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Sodium in PDB 4pmo: Crystal Structure of the Mycobacterium Tuberculosis Tat-Secreted Protein RV2525C, Monoclinic Crystal Form I

Protein crystallography data

The structure of Crystal Structure of the Mycobacterium Tuberculosis Tat-Secreted Protein RV2525C, Monoclinic Crystal Form I, PDB code: 4pmo was solved by M.Bellinzoni, A.Haouz, W.Shepard, P.M.Alzari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.95 / 1.33
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.442, 73.679, 74.415, 90.00, 130.85, 90.00
R / Rfree (%) 15 / 16.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Mycobacterium Tuberculosis Tat-Secreted Protein RV2525C, Monoclinic Crystal Form I (pdb code 4pmo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of the Mycobacterium Tuberculosis Tat-Secreted Protein RV2525C, Monoclinic Crystal Form I, PDB code: 4pmo:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4pmo

Go back to Sodium Binding Sites List in 4pmo
Sodium binding site 1 out of 6 in the Crystal Structure of the Mycobacterium Tuberculosis Tat-Secreted Protein RV2525C, Monoclinic Crystal Form I


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 the Mycobacterium Tuberculosis Tat-Secreted Protein RV2525C, Monoclinic Crystal Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na310

b:8.1
occ:1.00
 O A:GLY35 2.3 9.9 1.0
O1 A:FMT305 2.3 9.7 1.0
O A:GLY36 2.4 9.8 1.0
O A:HOH412 2.5 7.2 1.0
C A:FMT305 3.1 8.0 1.0
C A:GLY35 3.2 9.4 1.0
C A:GLY36 3.2 9.3 1.0
CD2 A:LEU38 3.3 9.9 1.0
CA A:GLY36 3.6 9.4 1.0
N A:GLY36 3.8 9.4 1.0
CG A:LEU38 4.0 9.4 1.0
O A:SER37 4.1 8.7 1.0
O A:HOH424 4.1 9.5 1.0
CA A:GLY35 4.3 9.3 1.0
C A:SER37 4.3 8.6 1.0
N A:SER37 4.3 9.0 1.0
O2 A:FMT305 4.4 9.7 1.0
N A:LEU38 4.7 8.7 1.0
CA A:SER37 4.8 8.8 1.0
CD1 A:LEU38 5.0 10.2 1.0

Sodium binding site 2 out of 6 in 4pmo

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Sodium binding site 2 out of 6 in the Crystal Structure of the Mycobacterium Tuberculosis Tat-Secreted Protein RV2525C, Monoclinic Crystal Form I


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 the Mycobacterium Tuberculosis Tat-Secreted Protein RV2525C, Monoclinic Crystal Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na311

b:8.5
occ:1.00
 O A:HOH438 2.3 8.7 1.0
O A:GLN34 2.3 9.8 1.0
O A:HOH424 2.4 9.5 1.0
O A:HOH485 2.4 8.3 1.0
O3 A:GOL302 2.4 9.1 1.0
OE1 A:GLN34 2.5 9.9 1.0
NA A:NA312 3.1 9.6 1.0
CD A:GLN34 3.1 9.7 1.0
C3 A:GOL302 3.3 9.5 1.0
C A:GLN34 3.4 9.7 1.0
NE2 A:GLN34 3.5 9.6 1.0
CA A:GLY35 4.0 9.3 1.0
O A:LEU232 4.1 9.1 1.0
N A:GLY35 4.2 9.4 1.0
CG A:GLN34 4.3 9.7 1.0
O2 A:GOL302 4.3 12.5 1.0
O2 A:FMT305 4.3 9.7 1.0
CB A:GLN34 4.3 9.9 1.0
O1 A:FMT305 4.4 9.7 1.0
CA A:GLN34 4.5 9.7 1.0
C2 A:GOL302 4.5 10.8 1.0
O A:HOH507 4.5 16.5 1.0
C A:FMT305 4.6 8.0 1.0
O A:HOH420 4.6 10.6 1.0
C A:GLY35 4.8 9.4 1.0
O A:HOH542 4.9 9.5 1.0

Sodium binding site 3 out of 6 in 4pmo

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Sodium binding site 3 out of 6 in the Crystal Structure of the Mycobacterium Tuberculosis Tat-Secreted Protein RV2525C, Monoclinic Crystal Form I


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 the Mycobacterium Tuberculosis Tat-Secreted Protein RV2525C, Monoclinic Crystal Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na312

b:9.6
occ:1.00
 O A:HOH541 2.2 9.0 1.0
OE1 A:GLN34 2.4 9.9 1.0
O A:HOH542 2.4 9.5 1.0
O3 A:GOL302 2.4 9.1 1.0
O A:HOH485 2.5 8.3 1.0
O2 A:GOL302 2.6 12.5 1.0
NA A:NA311 3.1 8.5 1.0
C3 A:GOL302 3.3 9.5 1.0
C2 A:GOL302 3.3 10.8 1.0
CD A:GLN34 3.6 9.7 1.0
CA A:PRO207 4.1 9.9 1.0
O A:PRO207 4.2 10.4 1.0
CG A:GLN34 4.3 9.7 1.0
O A:GLN34 4.3 9.8 1.0
O A:HIS206 4.3 8.6 1.0
CB A:GLN34 4.4 9.9 1.0
CG2 A:THR205 4.4 10.7 1.0
C A:PRO207 4.5 9.8 1.0
O A:HOH507 4.6 16.5 1.0
NE2 A:GLN34 4.6 9.6 1.0
CB A:LEU232 4.6 9.1 1.0
O A:HOH424 4.7 9.5 1.0
O A:ALA209 4.7 8.5 1.0
C1 A:GOL302 4.8 13.5 1.0
CD1 A:LEU232 4.8 10.3 1.0
CB A:PRO207 4.9 11.2 1.0
C A:HIS206 4.9 8.8 1.0
O A:LEU232 5.0 9.1 1.0
N A:PRO207 5.0 9.4 1.0
O A:HOH438 5.0 8.7 1.0

