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Sodium in PDB 7ahb: Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis

Enzymatic activity of Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis

All present enzymatic activity of Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis:
2.3.1.292;

Protein crystallography data

The structure of Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis, PDB code: 7ahb 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) 48.12 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 51.374, 58.355, 65.857, 65.84, 73.28, 71.02
R / Rfree (%) 18.8 / 22.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis (pdb code 7ahb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis, PDB code: 7ahb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 7ahb

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Sodium binding site 1 out of 8 in the Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1013

b:31.7
occ:1.00
HE21 A:GLN783 1.9 29.9 1.0
NE2 A:GLN783 2.7 24.9 1.0
O A:THR781 2.8 19.3 1.0
O B:HOH1244 2.8 32.0 1.0
HG2 A:GLN783 2.9 25.9 1.0
OH B:TYR857 2.9 25.1 1.0
HG22 A:THR781 3.1 30.1 1.0
HE22 A:GLN783 3.2 29.9 1.0
HH B:TYR857 3.2 30.2 1.0
CG A:GLN783 3.6 21.6 1.0
CD A:GLN783 3.6 24.8 1.0
HB A:THR781 3.6 27.1 1.0
O A:HOH1172 3.8 17.8 1.0
HE1 B:TYR857 3.8 31.9 1.0
C A:THR781 3.9 21.3 1.0
HE22 A:GLN677 3.9 22.6 1.0
HG3 A:GLN783 3.9 25.9 1.0
CZ B:TYR857 3.9 24.6 1.0
CG2 A:THR781 3.9 25.1 1.0
O A:PRO782 3.9 21.9 1.0
HB2 B:ALA831 4.0 28.6 1.0
HG21 A:THR781 4.1 30.1 1.0
CB A:THR781 4.2 22.6 1.0
CE1 B:TYR857 4.2 26.6 1.0
HB3 B:SER856 4.2 37.6 1.0
C A:PRO782 4.3 18.8 1.0
O B:ALA827 4.4 20.4 1.0
HA A:PRO782 4.5 22.0 1.0
O A:HOH1340 4.5 21.4 1.0
NE2 A:GLN677 4.6 18.8 1.0
CA A:THR781 4.7 19.4 1.0
HG23 A:THR781 4.7 30.1 1.0
N A:PRO782 4.7 19.4 1.0
HB1 B:ALA827 4.7 23.9 1.0
CA A:PRO782 4.7 18.3 1.0
OG B:SER856 4.7 29.9 1.0
HA B:HIS828 4.8 28.3 1.0
OE1 A:GLN783 4.8 27.1 1.0
N A:GLN783 4.8 19.3 1.0
CB B:SER856 4.9 31.4 1.0
CB A:GLN783 4.9 23.3 1.0
CB B:ALA831 4.9 23.9 1.0
CE2 B:TYR857 5.0 26.2 1.0

Sodium binding site 2 out of 8 in 7ahb

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Sodium binding site 2 out of 8 in the Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1014

b:25.4
occ:1.00
H A:ALA676 2.2 22.3 1.0
O A:HOH1329 2.6 52.1 1.0
HB2 A:ALA676 2.7 24.7 1.0
HD2 A:PRO675 2.8 21.3 1.0
HB A:THR674 2.9 25.1 1.0
N A:ALA676 3.0 18.5 1.0
HB3 A:ALA676 3.1 24.7 1.0
CB A:ALA676 3.2 20.6 1.0
O B:HOH1201 3.3 32.0 1.0
HB2 A:PRO675 3.3 23.2 1.0
CD A:PRO675 3.6 17.8 1.0
HG1 A:THR674 3.7 18.8 1.0
CA A:ALA676 3.7 19.4 1.0
CB A:THR674 3.7 20.9 1.0
N A:PRO675 3.8 15.3 1.0
OG1 A:THR674 3.8 15.7 1.0
CB A:PRO675 4.0 19.3 1.0
C A:PRO675 4.0 20.3 1.0
HB1 A:ALA676 4.1 24.7 1.0
HG2 A:PRO675 4.1 26.2 1.0
CA A:PRO675 4.1 17.6 1.0
CG A:PRO675 4.2 21.8 1.0
HA A:ALA676 4.2 23.2 1.0
C A:THR674 4.3 19.6 1.0
HD3 A:PRO675 4.4 21.3 1.0
O A:HOH1163 4.4 35.7 1.0
H A:GLN677 4.5 17.7 1.0
CA A:THR674 4.6 17.0 1.0
HG21 A:THR674 4.6 24.2 1.0
O B:HOH1243 4.6 36.3 1.0
O B:HOH1213 4.7 41.5 1.0
CG2 A:THR674 4.8 20.2 1.0
HA A:THR674 4.8 20.4 1.0
HB3 A:PRO675 4.9 23.2 1.0
HG3 A:GLU606 4.9 37.2 1.0
C A:ALA676 5.0 21.5 1.0

