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Calcium 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:

Sodium (Na) 12 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium where determined in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product., PDB code: 5agv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5agv

Go back to Calcium Binding Sites List in 5agv
Calcium binding site 1 out of 6 in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca501

b:40.3
occ:1.00
 O A:HOH832 2.3 37.3 1.0
O6 A:BU3508 2.4 36.2 1.0
O A:THR389 2.5 31.9 1.0
O A:HOH849 2.5 36.2 1.0
O5 A:BU3508 2.6 33.0 1.0
O A:HOH917 2.6 40.6 1.0
O A:HOH823 2.8 58.8 1.0
O A:HOH897 2.9 66.8 1.0
C3 A:BU3508 3.4 33.7 1.0
C2 A:BU3508 3.4 32.5 1.0
C A:THR389 3.7 32.5 1.0
C1 A:BU3508 3.9 28.5 1.0
N A:THR389 4.0 34.2 1.0
C4 A:BU3508 4.2 32.9 1.0
OE1 A:GLU190 4.2 41.5 1.0
CA A:THR389 4.5 31.2 1.0
O A:HOH666 4.5 36.5 1.0
O A:HOH991 4.6 46.4 1.0
N A:ASP390 4.7 26.9 1.0
CA A:ASP390 4.7 26.7 1.0
OD1 A:ASP390 4.9 37.5 1.0
CG2 A:THR389 4.9 32.3 1.0

Calcium binding site 2 out of 6 in 5agv

Go back to Calcium Binding Sites List in 5agv
Calcium binding site 2 out of 6 in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
B:Ca502

b:50.6
occ:1.00
 O B:HOH670 2.4 35.1 1.0
O B:HOH987 2.5 40.9 1.0
O B:HOH765 2.6 44.7 1.0
NA B:NA507 2.8 69.9 1.0
O B:HOH977 2.8 55.3 1.0
O B:HOH1078 2.8 67.8 1.0
O B:HOH756 4.2 27.5 1.0
OD1 B:ASP303 4.3 30.9 1.0
O B:HOH758 4.5 22.9 1.0
OD2 B:ASP303 4.6 29.8 1.0
O B:HOH990 4.8 34.2 1.0
OD1 B:ASN379 4.9 31.8 1.0
CG B:ASP303 4.9 27.6 1.0

Calcium binding site 3 out of 6 in 5agv

Go back to Calcium Binding Sites List in 5agv
Calcium binding site 3 out of 6 in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
B:Ca503

b:30.3
occ:1.00
 O5 B:BU3513 2.4 31.5 1.0
O B:HOH862 2.4 51.0 1.0
O6 B:BU3513 2.4 30.0 1.0
O B:HOH762 2.5 36.1 1.0
O B:HOH961 2.5 36.5 1.0
O B:THR389 2.5 24.3 1.0
O B:HOH879 2.6 30.1 1.0
O B:HOH968 2.6 52.7 1.0
C2 B:BU3513 3.3 34.1 1.0
C3 B:BU3513 3.3 32.8 1.0
C B:THR389 3.7 24.4 1.0
C4 B:BU3513 3.9 30.7 1.0
C1 B:BU3513 3.9 36.3 1.0
N B:THR389 4.2 25.5 1.0
OE1 B:GLU190 4.4 33.3 1.0
O B:HOH939 4.4 48.9 1.0
O B:HOH767 4.6 28.0 1.0
CA B:THR389 4.6 24.1 1.0
N B:ASP390 4.7 23.2 1.0
CA B:ASP390 4.7 23.0 1.0
O B:HOH840 4.7 48.6 1.0
OD1 B:ASP390 4.8 36.4 1.0
CG2 B:THR389 4.8 25.2 1.0
O B:HOH1027 4.8 42.2 1.0
CD B:GLU190 4.9 37.3 1.0

