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Sodium in PDB 2wgg: Crystal Structure of Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm:
2.3.1.41;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm, PDB code: 2wgg was solved by S.R.Luckner, C.Kisker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.16 / 2.00
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 151.276, 151.276, 147.960, 90.00, 90.00, 120.00
R / Rfree (%) 13.7 / 17.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm (pdb code 2wgg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm, PDB code: 2wgg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 2wgg

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Sodium binding site 1 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm


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 Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1418

b:10.1
occ:1.00
 OE1 A:GLU354 2.5 18.1 1.0
OD1 A:ASN399 2.7 27.2 1.0
O A:ASN400 2.7 18.1 1.0
OD1 A:ASN309 2.8 19.6 1.0
O A:ASN309 2.8 24.1 1.0
O A:ALA310 3.0 19.6 1.0
C A:ALA310 3.2 17.6 1.0
C A:ASN309 3.4 30.6 1.0
N A:HIS311 3.5 19.4 1.0
CD A:GLU354 3.5 18.4 1.0
CB A:GLU354 3.6 16.3 1.0
CG A:ASN399 3.7 19.5 1.0
CG A:ASN309 3.8 18.7 1.0
CA A:HIS311 3.8 19.4 1.0
C A:ASN400 3.9 20.2 1.0
O A:HOH2130 3.9 20.8 1.0
N A:ALA310 3.9 20.5 1.0
N A:ASN400 3.9 17.4 1.0
CA A:ALA310 4.0 20.2 1.0
CG A:GLU354 4.1 17.5 1.0
CB A:ASN309 4.2 18.7 1.0
ND2 A:ASN399 4.4 25.1 1.0
CA A:ASN400 4.4 19.9 1.0
CA A:ASN309 4.4 23.4 1.0
OE2 A:GLU354 4.5 22.6 1.0
C A:ASN399 4.6 19.1 1.0
CA A:ASN399 4.7 17.2 1.0
OG A:SER401 4.7 26.1 1.0
CB A:ASN399 4.8 19.8 1.0
CB A:HIS311 4.8 17.2 1.0
CB A:ASN400 4.8 17.0 1.0
C A:HIS311 4.9 20.8 1.0
ND2 A:ASN309 4.9 20.5 1.0
N A:SER401 5.0 20.9 1.0
CA A:GLU354 5.0 16.5 1.0

Sodium binding site 2 out of 8 in 2wgg

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Sodium binding site 2 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm


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 Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1420

b:7.6
occ:1.00
 OD1 B:ASN399 2.6 18.3 1.0
O B:ASN400 2.7 19.1 1.0
OE1 B:GLU354 2.7 23.2 1.0
O B:ASN309 2.8 20.9 1.0
OD1 B:ASN309 2.8 22.9 1.0
O B:ALA310 3.2 16.0 1.0
C B:ALA310 3.3 19.7 1.0
C B:ASN309 3.4 17.5 1.0
N B:HIS311 3.6 18.8 1.0
CG B:ASN399 3.6 12.8 1.0
CD B:GLU354 3.6 14.3 1.0
CB B:GLU354 3.7 19.5 1.0
CG B:ASN309 3.7 20.6 1.0
O B:HOH2115 3.7 21.2 1.0
C B:ASN400 3.8 19.8 1.0
CA B:HIS311 3.8 21.1 1.0
N B:ALA310 3.9 15.6 1.0
N B:ASN400 3.9 16.5 1.0
CA B:ALA310 4.0 15.0 1.0
CB B:ASN309 4.1 18.0 1.0
CG B:GLU354 4.2 14.4 1.0
ND2 B:ASN399 4.2 19.8 1.0
CA B:ASN309 4.3 18.5 1.0
CA B:ASN400 4.4 19.0 1.0
C B:ASN399 4.6 20.3 1.0
OE2 B:GLU354 4.6 25.3 1.0
OG B:SER401 4.7 27.9 1.0
CA B:ASN399 4.7 15.8 1.0
CB B:ASN399 4.7 20.4 1.0
CB B:HIS311 4.8 13.9 1.0
CB B:ASN400 4.8 17.0 1.0
C B:HIS311 4.9 20.8 1.0
N B:SER401 4.9 15.2 1.0
ND2 B:ASN309 4.9 17.3 1.0

