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Sodium in PDB 4oki: X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis

Enzymatic activity of X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis

All present enzymatic activity of X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis:
2.3.1.41;

Protein crystallography data

The structure of X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis, PDB code: 4oki was solved by A.Faille, L.Mourey, J.D.Pedelacq, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.885, 78.743, 88.796, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.8

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis (pdb code 4oki). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis, PDB code: 4oki:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4oki

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Sodium binding site 1 out of 7 in the X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na901

b:45.9
occ:1.00
 O A:HOH1061 2.7 31.0 1.0
O A:HOH1075 2.8 29.3 1.0
O A:SER746 3.8 28.3 1.0
C A:ARG747 3.8 30.0 1.0
O A:ARG747 3.9 33.6 1.0
N A:SER748 4.0 26.9 1.0
O A:SER748 4.0 31.8 1.0
O A:HOH1055 4.1 33.8 1.0
C A:SER748 4.1 27.4 1.0
CA A:ARG747 4.2 27.7 1.0
CA A:SER748 4.3 31.1 1.0
CB A:ALA775 4.4 22.2 1.0
CG2 A:VAL749 4.5 34.7 1.0
O A:HOH1033 4.6 26.2 1.0
C A:SER746 4.6 24.9 1.0
O A:ALA772 4.7 28.5 1.0
O A:HOH1030 4.7 25.4 1.0
N A:VAL749 4.7 28.5 1.0
N A:ARG747 4.9 24.1 1.0

Sodium binding site 2 out of 7 in 4oki

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Sodium binding site 2 out of 7 in the X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:46.8
occ:1.00
 OH B:TYR798 2.4 41.8 1.0
O A:ALA809 3.0 20.4 1.0
O B:HOH1103 3.0 44.5 1.0
CG1 B:VAL816 3.5 22.9 1.0
CZ B:TYR798 3.6 47.3 1.0
O B:GLY793 3.8 34.2 1.0
N B:LYS795 3.9 47.7 1.0
C A:ALA809 4.0 19.6 1.0
CE2 B:TYR798 4.1 45.1 1.0
CA A:ALA809 4.1 21.1 1.0
CA B:LYS795 4.1 48.0 1.0
CB B:LYS795 4.2 45.6 1.0
CB A:ALA809 4.2 23.6 1.0
CB B:ASP818 4.3 21.8 1.0
OD2 B:ASP818 4.3 28.5 1.0
C B:LYS794 4.4 50.0 1.0
CA B:LYS794 4.7 53.5 1.0
CG B:ASP818 4.7 26.4 1.0
CE1 B:TYR798 4.7 48.2 1.0
C B:GLY793 4.9 42.7 1.0
CB B:VAL816 4.9 18.4 1.0

Sodium binding site 3 out of 7 in 4oki

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Sodium binding site 3 out of 7 in the X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na901

b:41.0
occ:1.00
 O B:ASP745 2.5 32.4 1.0
O B:HOH1055 2.8 32.8 1.0
N B:PHE751 2.8 30.6 1.0
O B:SER748 3.2 34.8 1.0
N B:ASP750 3.3 33.6 1.0
C B:SER748 3.5 35.0 1.0
OG B:SER748 3.5 42.0 1.0
C B:ASP745 3.5 29.4 1.0
CB B:SER748 3.5 34.2 1.0
CB B:PHE751 3.6 27.4 1.0
CD2 B:PHE751 3.6 26.5 1.0
C B:ASP750 3.6 32.1 1.0
N B:ASP745 3.7 26.6 1.0
CB B:ASP750 3.7 34.6 1.0
CA B:PHE751 3.7 29.6 1.0
CA B:ASP750 3.7 31.2 1.0
CB B:ASP745 3.8 34.5 1.0
CA B:ASP745 3.9 30.5 1.0
CA B:SER748 4.0 34.4 1.0
N B:VAL749 4.0 38.1 1.0
C B:VAL749 4.1 33.0 1.0
CG B:PHE751 4.1 25.5 1.0
N B:SER748 4.2 32.8 1.0
CA B:VAL749 4.4 35.2 1.0
OH B:TYR742 4.7 31.3 1.0
N B:SER746 4.7 29.4 1.0
C B:GLY744 4.7 24.3 1.0
O B:ASP750 4.8 30.5 1.0
CG B:ASP750 4.8 40.6 1.0
CE2 B:PHE751 4.8 25.1 1.0
CG B:ASP745 4.8 38.4 1.0
O B:VAL749 4.8 29.0 1.0