Sodium binding site 3 out of 8 in 7ahb

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Sodium binding site 3 out of 8 in the Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1015

b:47.2
occ:1.00
H A:ALA595 2.1 34.6 1.0
HB3 A:ALA595 2.6 33.7 1.0
OE1 A:GLU593 2.9 32.5 1.0
N A:ALA595 2.9 28.9 1.0
HB2 A:ALA595 3.1 33.7 1.0
HB3 A:GLU593 3.1 37.6 1.0
HD2 A:PRO594 3.1 46.0 1.0
CB A:ALA595 3.2 28.1 1.0
HA A:GLU593 3.3 38.7 1.0
OG A:SER648 3.3 25.4 1.0
HD12 A:LEU645 3.4 27.9 1.0
N A:PRO594 3.4 36.1 1.0
C A:GLU593 3.5 31.3 1.0
HD13 A:LEU645 3.5 27.9 1.0
H A:PHE596 3.5 29.8 1.0
CA A:ALA595 3.6 26.8 1.0
CA A:GLU593 3.7 32.2 1.0
CD A:PRO594 3.8 38.3 1.0
CD1 A:LEU645 3.8 23.3 1.0
HG A:SER648 3.8 30.4 1.0
CB A:GLU593 3.8 31.4 1.0
HB2 A:SER648 3.8 31.1 1.0
HD11 A:LEU645 3.9 27.9 1.0
C A:PRO594 4.0 30.9 1.0
CB A:SER648 4.0 25.9 1.0
O A:GLU593 4.0 28.6 1.0
HB1 A:ALA595 4.0 33.7 1.0
HE2 A:TYR649 4.0 37.2 1.0
CD A:GLU593 4.1 34.8 1.0
HB3 A:SER648 4.1 31.1 1.0
CA A:PRO594 4.2 33.0 1.0
N A:PHE596 4.2 24.9 1.0
HB2 A:PRO594 4.2 42.9 1.0
HA A:LEU645 4.3 24.8 1.0
HA A:ALA595 4.4 32.1 1.0
N A:SCN1008 4.4 59.5 1.0
HD3 A:PRO594 4.4 46.0 1.0
CE2 A:TYR649 4.4 31.0 1.0
C A:ALA595 4.4 25.4 1.0
HH A:TYR649 4.5 42.1 1.0
CG A:GLU593 4.5 33.2 1.0
OH A:TYR649 4.6 35.1 1.0
HB2 A:GLU593 4.6 37.6 1.0
CB A:PRO594 4.6 35.8 1.0
CZ A:TYR649 4.7 33.4 1.0
CG A:PRO594 4.8 37.6 1.0
HG2 A:PRO594 4.9 45.1 1.0

