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Sodium in PDB 5agv: The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.

Enzymatic activity of The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.

All present enzymatic activity of The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.:
2.7.7.7;

Protein crystallography data

The structure of The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product., PDB code: 5agv was solved by P.Lukat, A.Kling, D.W.Heinz, R.Mueller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.80 / 1.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.869, 89.764, 81.928, 90.00, 95.14, 90.00
R / Rfree (%) 16.9 / 21

Other elements in 5agv:

The structure of The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product. also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product. (pdb code 5agv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product., PDB code: 5agv:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 5agv

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Sodium binding site 1 out of 12 in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:38.8
occ:1.00
 O A:HOH762 2.3 41.9 1.0
O A:HOH702 2.9 35.3 1.0
NE2 A:HIS269 2.9 24.0 1.0
O A:HOH803 3.0 35.7 1.0
CD2 A:HIS269 3.7 28.9 1.0
CB A:ALA386 3.7 35.7 1.0
CA A:ALA386 3.7 35.4 1.0
N A:VAL387 3.7 36.7 1.0
NE A:ARG366 3.8 34.2 1.0
CD A:ARG366 3.8 31.2 1.0
CD2 A:LEU364 3.8 30.4 1.0
CE1 A:HIS269 3.9 23.8 1.0
CD1 A:LEU364 4.0 31.9 1.0
C A:ALA386 4.2 35.5 1.0
CG A:LEU364 4.4 27.8 1.0
O A:VAL387 4.5 33.1 1.0
CG A:ARG366 4.6 23.4 1.0
CB A:LEU364 4.8 20.9 1.0
CA A:VAL387 4.8 37.4 1.0
CG A:HIS269 4.9 27.9 1.0
CA A:GLY355 4.9 22.8 1.0
OG A:SER353 4.9 29.2 1.0
CZ A:ARG366 5.0 34.3 1.0
ND1 A:HIS269 5.0 24.1 1.0

Sodium binding site 2 out of 12 in 5agv

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Sodium binding site 2 out of 12 in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:62.2
occ:1.00
 O A:HOH687 2.6 37.0 1.0
O A:HOH967 2.6 59.5 1.0
O A:HOH916 2.7 44.0 1.0
OD1 A:ASP292 2.9 65.5 1.0
OD2 A:ASP292 3.3 69.2 1.0
CG A:ASP292 3.5 64.8 1.0
O A:HOH678 3.7 45.9 1.0
O A:LEU289 4.3 24.1 1.0
CD2 A:LEU289 4.4 26.8 1.0
CA A:LEU289 4.5 21.6 1.0
O A:HOH852 4.5 63.5 1.0
O A:ALA288 4.6 21.1 1.0
O A:HOH729 4.8 36.0 1.0
C A:LEU289 4.8 23.7 1.0
CB A:ASP292 4.9 57.3 1.0

Sodium binding site 3 out of 12 in 5agv

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Sodium binding site 3 out of 12 in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:53.8
occ:1.00
 OG A:SER249 2.4 26.1 1.0
CB A:SER249 3.1 23.9 1.0
O A:HOH655 3.5 47.4 1.0
CB A:ALA214 3.8 28.4 1.0
NA A:NA505 4.1 50.4 1.0
CZ2 A:TRP28 4.3 38.8 1.0
CA A:SER249 4.6 30.7 1.0
CD1 A:ILE242 4.6 22.6 1.0
CA A:ALA214 4.7 27.7 1.0
O A:HOH680 4.7 49.1 1.0
OG1 A:THR210 4.7 48.1 0.5
CG1 A:VAL63 4.8 33.0 1.0
CG2 A:THR210 4.9 45.2 0.5
OG1 A:THR251 4.9 29.6 1.0
CB A:ILE242 4.9 21.2 1.0
CE2 A:TRP28 5.0 40.4 1.0
O A:THR210 5.0 36.8 1.0