Sodium binding site 3 out of 8 in 2wgg

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Sodium binding site 3 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm


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 Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1418

b:10.1
occ:1.00
 OE1 C:GLU354 2.6 22.3 1.0
OD1 C:ASN399 2.6 21.6 1.0
OD1 C:ASN309 2.7 21.2 1.0
O C:ASN400 2.8 17.4 1.0
O C:ASN309 2.8 26.1 1.0
O C:ALA310 3.1 24.1 1.0
C C:ALA310 3.2 30.2 1.0
C C:ASN309 3.4 24.0 1.0
N C:HIS311 3.4 24.4 1.0
CD C:GLU354 3.5 24.6 1.0
CB C:GLU354 3.6 19.6 1.0
CG C:ASN399 3.7 22.9 1.0
CG C:ASN309 3.7 19.7 1.0
O C:HOH2110 3.7 25.6 1.0
CA C:HIS311 3.8 16.7 1.0
N C:ASN400 3.8 17.3 1.0
C C:ASN400 3.8 19.6 1.0
N C:ALA310 3.9 23.9 1.0
CA C:ALA310 4.0 25.4 1.0
CG C:GLU354 4.0 15.3 1.0
CB C:ASN309 4.2 15.2 1.0
ND2 C:ASN399 4.3 25.8 1.0
CA C:ASN400 4.4 21.3 1.0
CA C:ASN309 4.4 22.6 1.0
C C:ASN399 4.5 22.0 1.0
OE2 C:GLU354 4.5 28.2 1.0
CA C:ASN399 4.6 19.9 1.0
CB C:ASN399 4.7 24.7 1.0
CB C:HIS311 4.7 14.5 1.0
OG C:SER401 4.7 31.4 1.0
ND2 C:ASN309 4.8 21.2 1.0
C C:HIS311 4.9 21.8 1.0
CB C:ASN400 4.9 18.6 1.0
CG C:PRO339 5.0 22.6 1.0
N C:SER401 5.0 21.1 1.0
CA C:GLU354 5.0 22.1 1.0

Sodium binding site 4 out of 8 in 2wgg

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Sodium binding site 4 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm


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 Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1418

b:11.6
occ:1.00
 OE1 D:GLU354 2.5 26.7 1.0
OD1 D:ASN399 2.6 24.7 1.0
O D:ASN400 2.6 17.9 1.0
O D:ASN309 2.8 21.1 1.0
OD1 D:ASN309 2.8 25.2 1.0
O D:ALA310 3.2 21.1 1.0
C D:ALA310 3.3 20.1 1.0
C D:ASN309 3.4 28.1 1.0
CD D:GLU354 3.5 20.6 1.0
N D:HIS311 3.5 22.9 1.0
CB D:GLU354 3.6 19.2 1.0
CG D:ASN399 3.6 21.6 1.0
C D:ASN400 3.7 16.1 1.0
O D:HOH2113 3.8 18.7 1.0
CG D:ASN309 3.8 23.4 1.0
CA D:HIS311 3.8 18.4 1.0
N D:ASN400 3.8 21.9 1.0
N D:ALA310 3.9 22.7 1.0
CA D:ALA310 4.0 20.1 1.0
CG D:GLU354 4.1 14.3 1.0
CB D:ASN309 4.1 17.5 1.0
ND2 D:ASN399 4.2 23.4 1.0
CA D:ASN400 4.3 20.3 1.0
CA D:ASN309 4.4 19.6 1.0
OE2 D:GLU354 4.5 21.2 1.0
C D:ASN399 4.6 19.1 1.0
CA D:ASN399 4.7 18.3 1.0
CB D:HIS311 4.7 24.6 1.0
CB D:ASN399 4.7 24.2 1.0
CB D:ASN400 4.8 22.6 1.0
OG D:SER401 4.9 25.4 1.0
N D:SER401 4.9 18.5 1.0
ND2 D:ASN309 4.9 20.6 1.0
C D:HIS311 4.9 18.7 1.0
CA D:GLU354 5.0 18.8 1.0

