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Sodium in PDB 3oqt: Crystal Structure of RV1498A Protein From Mycobacterium Tuberculosis

Protein crystallography data

The structure of Crystal Structure of RV1498A Protein From Mycobacterium Tuberculosis, PDB code: 3oqt was solved by F.Liu, J.Xiong, S.Kumar, C.Yang, S.Li, S.Ge, N.Xia, K.Swaminathan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.88
Space group P 21 3 1
Cell size a, b, c (Å), α, β, γ (°) 143.946, 143.946, 143.946, 90.00, 90.00, 90.00
R / Rfree (%) 25.2 / 28.3

Other elements in 3oqt:

The structure of Crystal Structure of RV1498A Protein From Mycobacterium Tuberculosis also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of RV1498A Protein From Mycobacterium Tuberculosis (pdb code 3oqt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of RV1498A Protein From Mycobacterium Tuberculosis, PDB code: 3oqt:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 3oqt

Go back to Sodium Binding Sites List in 3oqt
Sodium binding site 1 out of 5 in the Crystal Structure of RV1498A Protein 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 Crystal Structure of RV1498A Protein From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na111

b:59.6
occ:1.00
O C:HOH201 2.2 20.0 1.0
OD2 C:ASP20 3.6 25.1 1.0
CG C:ASP20 3.9 23.8 1.0
CB C:VAL19 4.1 22.5 1.0
N C:ASP20 4.2 21.6 1.0
OD1 C:ASP20 4.3 25.0 1.0
CB C:ASP20 4.5 22.2 1.0
CG2 C:VAL19 4.8 22.3 1.0
N C:VAL19 4.8 23.3 1.0
CG1 C:VAL19 4.9 22.1 1.0
CA C:VAL19 4.9 22.4 1.0
CA C:ASP20 4.9 21.4 1.0

Sodium binding site 2 out of 5 in 3oqt

Go back to Sodium Binding Sites List in 3oqt
Sodium binding site 2 out of 5 in the Crystal Structure of RV1498A Protein 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 Crystal Structure of RV1498A Protein From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na112

b:40.3
occ:1.00
OD2 H:ASP20 3.6 27.3 1.0
CG H:ASP20 3.9 25.4 1.0
OD1 H:ASP20 4.3 25.8 1.0
N H:ASP20 4.4 23.5 1.0
CB H:VAL19 4.5 23.4 1.0
CB H:ASP20 4.6 24.0 1.0
N H:VAL19 4.9 24.6 1.0
CG2 H:VAL19 5.0 22.7 1.0

Sodium binding site 3 out of 5 in 3oqt

Go back to Sodium Binding Sites List in 3oqt
Sodium binding site 3 out of 5 in the Crystal Structure of RV1498A Protein 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 Crystal Structure of RV1498A Protein From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na114

b:37.9
occ:0.33
OD2 I:ASP20 2.4 28.6 1.0
CG I:ASP20 3.3 26.9 1.0
OD1 I:ASP20 3.7 27.6 1.0
N I:ASP20 4.4 24.8 1.0
CB I:VAL19 4.5 25.1 1.0
CB I:ASP20 4.5 25.2 1.0
CG2 I:VAL19 5.0 24.3 1.0

Sodium binding site 4 out of 5 in 3oqt

Go back to Sodium Binding Sites List in 3oqt
Sodium binding site 4 out of 5 in the Crystal Structure of RV1498A Protein 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 Crystal Structure of RV1498A Protein From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na113

b:22.4
occ:1.00
OD2 L:ASP20 3.1 26.9 1.0
CG L:ASP20 3.6 24.8 1.0
OD1 L:ASP20 4.1 25.7 1.0
CB L:ASP20 4.4 22.9 1.0
N L:ASP20 4.5 22.6 1.0
CB L:VAL19 4.8 23.8 1.0

Sodium binding site 5 out of 5 in 3oqt

Go back to Sodium Binding Sites List in 3oqt
Sodium binding site 5 out of 5 in the Crystal Structure of RV1498A Protein 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 Crystal Structure of RV1498A Protein From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na115

b:46.9
occ:1.00
O P:HOH203 2.3 10.0 1.0
OD2 P:ASP20 3.8 26.6 1.0
CG P:ASP20 4.0 25.1 1.0
OD1 P:ASP20 4.2 26.1 1.0
N P:ASP20 4.7 24.1 1.0
CB P:ASP20 4.7 24.1 1.0
CB P:VAL19 4.9 24.7 1.0

Reference:

F.Liu, J.Xiong, S.Kumar, C.Yang, S.Ge, S.Li, N.Xia, K.Swaminathan. Structural and Biophysical Characterization of Mycobacterium Tuberculosis Dodecin RV1498A. J.Struct.Biol. V. 175 31 2011.
ISSN: ISSN 1047-8477
PubMed: 21539921
DOI: 10.1016/J.JSB.2011.04.013
Page generated: Tue Dec 15 06:20:25 2020

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