Sodium binding site 4 out of 12 in 5agv

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Sodium binding site 4 out of 12 in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:50.4
occ:1.00
 OG1 A:THR251 2.8 29.6 1.0
OG A:SER249 2.9 26.1 1.0
O A:LEU240 2.9 22.6 1.0
O A:SER249 3.1 29.9 1.0
CG1 A:ILE242 3.3 21.3 1.0
N A:THR251 3.3 21.9 1.0
C A:SER249 3.4 30.9 1.0
C A:THR250 3.4 33.3 1.0
CD1 A:ILE242 3.5 22.6 1.0
CA A:THR250 3.5 30.2 1.0
N A:THR250 3.6 29.0 1.0
CB A:THR251 3.6 28.5 1.0
N A:ILE242 3.7 22.4 1.0
CB A:ILE242 3.8 21.2 1.0
CB A:SER249 3.9 23.9 1.0
C A:LEU240 4.0 25.6 1.0
CA A:THR251 4.1 24.0 1.0
O A:THR250 4.1 29.8 1.0
NA A:NA504 4.1 53.8 1.0
C A:GLY241 4.2 27.6 1.0
CA A:SER249 4.2 30.7 1.0
CA A:GLY241 4.3 23.2 1.0
CA A:ILE242 4.4 22.0 1.0
N A:GLY241 4.6 22.8 1.0
CG A:LEU240 4.6 23.2 1.0
CD2 A:LEU240 4.8 23.4 1.0
CB A:LEU240 4.9 21.3 1.0
O A:GLY241 5.0 22.3 1.0
CB A:THR250 5.0 30.7 1.0
N A:SER249 5.0 30.6 1.0

Sodium binding site 5 out of 12 in 5agv

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Sodium binding site 5 out of 12 in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:0.8
occ:1.00
 OD2 A:ASP88 2.8 35.2 1.0
O A:HOH1019 2.9 50.9 1.0
CD1 A:LEU85 3.1 36.9 1.0
CA A:LEU85 3.3 30.8 1.0
CG A:ARG84 3.7 53.9 1.0
CG A:ASP88 3.7 34.4 1.0
N A:LEU85 3.7 33.7 1.0
CB A:LEU85 3.8 37.4 1.0
CD A:ARG84 3.8 65.0 1.0
O A:ARG84 3.9 32.0 1.0
C A:ARG84 4.0 36.1 1.0
CB A:ASP88 4.0 26.9 1.0
CG A:LEU85 4.0 37.3 1.0
C A:LEU85 4.5 27.3 1.0
O A:LEU85 4.7 27.2 1.0
OD1 A:ASP88 4.8 38.7 1.0
CB A:ARG84 4.8 41.3 1.0
CD2 A:LEU85 5.0 35.7 1.0

Sodium binding site 6 out of 12 in 5agv

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Sodium binding site 6 out of 12 in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na507

b:46.1
occ:1.00
 O A:HOH691 2.3 48.9 1.0
O A:HOH889 2.3 57.4 1.0
O A:THR120 2.4 32.5 1.0
O A:HOH950 2.4 51.1 1.0
O A:HOH1036 2.6 57.0 1.0
O A:HOH942 2.7 52.0 1.0
C A:THR120 3.7 33.6 1.0
O A:HOH858 4.0 50.9 1.0
N A:THR120 4.3 29.6 1.0
O A:HOH1016 4.4 49.1 1.0
CA A:MET121 4.4 37.3 1.0
N A:MET121 4.5 36.2 1.0
CA A:THR120 4.6 28.8 1.0
CB A:PRO119 4.7 37.4 1.0
O A:ASN105 4.7 37.0 1.0
CG A:MET121 4.7 44.3 1.0
C A:PRO119 4.9 33.3 1.0

Sodium binding site 7 out of 12 in 5agv

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Sodium binding site 7 out of 12 in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:43.6
occ:1.00
 O A:GLY221 2.6 49.5 1.0
O A:HOH624 2.8 34.6 1.0
O B:HOH768 2.9 40.0 1.0
OE2 B:GLU142 3.0 59.1 1.0
O A:GLY220 3.1 44.0 1.0
O A:HOH717 3.1 61.7 1.0
C A:GLY220 3.3 44.7 1.0
CG B:GLU142 3.5 48.6 1.0
C A:GLY221 3.7 49.0 1.0
CD B:GLU142 3.7 56.9 1.0
N A:GLY221 3.8 41.9 1.0
O A:HOH863 3.9 53.9 1.0
O A:HOH722 4.0 38.2 1.0
CA A:GLY220 4.0 45.9 1.0
CA A:GLY221 4.2 49.0 1.0
O A:HOH761 4.4 39.5 1.0
OE1 A:GLU142 4.5 32.5 1.0
O B:HOH854 4.6 32.2 1.0
N B:GLY220 4.6 37.9 1.0
N A:GLY220 4.7 45.4 1.0
N A:SER222 4.8 47.2 1.0
CG2 B:ILE219 4.9 36.9 1.0
CB A:ALA141 4.9 27.1 1.0
OE1 B:GLU142 4.9 56.5 1.0
CB B:GLU142 4.9 37.0 1.0
O A:HOH732 5.0 44.5 1.0
O B:GLY221 5.0 41.7 1.0