Calcium binding site 4 out of 6 in 5agv

Go back to Calcium Binding Sites List in 5agv
Calcium binding site 4 out of 6 in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
B:Ca504

b:24.7
occ:1.00
 O B:HOH836 2.4 25.2 1.0
O B:HOH776 2.5 25.3 1.0
O B:GLY380 2.5 23.3 1.0
O B:ASN379 2.6 24.6 1.0
O B:HOH801 2.6 20.4 1.0
O B:HOH710 2.6 18.9 1.0
C B:ASN379 3.4 27.0 1.0
C B:GLY380 3.5 25.5 1.0
CA B:GLY380 4.1 27.9 1.0
N B:GLY380 4.1 25.9 1.0
O B:HOH758 4.4 22.9 1.0
CA B:ASN379 4.4 26.6 1.0
OD1 B:ASN379 4.6 31.8 1.0
N B:ASN381 4.6 25.7 1.0
N B:GLY328 4.7 20.1 1.0
O B:LEU378 4.7 26.3 1.0
O B:HOH619 4.8 42.6 1.0
O B:HOH798 4.8 24.9 1.0
O B:HOH757 4.9 35.5 1.0
CA B:ASN381 4.9 26.6 1.0

Calcium binding site 5 out of 6 in 5agv

Go back to Calcium Binding Sites List in 5agv
Calcium binding site 5 out of 6 in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
B:Ca505

b:46.6
occ:1.00
 O B:ALA35 2.2 39.4 1.0
O B:LEU33 2.3 25.8 1.0
O5 B:BU3512 2.5 41.1 1.0
O B:HOH741 2.5 32.9 1.0
O B:HOH682 2.6 45.6 1.0
O B:HOH636 2.7 58.0 1.0
O6 B:BU3512 2.7 46.2 1.0
C B:ALA35 3.4 43.0 1.0
C2 B:BU3512 3.4 43.8 1.0
C B:LEU33 3.4 29.2 1.0
C3 B:BU3512 3.6 44.5 1.0
C B:PRO34 3.9 35.7 1.0
N B:ALA35 3.9 35.4 1.0
CB B:LEU33 4.0 28.9 1.0
O B:PRO34 4.0 37.1 1.0
CA B:ALA35 4.3 40.0 1.0
CA B:LEU33 4.3 27.5 1.0
N B:ARG36 4.3 45.1 1.0
N B:PRO34 4.3 30.0 1.0
CD B:PRO37 4.4 41.8 1.0
CA B:ARG36 4.4 46.3 1.0
CA B:PRO34 4.4 30.8 1.0
O B:HOH628 4.4 46.0 1.0
O B:HOH759 4.6 57.6 1.0
O B:HOH669 4.6 45.3 1.0
O B:HOH641 4.7 32.5 1.0
C1 B:BU3512 4.7 44.3 1.0
O B:HOH893 4.8 35.0 1.0
O B:HOH975 4.8 38.8 1.0
C4 B:BU3512 4.9 42.1 1.0

Calcium binding site 6 out of 6 in 5agv

Go back to Calcium Binding Sites List in 5agv
Calcium binding site 6 out of 6 in the The Sliding Clamp of Mycobacterium Tuberculosis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
B:Ca506

b:70.0
occ:1.00
 O B:HOH802 2.2 26.4 1.0
O B:HOH830 2.8 49.3 1.0
N B:VAL387 3.0 26.3 1.0
NE B:ARG366 3.1 31.6 1.0
O B:HOH689 3.1 35.8 1.0
CB B:VAL387 3.6 32.4 1.0
CG2 B:VAL387 3.7 34.1 1.0
O B:HOH850 3.7 33.2 1.0
CA B:ALA386 3.7 23.7 1.0
C B:ALA386 3.8 30.1 1.0
CD B:ARG366 3.8 28.4 1.0
CA B:VAL387 3.9 29.2 1.0
CZ B:ARG366 4.0 31.4 1.0
NH2 B:ARG366 4.0 27.0 1.0
O B:HOH751 4.1 29.6 1.0
NE2 B:HIS269 4.1 21.0 1.0
CD2 B:HIS269 4.2 24.1 1.0
OG B:SER353 4.2 30.5 1.0
CB B:ALA386 4.4 22.4 1.0
O B:VAL387 4.4 26.5 1.0
O B:PRO385 4.4 32.1 1.0
C B:VAL387 4.7 26.5 1.0
N B:ALA386 4.8 25.1 1.0
CG B:ARG366 4.9 25.8 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: Wed Jul 9 04:13:13 2025

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