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Calcium in PDB 3s82: Structure of A S-Adenosylmethionine Synthetase From Mycobacterium Avium

Enzymatic activity of Structure of A S-Adenosylmethionine Synthetase From Mycobacterium Avium

All present enzymatic activity of Structure of A S-Adenosylmethionine Synthetase From Mycobacterium Avium:
2.5.1.6;

Protein crystallography data

The structure of Structure of A S-Adenosylmethionine Synthetase From Mycobacterium Avium, PDB code: 3s82 was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural 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) 20.00 / 1.73
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.030, 88.180, 184.190, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 17.7

Other elements in 3s82:

The structure of Structure of A S-Adenosylmethionine Synthetase From Mycobacterium Avium also contains other interesting chemical elements:

Uranium (U) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of A S-Adenosylmethionine Synthetase From Mycobacterium Avium (pdb code 3s82). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of A S-Adenosylmethionine Synthetase From Mycobacterium Avium, PDB code: 3s82:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3s82

Go back to Calcium Binding Sites List in 3s82
Calcium binding site 1 out of 4 in the Structure of A S-Adenosylmethionine Synthetase From Mycobacterium Avium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A S-Adenosylmethionine Synthetase From Mycobacterium Avium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:21.6
occ:1.00
O A:HOH1792 2.3 22.2 1.0
O A:HOH1647 2.3 25.6 1.0
OD1 A:ASP234 2.4 22.9 1.0
O A:HOH1651 2.4 14.1 1.0
OD2 A:ASP234 2.7 23.1 1.0
CG A:ASP234 2.9 20.6 1.0
O A:ALA232 4.2 17.5 1.0
CB A:ASP234 4.4 19.5 1.0
O A:HOH455 4.8 14.3 1.0
O A:HOH1038 4.8 35.3 1.0
CA A:ASP234 5.0 19.5 1.0
N A:ASP234 5.0 18.4 1.0

Calcium binding site 2 out of 4 in 3s82

Go back to Calcium Binding Sites List in 3s82
Calcium binding site 2 out of 4 in the Structure of A S-Adenosylmethionine Synthetase From Mycobacterium Avium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A S-Adenosylmethionine Synthetase From Mycobacterium Avium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:24.2
occ:1.00
O A:HOH741 2.4 25.7 1.0
O A:ASN394 2.4 11.1 1.0
OD1 A:ASP398 2.4 21.5 1.0
OD1 A:ASP397 2.4 21.8 1.0
O A:HOH696 2.5 33.3 1.0
O A:HOH1140 2.6 33.9 1.0
O A:HOH848 2.6 31.3 1.0
OD2 A:ASP397 2.9 24.1 1.0
CG A:ASP397 3.0 17.9 1.0
CG A:ASP398 3.5 18.7 1.0
C A:ASN394 3.5 11.8 1.0
OD2 A:ASP398 3.9 25.0 1.0
O A:HOH453 4.3 13.5 1.0
N A:LYS395 4.4 10.9 1.0
CA A:LYS395 4.4 10.5 1.0
CA A:ASN394 4.5 11.8 1.0
N A:ASP398 4.5 11.9 1.0
CB A:ASP397 4.6 14.2 1.0
O A:HOH1274 4.6 37.9 1.0
O A:HOH953 4.7 43.4 1.0
CB A:ASN394 4.8 12.8 1.0
CB A:ASP398 4.8 13.7 1.0
NH2 A:ARG401 4.9 19.4 1.0
CD A:LYS395 4.9 20.3 1.0

Calcium binding site 3 out of 4 in 3s82

Go back to Calcium Binding Sites List in 3s82
Calcium binding site 3 out of 4 in the Structure of A S-Adenosylmethionine Synthetase From Mycobacterium Avium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of A S-Adenosylmethionine Synthetase From Mycobacterium Avium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:24.5
occ:1.00
O B:HOH1773 2.3 30.8 1.0
OD1 B:ASP398 2.4 23.7 1.0
O B:HOH1774 2.4 29.7 1.0
OD1 B:ASP397 2.4 22.4 1.0
O B:ASN394 2.5 14.4 1.0
O B:HOH1744 2.7 40.0 1.0
OD2 B:ASP397 2.8 24.8 1.0
CG B:ASP397 3.0 20.8 1.0
CG B:ASP398 3.4 20.5 1.0
C B:ASN394 3.6 15.1 1.0
OD2 B:ASP398 3.8 25.6 1.0
O B:HOH534 4.3 17.7 1.0
CA B:LYS395 4.4 14.4 1.0
N B:LYS395 4.5 14.4 1.0
CB B:ASP397 4.5 17.3 1.0
N B:ASP398 4.5 15.6 1.0
CA B:ASN394 4.6 14.9 1.0
CB B:ASP398 4.8 16.1 1.0
NH2 B:ARG401 4.8 21.6 1.0
CB B:ASN394 4.9 15.6 1.0
CD B:LYS395 5.0 21.6 1.0

Calcium binding site 4 out of 4 in 3s82

Go back to Calcium Binding Sites List in 3s82
Calcium binding site 4 out of 4 in the Structure of A S-Adenosylmethionine Synthetase From Mycobacterium Avium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of A S-Adenosylmethionine Synthetase From Mycobacterium Avium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca406

b:33.8
occ:1.00
O B:HOH1803 2.2 35.7 1.0
O B:HOH1804 2.2 37.5 1.0
O B:ARG401 2.3 20.7 1.0
O B:HOH690 3.2 35.4 1.0
C B:ARG401 3.5 20.9 1.0
CA B:ARG401 4.2 20.2 1.0
OXT B:ILE403 4.2 31.4 1.0
N B:ALA402 4.5 20.9 1.0
CB B:ARG401 4.7 20.4 1.0
CA B:ALA402 4.7 22.3 1.0
C B:ALA402 4.9 23.9 1.0

Reference:

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
Page generated: Wed Oct 28 08:23:34 2020

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