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Magnesium in PDB 3tav: Crystal Structure of A Methionine Aminopeptidase From Mycobacterium Abscessus

Enzymatic activity of Crystal Structure of A Methionine Aminopeptidase From Mycobacterium Abscessus

All present enzymatic activity of Crystal Structure of A Methionine Aminopeptidase From Mycobacterium Abscessus:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of A Methionine Aminopeptidase From Mycobacterium Abscessus, PDB code: 3tav 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 / 2.15
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 119.640, 119.640, 96.190, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 21.6

Other elements in 3tav:

The structure of Crystal Structure of A Methionine Aminopeptidase From Mycobacterium Abscessus also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Methionine Aminopeptidase From Mycobacterium Abscessus (pdb code 3tav). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A Methionine Aminopeptidase From Mycobacterium Abscessus, PDB code: 3tav:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3tav

Go back to Magnesium Binding Sites List in 3tav
Magnesium binding site 1 out of 4 in the Crystal Structure of A Methionine Aminopeptidase From Mycobacterium Abscessus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Methionine Aminopeptidase From Mycobacterium Abscessus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg266

b:36.9
occ:1.00
 O A:HOH409 2.1 55.4 1.0
OD2 A:ASP115 2.2 46.8 1.0
NE2 A:HIS184 2.2 38.0 1.0
OE2 A:GLU248 2.3 44.9 1.0
OE2 A:GLU217 2.4 48.8 1.0
O A:HOH349 2.8 48.5 1.0
CD2 A:HIS184 3.1 38.8 1.0
CD A:GLU217 3.1 50.0 1.0
CD A:GLU248 3.2 43.9 1.0
CE1 A:HIS184 3.3 37.9 1.0
CG A:ASP115 3.3 45.0 1.0
MG A:MG269 3.4 50.2 1.0
OE1 A:GLU217 3.5 50.8 1.0
OE1 A:GLU248 3.5 46.5 1.0
OD1 A:ASP115 4.0 49.5 1.0
CB A:ALA215 4.1 37.3 1.0
CB A:ASP115 4.3 38.8 1.0
CG A:GLU217 4.3 45.4 1.0
CG A:HIS184 4.3 37.5 1.0
ND1 A:HIS184 4.4 37.3 1.0
NE2 A:HIS191 4.5 43.0 1.0
CG A:GLU248 4.6 40.4 1.0
CD2 A:HIS191 4.8 43.6 1.0

Magnesium binding site 2 out of 4 in 3tav

Go back to Magnesium Binding Sites List in 3tav
Magnesium binding site 2 out of 4 in the Crystal Structure of A Methionine Aminopeptidase From Mycobacterium Abscessus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Methionine Aminopeptidase From Mycobacterium Abscessus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg269

b:50.2
occ:1.00
 OE1 A:GLU248 2.0 46.5 1.0
OD1 A:ASP115 2.0 49.5 1.0
OD1 A:ASP104 2.1 42.0 1.0
O A:HOH409 2.2 55.4 1.0
CG A:ASP115 2.7 45.0 1.0
OD2 A:ASP115 2.8 46.8 1.0
CD A:GLU248 3.0 43.9 1.0
CG A:ASP104 3.0 42.1 1.0
OD2 A:ASP104 3.2 45.9 1.0
OE2 A:GLU248 3.3 44.9 1.0
MG A:MG266 3.4 36.9 1.0
O A:SER116 3.9 38.6 1.0
CZ A:PHE66 4.0 41.7 1.0
N A:SER116 4.0 36.0 1.0
CB A:ASP115 4.0 38.8 1.0
C A:SER116 4.2 36.0 1.0
OE1 A:GLU217 4.2 50.8 1.0
C A:ASP115 4.3 36.7 1.0
O A:CYS105 4.3 37.0 1.0
CG A:GLU248 4.3 40.4 1.0
CB A:ASP104 4.4 40.6 1.0
CA A:ASP115 4.4 35.9 1.0
N A:CYS105 4.5 38.0 1.0
CA A:SER116 4.5 35.9 1.0
CB A:ALA117 4.7 35.4 1.0
CE1 A:HIS246 4.7 38.5 1.0
CE1 A:PHE66 4.8 42.5 1.0
O A:HOH349 4.8 48.5 1.0
CB A:GLU248 4.8 37.9 1.0
CD A:GLU217 4.8 50.0 1.0
CA A:ASP104 4.9 38.0 1.0
CE2 A:PHE66 4.9 43.2 1.0
OE2 A:GLU217 4.9 48.8 1.0
N A:ALA117 4.9 36.9 1.0
O A:ASP115 4.9 34.8 1.0
NE2 A:HIS246 5.0 39.0 1.0