Sodium binding site 4 out of 8 in 7ahb

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Sodium binding site 4 out of 8 in the Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1016

b:27.2
occ:1.00
HA A:ALA644 2.6 24.7 1.0
O B:LEU801 2.9 29.2 1.0
HD3 A:ARG647 3.0 40.8 1.0
HB3 B:SER800 3.0 38.7 1.0
C1 A:GOL1001 3.1 45.2 1.0
O1 A:GOL1001 3.1 24.9 1.0
HB2 A:ALA644 3.2 26.6 1.0
H32 A:GOL1001 3.3 41.5 1.0
CA A:ALA644 3.4 20.6 1.0
HB2 B:LEU801 3.6 35.5 1.0
CB A:ALA644 3.7 22.2 1.0
HG22 A:THR643 3.7 18.9 1.0
C B:LEU801 3.8 29.0 1.0
N A:ALA644 3.8 19.3 1.0
HB1 A:ALA644 3.8 26.6 1.0
CD A:ARG647 3.8 34.0 1.0
H B:LEU801 3.9 30.5 1.0
HB3 A:ARG647 3.9 40.6 1.0
HD2 A:ARG647 3.9 40.8 1.0
CB B:SER800 3.9 32.2 1.0
N B:LEU801 4.0 25.4 1.0
HB2 A:ARG647 4.1 40.6 1.0
H A:ALA644 4.1 23.1 1.0
S B:SCN901 4.1 42.0 1.0
C3 A:GOL1001 4.2 34.6 1.0
C2 A:GOL1001 4.2 27.1 1.0
C A:THR643 4.2 17.3 1.0
CA B:LEU801 4.3 27.8 1.0
O A:THR643 4.3 18.0 1.0
HB2 B:SER800 4.3 38.7 1.0
CB B:LEU801 4.4 29.5 1.0
CB A:ARG647 4.4 33.9 1.0
HE A:ARG647 4.4 44.6 1.0
OG B:SER800 4.4 38.3 1.0
C B:SER800 4.5 32.1 1.0
O B:HOH1076 4.6 39.7 1.0
HB3 A:ALA644 4.6 26.6 1.0
HB A:THR643 4.6 20.2 1.0
HA3 B:GLY802 4.6 36.1 1.0
CG2 A:THR643 4.6 15.8 1.0
NE A:ARG647 4.7 37.1 1.0
C A:ALA644 4.7 23.1 1.0
CG A:ARG647 4.7 32.5 1.0
HB3 B:LEU801 4.7 35.5 1.0
O B:HOH1005 4.7 46.9 1.0
CA B:SER800 4.8 28.8 1.0
O A:HOH1355 4.8 28.1 1.0
O3 A:GOL1001 4.8 36.6 1.0
N B:GLY802 4.9 29.4 1.0
O A:LEU640 4.9 15.6 1.0
HG2 A:ARG647 4.9 39.0 1.0
O A:ALA644 4.9 20.5 1.0
H31 A:GOL1001 5.0 41.5 1.0
HG21 A:THR643 5.0 18.9 1.0

Sodium binding site 5 out of 8 in 7ahb

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Sodium binding site 5 out of 8 in the Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na910

b:26.9
occ:1.00
O B:HOH1208 2.6 52.4 1.0
HD2 B:ARG774 3.0 36.0 1.0
HB3 B:ALA813 3.1 24.8 1.0
HG3 B:GLU810 3.3 33.8 1.0
HG1 B:THR814 3.3 19.9 1.0
HH11 B:ARG774 3.4 41.8 1.0
HB1 B:ALA813 3.4 24.8 1.0
O B:HOH1157 3.5 44.0 1.0
OG1 B:THR814 3.6 16.7 1.0
HB3 B:GLN770 3.7 22.0 1.0
CB B:ALA813 3.7 20.6 1.0
NE2 B:GLN770 3.8 18.2 1.0
HE22 B:GLN770 3.8 21.9 1.0
HE21 B:GLN770 3.9 21.9 1.0
HA B:GLU810 3.9 31.6 1.0
CD B:ARG774 4.0 30.0 1.0
CD B:GLN770 4.0 19.3 1.0
NH1 B:ARG774 4.0 34.8 1.0
O B:GLU810 4.1 16.3 1.0
CG B:GLU810 4.2 28.1 1.0
N B:THR814 4.3 15.9 1.0
H B:THR814 4.3 19.0 1.0
HD3 B:ARG774 4.4 36.0 1.0
HA B:THR814 4.4 25.9 1.0
OE1 B:GLN770 4.4 20.4 1.0
HB2 B:ALA813 4.4 24.8 1.0
C B:ALA813 4.4 19.9 1.0
HH12 B:ARG774 4.4 41.8 1.0
HG2 B:GLN770 4.4 21.3 1.0
CB B:GLN770 4.5 18.3 1.0
HG3 B:ARG774 4.5 31.3 1.0
HG2 B:GLU810 4.5 33.8 1.0
CG B:GLN770 4.6 17.8 1.0
CA B:GLU810 4.7 26.4 1.0
HG2 B:ARG774 4.7 31.3 1.0
CG B:ARG774 4.7 26.1 1.0
CA B:THR814 4.7 21.6 1.0
CA B:ALA813 4.7 20.2 1.0
NE B:ARG774 4.8 33.2 1.0
CB B:THR814 4.8 19.2 1.0
CZ B:ARG774 4.8 31.6 1.0
O B:HOH1168 4.8 32.5 1.0
C B:GLU810 4.8 22.9 1.0
O B:ALA813 4.8 18.1 1.0
OE2 B:GLU810 4.9 33.3 1.0
O B:HOH1224 4.9 42.7 1.0
HB2 B:GLN770 4.9 22.0 1.0
CB B:GLU810 4.9 26.2 1.0

