VAL178 4.9 16.5 1.0
CG2 C:THR99 5.0 20.4 1.0

Sodium binding site 8 out of 13 in 7sh5

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Sodium binding site 8 out of 13 in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na505

b:50.0
occ:1.00
 OD1 C:ASP115 2.3 44.3 1.0
CD C:ARG364 2.7 31.0 1.0
NH1 C:ARG364 2.7 28.8 1.0
NH2 C:ARG360 2.8 52.0 1.0
NE C:ARG360 2.8 48.8 1.0
CZ C:ARG360 3.1 48.4 1.0
CG C:ASP115 3.4 36.4 1.0
CA C:ASP115 3.4 23.1 1.0
NE C:ARG364 3.5 28.7 1.0
CZ C:ARG364 3.6 28.8 1.0
CB C:ARG360 3.6 25.4 1.0
CD1 C:ILE118 3.7 19.5 1.0
CB C:ASP115 3.8 25.0 1.0
CG C:ARG364 3.9 29.3 1.0
CD C:ARG360 4.0 42.3 1.0
N C:ASP115 4.0 21.9 1.0
CG C:ARG360 4.0 35.5 1.0
CB C:ILE118 4.3 21.5 1.0
NH1 C:ARG360 4.3 51.6 1.0
O C:CYS114 4.4 16.1 1.0
OD2 C:ASP115 4.4 47.0 1.0
C C:CYS114 4.4 21.6 1.0
CG1 C:ILE118 4.4 20.3 1.0
C C:ASP115 4.5 23.0 1.0
O C:ASP115 4.5 24.1 1.0
CG2 C:ILE118 4.6 22.3 1.0
O C:ARG360 4.6 22.9 1.0
CA C:ARG360 4.7 20.6 1.0
CD2 C:LEU401 4.7 45.4 1.0
CB C:ARG364 4.7 26.9 1.0
NH2 C:ARG364 4.8 30.6 1.0
C C:ARG360 4.9 23.4 1.0

Sodium binding site 9 out of 13 in 7sh5

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Sodium binding site 9 out of 13 in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na506

b:39.7
occ:1.00
 O C:HOH991 2.5 40.1 1.0
O C:ILE7 2.7 33.2 1.0
O C:HOH706 3.1 37.5 1.0
CG C:PRO9 3.5 30.7 1.0
CA C:ALA27 3.5 22.6 1.0
O C:GLU26 3.6 25.9 0.5
CB C:PRO9 3.7 29.5 1.0
O C:GLU26 3.7 25.9 0.5
N C:ALA27 3.8 24.2 1.0
N C:PRO9 3.8 32.6 1.0
C C:ILE7 3.8 33.5 1.0
C C:GLU26 3.8 24.9 0.5
CA C:PRO9 3.8 30.2 1.0
C C:GLU26 3.9 24.9 0.5
CG2 C:ILE7 3.9 38.4 1.0
CD C:PRO9 4.0 28.5 1.0
CB C:ALA27 4.1 23.1 1.0
C C:LYS8 4.2 33.4 1.0
CB C:TRP30 4.4 27.0 1.0
N C:ILE7 4.5 33.3 1.0
O C:LYS8 4.5 29.9 1.0
CB C:GLU26 4.6 29.8 0.5
CA C:ILE7 4.6 29.0 1.0
C C:ALA27 4.7 23.2 1.0
CB C:GLU26 4.7 30.1 0.5
N C:LYS8 4.7 26.4 1.0
CA C:LYS8 4.8 27.4 1.0
O C:ALA27 4.9 22.5 1.0
CA C:GLU26 4.9 26.7 0.5
CA C:GLU26 4.9 26.6 0.5
CB C:ILE7 4.9 34.4 1.0

Sodium binding site 10 out of 13 in 7sh5

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Sodium binding site 10 out of 13 in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na503

b:38.7
occ:1.00
 N D:ARG22 2.4 35.8 1.0
O D:HOH682 2.7 24.4 1.0
CA D:ARG22 2.9 38.9 1.0
N D:ALA24 3.1 26.6 1.0
CB D:ALA24 3.1 21.4 1.0
O D:PHE18 3.1 20.4 1.0
N D:GLN23 3.3 41.9 1.0
OG D:SER21 3.4 34.5 1.0
N D:SER21 3.4 35.6 1.0
C D:ARG22 3.4 39.0 1.0
C D:SER21 3.4 40.2 1.0
O D:HOH867 3.6 24.1 1.0
CA D:ALA24 3.7 26.6 1.0
CA D:SER21 3.8 40.7 1.0
O D:TYR19 3.8 19.7 1.0
C D:TYR19 3.9 18.1 1.0
C D:ALA20 4.0 30.6 1.0
C D:GLN23 4.1 29.5 1.0
CB D:SER21 4.2 37.0 1.0
N D:ALA20 4.2 21.0 1.0
O D:HOH626 4.2 25.9 1.0
C D:PHE18 4.2 19.1 1.0
CA D:TYR19 4.3 17.1 1.0
CA D:GLN23 4.3 37.6 1.0
CB D:ARG22 4.3 43.0 1.0
O D:ARG22 4.5 35.9 1.0
O D:SER21 4.5 43.9 1.0
CA D:ALA20 4.5 21.9 1.0
O D:ALA20 4.7 29.6 1.0
N D:TYR19 4.7 19.2 1.0
CG D:ARG22 4.7 41.5 1.0
C D:ALA24 4.8 20.1 1.0
N D:ARG25 4.9 19.0 1.0

Reference:

A.Ghith, D.Z.Doherty, J.B.Bruning, R.A.Russell, J.J.De Voss, S.G.Bell. The Structures of the Steroid Binding CYP142 Cytochrome P450 Enzymes From Mycobacterium Ulcerans and Mycobacterium Marinum. Acs Infect Dis. V. 8 1606 2022.
ISSN: ESSN 2373-8227
PubMed: 35881654
DOI: 10.1021/ACSINFECDIS.2C00215
Page generated: Wed Oct 9 08:57:26 2024

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