Magnesium binding site 3 out of 4 in 3tav

Go back to Magnesium Binding Sites List in 3tav
Magnesium binding site 3 out of 4 in the Crystal Structure of A Methionine Aminopeptidase From Mycobacterium Abscessus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Methionine Aminopeptidase From Mycobacterium Abscessus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg267

b:38.5
occ:1.00
 OD2 B:ASP115 2.2 46.8 1.0
NE2 B:HIS184 2.3 35.4 1.0
OE2 B:GLU217 2.3 49.4 1.0
OE2 B:GLU248 2.3 47.1 1.0
O B:HOH410 2.4 54.6 1.0
O B:HOH332 2.8 51.2 1.0
CD B:GLU217 3.1 49.4 1.0
CD2 B:HIS184 3.2 37.0 1.0
CG B:ASP115 3.2 44.5 1.0
CD B:GLU248 3.2 44.5 1.0
CE1 B:HIS184 3.3 35.8 1.0
MG B:MG270 3.3 51.7 1.0
OE1 B:GLU248 3.5 47.6 1.0
OE1 B:GLU217 3.5 50.5 1.0
OD1 B:ASP115 3.8 47.5 1.0
CB B:ALA215 4.2 37.6 1.0
CB B:ASP115 4.3 39.2 1.0
CG B:GLU217 4.3 46.1 1.0
CG B:HIS184 4.4 36.5 1.0
ND1 B:HIS184 4.4 36.2 1.0
NE2 B:HIS191 4.5 44.0 1.0
CG B:GLU248 4.6 39.8 1.0
CD2 B:HIS191 4.8 44.5 1.0

Magnesium binding site 4 out of 4 in 3tav

Go back to Magnesium Binding Sites List in 3tav
Magnesium binding site 4 out of 4 in the Crystal Structure of A Methionine Aminopeptidase From Mycobacterium Abscessus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Methionine Aminopeptidase From Mycobacterium Abscessus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg270

b:51.7
occ:1.00
 OD1 B:ASP115 2.0 47.5 1.0
OE1 B:GLU248 2.0 47.6 1.0
OD1 B:ASP104 2.0 41.8 1.0
O B:HOH410 2.1 54.6 1.0
CG B:ASP115 2.8 44.5 1.0
CG B:ASP104 2.9 42.5 1.0
OD2 B:ASP115 3.0 46.8 1.0
CD B:GLU248 3.1 44.5 1.0
OD2 B:ASP104 3.1 44.3 1.0
MG B:MG267 3.3 38.5 1.0
OE2 B:GLU248 3.4 47.1 1.0
CZ B:PHE66 4.0 40.4 1.0
O B:SER116 4.0 38.4 1.0
N B:SER116 4.1 36.2 1.0
CB B:ASP115 4.1 39.2 1.0
OE1 B:GLU217 4.2 50.5 1.0
C B:SER116 4.3 35.9 1.0
CB B:ASP104 4.3 41.4 1.0
CG B:GLU248 4.4 39.8 1.0
C B:ASP115 4.4 37.1 1.0
O B:CYS105 4.4 38.4 1.0
N B:CYS105 4.5 39.7 1.0
CA B:ASP115 4.6 36.4 1.0
CE1 B:HIS246 4.6 39.5 1.0
CB B:ALA117 4.6 35.3 1.0
CA B:SER116 4.6 36.0 1.0
O B:HOH332 4.7 51.2 1.0
OE2 B:GLU217 4.7 49.4 1.0
CB B:GLU248 4.7 38.3 1.0
CD B:GLU217 4.7 49.4 1.0
CE1 B:PHE66 4.8 41.9 1.0
CA B:ASP104 4.8 39.1 1.0
CE2 B:PHE66 4.9 42.4 1.0
NE2 B:HIS246 4.9 41.1 1.0
C B:ASP104 5.0 39.0 1.0
N B:ALA117 5.0 37.2 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: Mon Dec 14 08:54:00 2020

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