Sodium binding site 6 out of 8 in 7ahb

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Sodium binding site 6 out of 8 in the Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na911

b:34.9
occ:1.00
HZ3 B:LYS744 2.1 37.4 1.0
HZ2 B:LYS744 2.4 37.4 1.0
NZ B:LYS744 2.6 31.2 1.0
O B:LEU711 2.7 22.9 1.0
HD3 B:LYS744 2.7 35.7 1.0
HD2 B:LYS744 2.7 35.7 1.0
HE1 B:TYR715 2.8 32.8 1.0
CD B:LYS744 3.1 29.7 1.0
HD12 B:LEU711 3.2 27.9 1.0
HZ1 B:LYS744 3.4 37.4 1.0
HG B:LEU711 3.4 26.4 1.0
CE B:LYS744 3.4 31.4 1.0
HA B:LEU711 3.5 26.3 1.0
CE1 B:TYR715 3.6 27.4 1.0
HD21 B:LEU741 3.7 28.2 1.0
HD23 B:LEU741 3.7 28.2 1.0
O B:HOH1049 3.7 29.1 1.0
C B:LEU711 3.7 21.9 1.0
CD1 B:LEU711 3.8 23.3 1.0
HD11 B:LEU711 3.8 27.9 1.0
HD22 B:LEU741 3.9 28.2 1.0
CD2 B:LEU741 3.9 23.6 1.0
HE2 B:LYS744 4.0 37.7 1.0
CG B:LEU711 4.0 22.0 1.0
CA B:LEU711 4.0 21.9 1.0
HE3 B:LYS744 4.1 37.7 1.0
OH B:TYR715 4.3 31.6 1.0
HD1 B:TYR715 4.3 34.2 1.0
CZ B:TYR715 4.4 29.3 1.0
CD1 B:TYR715 4.4 28.5 1.0
CG B:LYS744 4.5 29.5 1.0
CB B:LEU711 4.6 21.4 1.0
HD13 B:LEU711 4.7 27.9 1.0
HA B:ILE712 4.7 25.0 1.0
HG2 B:LYS744 4.7 35.4 1.0
HB3 B:LYS744 4.8 33.4 1.0
N B:ILE712 4.9 20.9 1.0