Sodium binding site 4 out of 6 in 4pmo

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Sodium binding site 4 out of 6 in the Crystal Structure of the Mycobacterium Tuberculosis Tat-Secreted Protein RV2525C, Monoclinic Crystal Form I


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 the Mycobacterium Tuberculosis Tat-Secreted Protein RV2525C, Monoclinic Crystal Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na308

b:8.5
occ:1.00
 O B:GLY35 2.3 10.4 1.0
O B:GLY36 2.4 10.5 1.0
O B:HOH414 2.5 7.4 1.0
C B:GLY35 3.2 9.9 1.0
C B:GLY36 3.2 9.7 1.0
CD2 B:LEU38 3.3 9.8 1.0
CA B:GLY36 3.6 10.0 1.0
N B:GLY36 3.7 10.0 1.0
CG B:LEU38 4.0 9.4 1.0
O B:SER37 4.1 8.4 1.0
CA B:GLY35 4.2 9.9 1.0
C B:SER37 4.3 8.6 1.0
N B:SER37 4.3 9.3 1.0
N B:LEU38 4.7 8.5 1.0
CA B:SER37 4.8 8.9 1.0
CD1 B:LEU38 5.0 9.8 1.0

Sodium binding site 5 out of 6 in 4pmo

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Sodium binding site 5 out of 6 in the Crystal Structure of the Mycobacterium Tuberculosis Tat-Secreted Protein RV2525C, Monoclinic Crystal Form I


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 the Mycobacterium Tuberculosis Tat-Secreted Protein RV2525C, Monoclinic Crystal Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na309

b:9.8
occ:1.00
 O B:GLN34 2.3 10.4 1.0
O3 B:GOL302 2.4 11.4 1.0
O B:HOH434 2.4 9.4 1.0
OE1 B:GLN34 2.5 11.1 1.0
NA B:NA310 3.1 11.8 1.0
CD B:GLN34 3.1 10.7 1.0
C3 B:GOL302 3.3 13.4 1.0
NE2 B:GLN34 3.4 11.1 1.0
C B:GLN34 3.5 10.3 1.0
CA B:GLY35 4.0 9.9 1.0
O B:LEU232 4.1 9.1 1.0
N B:GLY35 4.2 9.9 1.0
CG B:GLN34 4.3 10.9 1.0
CB B:GLN34 4.4 10.8 1.0
O2 B:GOL302 4.4 14.1 1.0
C2 B:GOL302 4.4 15.5 1.0
CA B:GLN34 4.5 10.4 1.0
O B:HOH416 4.5 19.9 1.0
O B:HOH530 4.9 12.0 1.0
C B:GLY35 4.9 9.9 1.0

Sodium binding site 6 out of 6 in 4pmo

Go back to Sodium Binding Sites List in 4pmo
Sodium binding site 6 out of 6 in the Crystal Structure of the Mycobacterium Tuberculosis Tat-Secreted Protein RV2525C, Monoclinic Crystal Form I


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 the Mycobacterium Tuberculosis Tat-Secreted Protein RV2525C, Monoclinic Crystal Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na310

b:11.8
occ:1.00
 O B:HOH479 2.2 9.7 1.0
OE1 B:GLN34 2.3 11.1 1.0
O B:HOH530 2.3 12.0 1.0
O3 B:GOL302 2.4 11.4 1.0
O B:HOH434 2.5 9.4 1.0
O2 B:GOL302 2.7 14.1 1.0
NA B:NA309 3.1 9.8 1.0
C3 B:GOL302 3.3 13.4 1.0
C2 B:GOL302 3.3 15.5 1.0
CD B:GLN34 3.5 10.7 1.0
CA B:PRO207 4.2 10.8 1.0
CG B:GLN34 4.2 10.9 1.0
O B:PRO207 4.3 11.2 1.0
O B:GLN34 4.3 10.4 1.0
O B:HIS206 4.4 8.6 1.0
CB B:GLN34 4.4 10.8 1.0
CG2 B:THR205 4.5 10.7 1.0
NE2 B:GLN34 4.5 11.1 1.0
C B:PRO207 4.6 10.5 1.0
CB B:LEU232 4.6 9.2 1.0
O B:HOH416 4.7 19.9 1.0
O B:ALA209 4.7 8.8 1.0
C1 B:GOL302 4.8 19.0 1.0
CD1 B:LEU232 4.8 10.2 1.0
C B:HIS206 4.9 9.6 1.0
O B:LEU232 5.0 9.1 1.0
CB B:PRO207 5.0 11.6 1.0
N B:PRO207 5.0 10.1 1.0

Reference:

M.Bellinzoni, A.Haouz, I.Miras, S.Magnet, G.Andre-Leroux, R.Mukherjee, W.Shepard, S.T.Cole, P.M.Alzari. Structural Studies Suggest A Peptidoglycan Hydrolase Function For the Mycobacterium Tuberculosis Tat-Secreted Protein RV2525C. J.Struct.Biol. 2014.
ISSN: ESSN 1095-8657
PubMed: 25260828
DOI: 10.1016/J.JSB.2014.09.003
Page generated: Mon Oct 7 17:45:13 2024

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