Sodium binding site 8 out of 12 in 5agv

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Sodium binding site 8 out of 12 in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na507

b:69.9
occ:1.00
 OD1 B:ASP325 2.3 46.9 1.0
O B:HOH977 2.4 55.3 1.0
O B:HOH987 2.8 40.9 1.0
CA B:CA502 2.8 50.6 1.0
O B:HOH756 3.1 27.5 1.0
O B:HOH670 3.1 35.1 1.0
O B:HOH625 3.2 34.8 1.0
O B:TYR326 3.4 25.2 1.0
CG B:ASP325 3.5 45.4 1.0
N B:TYR326 3.7 19.6 1.0
O B:HOH990 3.7 34.2 1.0
O B:HOH765 3.8 44.7 1.0
O B:HOH758 4.0 22.9 1.0
CA B:ASP325 4.0 22.5 1.0
C B:ASP325 4.0 19.1 1.0
CB B:ASP325 4.3 30.7 1.0
C B:TYR326 4.3 22.9 1.0
OD2 B:ASP325 4.4 54.2 1.0
O B:HOH1078 4.5 67.8 1.0
CA B:TYR326 4.6 18.5 1.0
O B:HOH633 4.7 37.5 1.0
O B:ASP325 4.9 20.4 1.0

Sodium binding site 9 out of 12 in 5agv

Go back to Sodium Binding Sites List in 5agv
Sodium binding site 9 out of 12 in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na508

b:67.3
occ:1.00
 O B:HOH627 2.6 45.5 1.0
O B:HOH950 2.8 60.5 1.0
O B:HOH780 3.0 34.8 1.0
CG1 B:VAL69 3.1 31.3 1.0
OG B:SER21 3.3 32.8 1.0
O B:SER21 3.3 20.9 1.0
OD2 B:ASP24 3.7 27.4 0.5
CA B:SER21 3.7 23.2 1.0
CB B:ASP24 3.9 25.2 0.5
C B:SER21 3.9 20.4 1.0
CB B:SER21 4.0 29.0 1.0
CB B:ASP24 4.0 25.6 0.5
O B:HOH778 4.2 33.5 1.0
CG B:ASP24 4.2 27.6 0.5
CB B:VAL69 4.3 28.6 1.0
N B:ALA25 4.5 22.5 1.0
O B:HOH982 4.7 42.8 1.0
O B:HOH638 4.8 51.4 1.0
CB B:ALA25 4.9 20.1 1.0
C B:ASP24 4.9 22.6 0.5
OD2 B:ASP24 4.9 30.7 0.5
O B:HOH868 5.0 31.9 1.0

Sodium binding site 10 out of 12 in 5agv

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Sodium binding site 10 out of 12 in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na509

b:61.9
occ:1.00
 OG B:SER57 2.4 34.2 1.0
O B:HOH808 2.5 24.3 1.0
O B:HOH996 2.6 63.2 1.0
OE1 B:GLU66 2.8 46.5 1.0
CB B:SER57 3.2 32.3 1.0
CG2 B:THR55 3.6 25.3 0.5
CD2 B:LEU46 3.9 28.2 1.0
CD B:GLU66 3.9 46.4 1.0
OG1 B:THR55 4.0 22.7 0.5
O B:HOH928 4.1 54.7 1.0
CA B:SER57 4.4 29.2 1.0
N B:SER57 4.4 25.4 1.0
CG B:GLU66 4.5 34.4 1.0
CD2 B:LEU129 4.5 38.0 1.0
CG B:LEU46 4.5 24.6 1.0
CB B:THR55 4.6 26.4 0.5
CB B:THR55 4.6 26.6 0.5
OG1 B:THR48 4.6 28.6 1.0
O B:LEU46 4.6 29.2 1.0
CB B:LEU46 4.7 24.8 1.0
CD1 B:LEU129 4.7 51.1 1.0
O B:HOH1044 4.8 49.9 1.0
OE2 B:GLU66 4.8 50.4 1.0

Reference:

A.Kling, P.Lukat, D.V.Almeida, A.Bauer, E.Fontaine, S.Sordello, N.Zaburannyi, J.Herrmann, S.C.Wenzel, C.Konig, N.C.Ammerman, M.B.Barrio, K.Borchers, F.Bordon-Pallier, M.Bronstrup, G.Courtemanche, M.Gerlitz, M.Geslin, P.Hammann, D.W.Heinz, H.Hoffmann, S.Klieber, M.Kohlmann, M.Kurz, C.Lair, H.Matter, E.Nuermberger, S.Tyagi, L.Fraisse, J.H.Grosset, S.Lagrange, R.Muller. Antibiotics. Targeting Dnan For Tuberculosis Therapy Using Novel Griselimycins. Science V. 348 1106 2015.
ISSN: ISSN 0036-8075
PubMed: 26045430
DOI: 10.1126/SCIENCE.AAA4690
Page generated: Mon Oct 7 19:53:12 2024

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