Sodium binding site 4 out of 7 in 4oki

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Sodium binding site 4 out of 7 in the X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na902

b:43.4
occ:1.00
 O B:HOH1105 2.6 43.9 1.0
O B:HOH1018 2.6 34.1 1.0
N B:GLY727 2.7 32.3 1.0
CA B:GLY727 3.5 39.6 1.0
CD B:LYS731 3.5 38.1 1.0
CA B:ALA726 3.6 28.9 1.0
C B:ALA726 3.6 31.1 1.0
OG B:SER746 3.8 32.0 1.0
O B:HOH1143 3.8 40.5 1.0
CB B:ALA726 3.8 30.7 1.0
CE B:LYS731 4.1 42.5 1.0
OG1 B:THR704 4.5 20.0 1.0
OG B:SER702 4.5 33.7 1.0
C B:GLY727 4.5 44.0 1.0
CA B:SER702 4.6 26.4 1.0
CB B:SER702 4.7 30.2 1.0
N B:SER728 4.7 39.4 1.0
O B:ALA726 4.7 31.4 1.0
CG B:LYS731 4.8 38.2 1.0
O B:HOH1047 4.8 43.3 1.0
CB B:SER746 4.8 32.4 1.0
CB B:LYS731 4.9 37.5 1.0
N B:ALA726 4.9 29.1 1.0
NZ B:LYS731 4.9 55.3 1.0

Sodium binding site 5 out of 7 in 4oki

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Sodium binding site 5 out of 7 in the X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na903

b:41.8
occ:1.00
 O B:HOH1130 2.8 40.0 1.0
O B:HOH1002 2.8 21.0 1.0
O A:HOH1003 2.8 42.3 1.0
O B:ALA806 2.8 23.2 1.0
O B:ALA807 3.7 22.3 1.0
N B:ALA809 3.7 19.1 1.0
C B:ALA807 3.8 19.4 1.0
CE B:LYS810 3.9 38.9 1.0
CG B:LYS810 3.9 24.2 1.0
N B:LYS810 4.0 17.8 1.0
C B:ALA806 4.0 23.6 1.0
CA B:ALA807 4.0 22.3 1.0
CB B:ALA809 4.1 23.3 1.0
NZ A:LYS795 4.1 54.1 1.0
CD B:LYS810 4.3 30.4 1.0
CA B:ALA809 4.3 19.7 1.0
N B:LEU808 4.4 18.7 1.0
N B:ALA807 4.5 22.2 1.0
C B:ALA809 4.6 16.3 1.0
NZ B:LYS810 4.6 42.0 1.0
CB B:LYS810 4.6 20.8 1.0
C B:LEU808 4.6 18.5 1.0
O B:HOH1005 4.7 27.2 1.0
O B:HOH1045 4.8 27.2 1.0
O B:HOH1141 4.8 35.6 1.0
O B:HOH1088 4.8 42.0 1.0
CA B:LYS810 4.9 17.7 1.0
CA B:LEU808 5.0 17.9 1.0

Sodium binding site 6 out of 7 in 4oki

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Sodium binding site 6 out of 7 in the X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na904

b:47.1
occ:1.00
 O B:HOH1123 2.7 29.4 1.0
O A:HOH1025 3.2 33.6 1.0
NH1 B:ARG829 3.3 32.6 1.0
O A:HOH1006 3.4 20.5 1.0
O A:HOH1023 3.5 27.9 1.0
NH2 A:ARG788 3.8 17.6 1.0
OE2 A:GLU696 3.9 22.5 1.0
O B:HOH1030 4.0 31.4 1.0
O A:HOH1032 4.0 36.1 1.0
O B:HOH1125 4.2 22.3 1.0
CA A:GLY786 4.2 17.5 1.0
O B:HOH1041 4.3 23.9 1.0
O A:GLY786 4.4 17.7 1.0
CZ B:ARG829 4.4 38.0 1.0
O B:HOH1051 4.4 25.6 1.0
O B:HOH1029 4.4 24.8 1.0
O A:PRO785 4.5 18.5 1.0
NH2 B:ARG829 4.5 40.6 1.0
O A:HOH1041 4.6 27.4 1.0
C A:GLY786 4.7 15.7 1.0
CZ A:ARG788 4.7 14.7 1.0
O B:HOH1058 4.8 37.4 1.0
CG B:GLN826 4.9 29.9 1.0

Sodium binding site 7 out of 7 in 4oki

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Sodium binding site 7 out of 7 in the X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of X-Ray Structure of the Nucleotide-Binding Subdomain of the Enoylreductase Domain of Ppsc From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na905

b:36.3
occ:1.00
 O B:HOH1137 2.8 42.0 1.0
O B:HOH1138 2.8 39.1 1.0
CD1 B:PHE675 3.8 31.1 1.0
CG B:PHE675 4.0 27.6 1.0
CB B:PHE675 4.1 28.7 1.0
CE1 B:PHE675 4.5 33.8 1.0
O B:HOH1133 4.6 41.0 1.0
O B:HOH1139 4.8 33.2 1.0
CD2 B:PHE675 4.9 31.9 1.0

Reference:

A.Faille, N.Slama, A.Quemard, L.Mourey, J.D.Pedelacq. Insights Into the Catalytic Mechanism of the Dh Domain of the Mycobacterium Tuberculosis Polyketide Synthase Ppsc and Architecture of the Beta-Carbon Processing Domains To Be Published.
Page generated: Mon Oct 7 17:29:09 2024

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