Sodium binding site 5 out of 8 in 2wgg

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Sodium binding site 5 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm


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 Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1418

b:12.6
occ:1.00
 OE1 E:GLU354 2.5 21.5 1.0
O E:ASN309 2.7 25.0 1.0
OD1 E:ASN399 2.7 26.1 1.0
O E:ASN400 2.7 23.6 1.0
OD1 E:ASN309 2.8 25.8 1.0
O E:ALA310 3.0 23.8 1.0
C E:ALA310 3.2 23.2 1.0
C E:ASN309 3.4 30.8 1.0
CD E:GLU354 3.4 27.6 1.0
N E:HIS311 3.5 22.2 1.0
CB E:GLU354 3.6 22.2 1.0
CG E:ASN309 3.7 25.0 1.0
CA E:HIS311 3.8 21.3 1.0
C E:ASN400 3.8 26.6 1.0
N E:ASN400 3.8 24.8 1.0
CG E:ASN399 3.8 30.7 1.0
N E:ALA310 3.9 26.8 1.0
O E:HOH2107 4.0 21.9 1.0
CA E:ALA310 4.0 22.1 1.0
CG E:GLU354 4.0 26.8 1.0
CB E:ASN309 4.1 15.7 1.0
CA E:ASN400 4.3 19.7 1.0
CA E:ASN309 4.3 23.6 1.0
OE2 E:GLU354 4.4 25.9 1.0
ND2 E:ASN399 4.5 32.2 1.0
C E:ASN399 4.6 27.6 1.0
CB E:ASN400 4.7 21.9 1.0
CB E:HIS311 4.7 26.9 1.0
CA E:ASN399 4.8 28.1 1.0
OG E:SER401 4.8 31.4 1.0
C E:HIS311 4.8 19.3 1.0
CB E:ASN399 4.9 25.9 1.0
ND2 E:ASN309 4.9 22.4 1.0
N E:SER401 5.0 26.5 1.0

Sodium binding site 6 out of 8 in 2wgg

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Sodium binding site 6 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm


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 Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na1418

b:9.3
occ:1.00
 OE1 F:GLU354 2.4 20.8 1.0
OD1 F:ASN399 2.6 25.3 1.0
O F:ASN400 2.7 18.6 1.0
OD1 F:ASN309 2.8 19.2 1.0
O F:ASN309 2.9 16.9 1.0
O F:ALA310 3.1 21.3 1.0
C F:ALA310 3.2 26.9 1.0
C F:ASN309 3.4 22.8 1.0
N F:HIS311 3.4 21.1 1.0
CD F:GLU354 3.5 18.4 1.0
CG F:ASN399 3.6 16.4 1.0
CB F:GLU354 3.7 17.9 1.0
CA F:HIS311 3.8 19.8 1.0
CG F:ASN309 3.8 20.1 1.0
C F:ASN400 3.8 21.3 1.0
O F:HOH2127 3.8 25.3 1.0
N F:ALA310 3.8 25.3 1.0
N F:ASN400 3.9 16.4 1.0
CA F:ALA310 4.0 20.2 1.0
CG F:GLU354 4.1 19.9 1.0
CB F:ASN309 4.2 16.9 1.0
ND2 F:ASN399 4.2 20.9 1.0
CA F:ASN309 4.4 16.7 1.0
CA F:ASN400 4.4 18.6 1.0
OE2 F:GLU354 4.4 22.9 1.0
C F:ASN399 4.6 17.6 1.0
CB F:HIS311 4.7 22.7 1.0
CA F:ASN399 4.7 25.2 1.0
CB F:ASN399 4.8 21.4 1.0
CB F:ASN400 4.8 22.3 1.0
OG F:SER401 4.8 28.8 1.0
C F:HIS311 4.9 24.9 1.0
ND2 F:ASN309 4.9 13.4 1.0
N F:SER401 5.0 26.2 1.0

Sodium binding site 7 out of 8 in 2wgg

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Sodium binding site 7 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm


