Calcium in PDB 3rrv: Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis

The structure of Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis, PDB code: 3rrv was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.080, 134.050, 140.970, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 23.8

The structure of Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis (pdb code 3rrv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis, PDB code: 3rrv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca255 b:26.7 occ:1.00 O A:HOH331 2.1 12.4 1.0 O A:HOH294 2.3 7.5 1.0 OD1 A:ASP33 2.5 23.5 1.0 OD2 A:ASP33 2.5 22.9 1.0 O A:HOH330 2.5 2.8 1.0 CG A:ASP33 2.8 22.4 1.0 CA A:CA256 4.0 31.1 1.0 O A:HOH332 4.2 6.5 1.0 O A:HOH266 4.3 9.6 1.0 CB A:ASP33 4.3 21.8 1.0 O A:HOH333 4.4 11.3 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca256 b:31.1 occ:1.00 OD2 A:ASP33 2.2 22.9 1.0 O A:HOH333 2.3 11.3 1.0 O A:HOH332 2.6 6.5 1.0 OE2 A:GLU7 2.7 28.6 1.0 OE1 A:GLU7 3.3 28.6 1.0 CG A:ASP33 3.3 22.4 1.0 CD A:GLU7 3.3 28.6 1.0 CB A:ASP33 3.8 21.8 1.0 O A:HOH330 4.0 2.8 1.0 CA A:CA255 4.0 26.7 1.0 OD1 A:ASP33 4.4 23.5 1.0 O A:HOH266 4.4 9.6 1.0 O A:HOH294 4.5 7.5 1.0 ND2 A:ASN31 4.6 19.8 1.0 CG2 A:THR6 4.7 28.6 1.0 CG A:GLU7 4.8 28.4 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca257 b:27.5 occ:1.00 OE2 A:GLU234 2.1 26.9 1.0 NE2 A:HIS137 2.2 18.1 1.0 O A:HOH329 2.3 11.1 1.0 OD2 A:ASP146 2.7 31.1 0.5 CD A:GLU234 3.1 26.4 1.0 CD2 A:HIS137 3.1 16.4 1.0 CE1 A:HIS137 3.2 14.3 1.0 CG A:ASP146 3.2 30.4 0.5 OD1 A:ASP146 3.2 31.7 0.5 OE1 A:GLU234 3.4 26.3 1.0 O A:HOH327 3.5 44.7 1.0 CB A:ASP146 4.2 28.1 0.5 O A:HOH274 4.2 29.0 1.0 ND1 A:HIS137 4.3 17.2 1.0 CG A:HIS137 4.3 18.6 1.0 O A:HOH300 4.4 19.1 1.0 O A:HOH265 4.4 37.3 1.0 CG A:GLU234 4.5 23.6 1.0 CB A:ASP146 4.5 29.7 0.5 CG A:ASP146 4.6 26.5 0.5 CD1 A:LEU142 4.6 26.3 1.0 N A:ASP146 4.6 28.8 0.5 N A:ASP146 4.7 28.2 0.5 OD2 A:ASP146 4.7 28.0 0.5 O A:VAL143 4.7 23.9 1.0 O A:HOH328 4.9 35.1 1.0 CA A:ASP146 5.0 28.6 0.5 CA A:ASP146 5.0 29.7 0.5

Calcium binding site 4 out of 8 in the Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca255 b:25.1 occ:1.00 NE2 B:HIS137 2.1 21.8 1.0 OE2 B:GLU234 2.3 28.2 1.0 OD2 B:ASP146 2.4 34.2 0.6 CG B:ASP146 2.9 33.6 0.6 CD2 B:HIS137 3.0 21.4 1.0 OD1 B:ASP146 3.1 35.8 0.6 CE1 B:HIS137 3.1 20.1 1.0 CD B:GLU234 3.3 28.5 1.0 OE1 B:GLU234 3.6 31.0 1.0 CB B:ASP146 4.0 29.7 0.4 OD1 B:ASP146 4.1 28.0 0.4 CB B:ASP146 4.1 31.7 0.6 CG B:HIS137 4.2 21.3 1.0 ND1 B:HIS137 4.2 20.4 1.0 CG B:ASP146 4.4 28.1 0.4 CD1 B:LEU142 4.5 19.5 1.0 N B:ASP146 4.6 30.3 0.6 CG B:GLU234 4.6 22.8 1.0 N B:ASP146 4.6 29.6 0.4 CA B:ASP146 4.8 31.5 0.6 O B:VAL143 4.8 22.5 1.0 CA B:ASP146 4.9 30.1 0.4

