Calcium in PDB 3rv2: Crystal Structure of S-Adenosylmethionine Synthetase From Mycobacterium Marinum

All present enzymatic activity of Crystal Structure of S-Adenosylmethionine Synthetase From Mycobacterium Marinum:
2.5.1.6;

The structure of Crystal Structure of S-Adenosylmethionine Synthetase From Mycobacterium Marinum, PDB code: 3rv2 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 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.600, 196.230, 59.660, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 18.7

The binding sites of Calcium atom in the Crystal Structure of S-Adenosylmethionine Synthetase From Mycobacterium Marinum (pdb code 3rv2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of S-Adenosylmethionine Synthetase From Mycobacterium Marinum, PDB code: 3rv2:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of S-Adenosylmethionine Synthetase From Mycobacterium Marinum


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 S-Adenosylmethionine Synthetase From Mycobacterium Marinum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:36.1 occ:1.00 O A:HOH448 2.4 32.7 1.0 OD2 A:ASP259 2.4 19.9 1.0 O A:HOH447 2.4 22.8 1.0 O A:HOH601 2.6 27.0 1.0 O A:HOH482 2.6 32.9 1.0 O A:HOH506 2.6 21.3 1.0 CG A:ASP259 3.4 21.4 1.0 CB A:ASP259 3.8 19.7 1.0 O A:GLY255 4.4 17.5 1.0 O A:HOH527 4.5 29.5 1.0 OD2 A:ASP179 4.5 18.6 1.0 OD1 A:ASP259 4.5 26.8 1.0 O A:MET257 4.6 17.7 1.0 O A:HOH484 4.7 52.8 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of S-Adenosylmethionine Synthetase From Mycobacterium Marinum


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 S-Adenosylmethionine Synthetase From Mycobacterium Marinum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:39.4 occ:1.00 OD2 A:ASP398 2.2 37.9 1.0 O A:HOH478 2.2 29.4 1.0 O A:HOH454 2.4 31.9 1.0 O A:ASP394 2.5 20.4 1.0 O A:HOH455 2.6 20.6 1.0 OD1 A:ASP397 2.6 33.8 1.0 OD2 A:ASP397 2.9 38.1 1.0 CG A:ASP397 3.1 34.1 1.0 CG A:ASP398 3.4 35.2 1.0 C A:ASP394 3.6 21.3 1.0 OD1 A:ASP398 3.8 38.5 1.0 CA A:LYS395 4.3 21.1 1.0 O A:HOH456 4.3 20.8 1.0 N A:LYS395 4.4 20.7 1.0 N A:ASP398 4.5 30.1 1.0 CB A:ASP398 4.6 30.6 1.0 CB A:ASP397 4.7 31.5 1.0 CA A:ASP394 4.7 20.6 1.0 CD A:LYS395 4.7 23.2 1.0 NH2 A:ARG401 4.9 35.2 1.0 C A:LYS395 5.0 21.8 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of S-Adenosylmethionine Synthetase From Mycobacterium Marinum


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 S-Adenosylmethionine Synthetase From Mycobacterium Marinum within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:31.4 occ:1.00 OD2 B:ASP259 2.3 22.4 1.0 O B:HOH611 2.4 22.1 1.0 O B:HOH490 2.6 25.4 1.0 O B:HOH442 2.6 16.4 1.0 O B:HOH604 2.6 25.6 1.0 O B:HOH545 2.6 20.1 1.0 O B:HOH466 2.7 29.9 1.0 CG B:ASP259 3.4 19.7 1.0 CB B:ASP259 3.9 17.2 1.0 O B:HOH605 4.2 28.5 1.0 O B:HOH628 4.3 39.5 1.0 O B:GLY255 4.4 16.5 1.0 OD2 B:ASP179 4.5 17.0 1.0 OD1 B:ASP259 4.5 21.6 1.0 O B:MET257 4.8 17.0 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