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 Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na1420

b:16.0
occ:1.00
 OE1 G:GLU354 2.5 29.1 1.0
OD1 G:ASN399 2.5 27.8 1.0
O G:ASN400 2.7 26.6 1.0
O G:ASN309 2.8 33.7 1.0
OD1 G:ASN309 2.9 25.7 1.0
O G:ALA310 3.2 28.5 1.0
C G:ALA310 3.3 28.4 1.0
C G:ASN309 3.4 34.1 1.0
CD G:GLU354 3.5 23.2 1.0
N G:HIS311 3.5 25.4 1.0
CB G:GLU354 3.6 23.3 1.0
CG G:ASN399 3.6 29.8 1.0
CA G:HIS311 3.8 18.4 1.0
CG G:ASN309 3.8 25.3 1.0
C G:ASN400 3.8 25.2 1.0
N G:ASN400 3.9 26.2 1.0
N G:ALA310 4.0 30.8 1.0
CB G:ASN309 4.0 19.5 1.0
CG G:GLU354 4.1 22.0 1.0
O G:HOH2092 4.1 26.1 1.0
CA G:ALA310 4.1 29.9 1.0
ND2 G:ASN399 4.2 35.4 1.0
CA G:ASN309 4.3 34.4 1.0
CA G:ASN400 4.4 24.4 1.0
OE2 G:GLU354 4.5 25.3 1.0
C G:ASN399 4.6 24.6 1.0
CB G:HIS311 4.6 24.9 1.0
CA G:ASN399 4.7 24.4 1.0
CB G:ASN399 4.7 29.7 1.0
OG G:SER401 4.8 32.1 1.0
CB G:ASN400 4.8 16.4 1.0
C G:HIS311 4.9 22.6 1.0
N G:SER401 4.9 22.6 1.0
ND2 G:ASN309 4.9 23.3 1.0
CA G:GLU354 5.0 21.4 1.0

Sodium binding site 8 out of 8 in 2wgg

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Sodium binding site 8 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm


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 Mycobacterium Tuberculosis C171Q Kasa Variant with Bound Tlm within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1418

b:14.8
occ:1.00
 OE1 H:GLU354 2.6 23.6 1.0
O H:ASN400 2.6 20.0 1.0
OD1 H:ASN399 2.7 27.5 1.0
OD1 H:ASN309 2.7 28.4 1.0
O H:ASN309 2.7 26.0 1.0
O H:ALA310 3.1 21.8 1.0
C H:ALA310 3.3 23.4 1.0
C H:ASN309 3.4 26.9 1.0
CD H:GLU354 3.5 25.0 1.0
N H:HIS311 3.6 20.3 1.0
CB H:GLU354 3.6 19.1 1.0
CG H:ASN309 3.7 24.4 1.0
CG H:ASN399 3.7 24.5 1.0
C H:ASN400 3.7 20.9 1.0
CA H:HIS311 3.8 21.6 1.0
N H:ASN400 3.9 28.1 1.0
N H:ALA310 3.9 22.2 1.0
CG H:GLU354 4.0 23.6 1.0
CA H:ALA310 4.1 27.5 1.0
CB H:ASN309 4.2 25.8 1.0
CA H:ASN400 4.3 22.5 1.0
ND2 H:ASN399 4.4 28.3 1.0
CA H:ASN309 4.4 31.1 1.0
OE2 H:GLU354 4.5 27.8 1.0
C H:ASN399 4.6 30.7 1.0
CA H:ASN399 4.7 30.5 1.0
OG H:SER401 4.7 27.0 1.0
CB H:HIS311 4.7 17.5 1.0
CB H:ASN400 4.7 26.9 1.0
ND2 H:ASN309 4.8 17.9 1.0
CB H:ASN399 4.8 27.4 1.0
N H:SER401 4.9 21.7 1.0
C H:HIS311 4.9 25.6 1.0
CG H:PRO339 5.0 18.8 1.0

Reference:

S.R.Luckner, C.A.Machutta, P.J.Tonge, C.Kisker. Crystal Structures of Mycobacterium Tuberculosis Kasa Show Mode of Action Within Cell Wall Biosynthesis and Its Inhibition By Thiolactomycin Structure V. 17 1004 2009.
ISSN: ISSN 0969-2126
PubMed: 19604480
DOI: 10.1016/J.STR.2009.04.012
Page generated: Mon Oct 7 04:40:23 2024

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