Sodium binding site 7 out of 8 in 7ahb

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Sodium binding site 7 out of 8 in the Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na912

b:35.3
occ:1.00
O B:HOH1011 2.6 38.3 1.0
HG3 B:PRO819 2.8 29.2 1.0
OH B:TYR723 2.8 17.9 1.0
O B:HOH1107 3.0 32.2 1.0
HH B:TYR723 3.1 21.6 1.0
CG B:PRO819 3.7 24.3 1.0
HB3 B:LEU720 3.8 23.5 1.0
HE1 B:TYR723 3.9 23.6 1.0
CZ B:TYR723 3.9 19.8 1.0
HD22 B:LEU720 4.0 23.1 1.0
OE2 B:GLU709 4.0 21.0 0.5
HG2 B:PRO819 4.0 29.2 1.0
O B:HOH1255 4.0 32.3 1.0
HB3 B:PRO819 4.1 28.3 1.0
O B:HOH1152 4.2 42.7 1.0
HH22 B:ARG821 4.2 34.4 1.0
CE1 B:TYR723 4.3 19.6 1.0
CB B:PRO819 4.3 23.6 1.0
HB2 B:PRO819 4.4 28.3 1.0
O B:HOH1123 4.4 28.5 1.0
NH2 B:ARG821 4.5 28.6 1.0
HH21 B:ARG821 4.5 34.4 1.0
HD13 B:LEU720 4.5 22.8 1.0
OE2 B:GLU709 4.5 18.5 0.5
HD3 B:PRO819 4.6 24.3 1.0
CD B:PRO819 4.8 20.3 1.0
CB B:LEU720 4.8 19.6 1.0
O B:HOH1177 4.8 30.6 1.0
CD2 B:LEU720 4.8 19.3 1.0
O B:LEU720 4.9 13.7 1.0
HD21 B:LEU720 4.9 23.1 1.0

Sodium binding site 8 out of 8 in 7ahb

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Sodium binding site 8 out of 8 in the Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Acyltransferase Domain of the Polyketide Synthase Ppsc of Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na913

b:33.7
occ:1.00
H B:HIS847 2.4 35.8 1.0
O B:HOH1222 2.5 48.5 1.0
HG1 B:THR846 2.9 33.6 1.0
H B:THR846 3.0 31.6 1.0
HA B:LEU844 3.1 31.1 1.0
HB3 B:HIS847 3.1 44.8 1.0
N B:HIS847 3.2 29.8 1.0
C B:LEU844 3.2 27.5 1.0
OG1 B:THR846 3.3 28.0 1.0
O B:LEU844 3.3 26.3 1.0
N B:THR846 3.4 26.3 1.0
HB2 B:HIS847 3.5 44.8 1.0
O B:PRO843 3.5 38.6 1.0
CA B:LEU844 3.6 25.9 1.0
CB B:HIS847 3.7 37.3 1.0
O B:HOH1094 3.7 23.2 1.0
N B:LEU845 3.7 21.7 1.0
C B:PRO843 3.9 31.0 1.0
HB2 B:PRO843 4.0 38.0 1.0
N B:LEU844 4.0 24.1 1.0
C B:LEU845 4.0 30.5 1.0
CA B:HIS847 4.0 33.3 1.0
H B:LEU845 4.1 25.9 1.0
CA B:THR846 4.1 30.2 1.0
C B:THR846 4.1 33.4 1.0
CB B:THR846 4.3 31.3 1.0
CA B:LEU845 4.3 26.4 1.0
HA B:LEU845 4.4 31.7 1.0
H B:SER848 4.5 34.9 1.0
HA B:HIS847 4.6 40.0 1.0
H B:LEU844 4.7 28.9 1.0
HD23 B:LEU844 4.7 35.5 1.0
O B:LEU845 4.8 26.6 1.0
CB B:PRO843 4.8 31.6 1.0
HB B:THR846 4.9 37.6 1.0
CB B:LEU844 4.9 27.6 1.0
CA B:PRO843 5.0 29.2 1.0

Reference:

A.D.Grabowska, Y.Brison, L.Maveyraud, S.Gavalda, A.Faille, V.Nahoum, C.Bon, C.Guilhot, J.D.Pedelacq, C.Chalut, L.Mourey. Molecular Basis For Extender Unit Specificity of Mycobacterial Polyketide Synthases. Acs Chem.Biol. 2020.
ISSN: ESSN 1554-8937
PubMed: 33237724
DOI: 10.1021/ACSCHEMBIO.0C00772
Page generated: Tue Dec 15 17:21:11 2020

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