Calcium binding site 5 out of 8 in the Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca255 b:25.9 occ:1.00 NE2 C:HIS137 2.1 22.7 1.0 OE2 C:GLU234 2.2 27.5 1.0 O C:HOH260 2.2 15.4 1.0 OD2 C:ASP146 2.5 32.7 0.6 CG C:ASP146 2.8 31.8 0.6 OD1 C:ASP146 2.9 31.4 0.6 CD2 C:HIS137 3.0 22.3 1.0 CE1 C:HIS137 3.1 20.6 1.0 CD C:GLU234 3.1 29.1 1.0 OE1 C:GLU234 3.3 30.8 1.0 O C:HOH330 3.7 43.2 1.0 CB C:ASP146 3.9 32.2 0.6 O C:HOH412 4.0 41.0 1.0 CB C:ASP146 4.1 31.4 0.4 CG C:HIS137 4.1 22.4 1.0 ND1 C:HIS137 4.1 19.2 1.0 O C:HOH293 4.4 27.3 1.0 N C:ASP146 4.5 31.3 0.4 N C:ASP146 4.5 31.6 0.6 CG C:GLU234 4.5 26.2 1.0 CD1 C:LEU142 4.5 23.1 1.0 CA C:ASP146 4.8 31.7 0.4 CA C:ASP146 4.8 32.1 0.6 CG C:ASP146 4.8 29.8 0.4 O C:VAL143 4.8 25.1 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca255 b:26.2 occ:1.00 NE2 D:HIS137 2.2 25.1 1.0 OE2 D:GLU234 2.2 34.0 1.0 OD1 D:ASP146 2.3 34.7 0.6 CD2 D:HIS137 2.9 26.5 1.0 CD D:GLU234 3.0 33.9 1.0 CG D:ASP146 3.2 33.8 0.6 OE1 D:GLU234 3.2 36.4 1.0 CE1 D:HIS137 3.3 25.5 1.0 OD2 D:ASP146 3.4 36.2 0.6 CG D:HIS137 4.2 25.9 1.0 CB D:ASP146 4.3 31.4 0.4 ND1 D:HIS137 4.3 25.9 1.0 CG D:GLU234 4.5 29.4 1.0 CB D:ASP146 4.5 32.3 0.6 N D:ASP146 4.5 31.5 0.6 N D:ASP146 4.5 31.1 0.4 CD1 D:LEU142 4.6 28.3 1.0 O D:VAL143 4.8 26.0 1.0 CA D:ASP146 4.8 31.5 0.4 CA D:ASP146 4.8 32.2 0.6 CG D:ASP146 4.9 30.9 0.4

Calcium binding site 7 out of 8 in the Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca255 b:30.7 occ:1.00 OE2 E:GLU234 2.0 34.6 1.0 NE2 E:HIS137 2.1 26.9 1.0 O E:HOH289 2.4 14.5 1.0 OD1 E:ASP146 2.6 42.3 0.6 OD2 E:ASP146 2.9 40.7 0.6 CD E:GLU234 2.9 35.6 1.0 CG E:ASP146 2.9 40.1 0.6 OE1 E:GLU234 3.1 36.4 1.0 CD2 E:HIS137 3.1 27.3 1.0 CE1 E:HIS137 3.2 26.0 1.0 OD2 E:ASP146 4.1 36.8 0.4 CB E:ASP146 4.2 37.9 0.4 CB E:ASP146 4.2 39.0 0.6 CG E:HIS137 4.3 26.7 1.0 ND1 E:HIS137 4.3 26.7 1.0 CG E:GLU234 4.3 32.0 1.0 CG E:ASP146 4.4 36.8 0.4 CD1 E:LEU142 4.5 31.5 1.0 O E:HOH291 4.5 21.3 1.0 O E:VAL143 4.6 31.3 1.0 N E:ASP146 4.6 38.3 0.6 N E:ASP146 4.6 37.9 0.4 O E:HOH290 4.8 39.0 1.0 CA E:ASP146 4.9 38.6 0.6 CA E:ASP146 5.0 37.9 0.4 CZ E:PHE238 5.0 33.3 1.0 N E:ALA145 5.0 36.4 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of An Enoyl-Coa Hydratase/Isomerase From Mycobacterium Paratuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca255 b:24.1 occ:1.00 OE2 F:GLU234 2.1 26.2 1.0 NE2 F:HIS137 2.1 24.2 1.0 O F:HOH303 2.2 12.4 1.0 OD2 F:ASP146 2.5 34.3 1.0 CD2 F:HIS137 2.9 24.0 1.0 CD F:GLU234 3.1 28.9 1.0 CE1 F:HIS137 3.2 23.6 1.0 CG F:ASP146 3.5 35.4 1.0 OE1 F:GLU234 3.6 30.1 1.0 CG F:HIS137 4.2 22.2 1.0 ND1 F:HIS137 4.2 22.0 1.0 OD1 F:ASP146 4.3 34.6 1.0 CB F:ASP146 4.4 33.6 1.0 CG F:GLU234 4.4 24.9 1.0 O F:HOH397 4.5 26.7 1.0 O F:HOH396 4.6 40.6 1.0 CD1 F:LEU142 4.7 24.4 1.0 O F:VAL143 4.7 26.6 1.0 N F:ASP146 4.7 32.2 1.0 O F:HOH402 4.9 21.7 1.0

L.Baugh, I.Phan, D.W.Begley, M.C.Clifton, B.Armour, D.M.Dranow, B.M.Taylor, M.M.Muruthi, J.Abendroth, J.W.Fairman, D.Fox, S.H.Dieterich, B.L.Staker, A.S.Gardberg, R.Choi, S.N.Hewitt, A.J.Napuli, J.Myers, L.K.Barrett, Y.Zhang, M.Ferrell, E.Mundt, K.Thompkins, N.Tran, S.Lyons-Abbott, A.Abramov, A.Sekar, D.Serbzhinskiy, D.Lorimer, G.W.Buchko, R.Stacy, L.J.Stewart, T.E.Edwards, W.C.Van Voorhis, P.J.Myler. Increasing the Structural Coverage of Tuberculosis Drug Targets. Tuberculosis (Edinb) V. 95 142 2015.
ISSN: ISSN 1472-9792
PubMed: 25613812
DOI: 10.1016/J.TUBE.2014.12.003