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Magnesium in PDB 3ppi: Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium

Enzymatic activity of Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium

All present enzymatic activity of Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium:
1.1.1.178; 1.1.1.35;

Protein crystallography data

The structure of Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium, PDB code: 3ppi 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 (°) 118.810, 161.150, 65.570, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 17.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium (pdb code 3ppi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium, PDB code: 3ppi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3ppi

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Magnesium binding site 1 out of 8 in the Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium


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 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg300

b:39.8
occ:1.00
 O A:ALA56 2.2 34.5 1.0
O A:GLY53 2.3 39.1 1.0
O A:HOH714 2.4 37.4 1.0
O A:HOH715 2.4 43.2 1.0
O A:HOH712 2.5 38.7 1.0
O A:ALA49 2.6 35.7 1.0
C A:GLY53 3.2 40.4 1.0
C A:ALA49 3.4 36.1 1.0
C A:ALA56 3.4 33.8 1.0
CB A:ALA49 4.0 34.7 1.0
CA A:GLY53 4.0 40.1 1.0
N A:ASN54 4.1 41.4 1.0
CA A:ALA49 4.1 34.4 1.0
N A:GLY53 4.1 39.0 1.0
CA A:ASN54 4.1 42.4 1.0
N A:ASP50 4.2 37.6 1.0
CA A:ALA56 4.2 33.3 1.0
N A:ALA56 4.2 34.4 1.0
OE2 A:GLU57 4.3 45.6 1.0
CB A:ALA56 4.4 32.5 1.0
N A:GLU57 4.4 32.7 1.0
CA A:ASP50 4.4 39.7 1.0
O A:HOH716 4.5 37.0 1.0
CD A:GLU57 4.5 42.9 1.0
CA A:GLU57 4.6 33.8 1.0
C A:ASN54 4.6 40.8 1.0
OE1 A:GLU57 4.8 45.3 1.0
OD1 A:ASP50 4.8 44.2 1.0

Magnesium binding site 2 out of 8 in 3ppi

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Magnesium binding site 2 out of 8 in the Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium


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 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:58.6
occ:1.00
 O A:HOH868 2.3 33.1 1.0
O A:HOH286 2.4 32.5 1.0
O A:HOH270 2.4 21.3 1.0
O A:GLY15 2.6 23.5 1.0
O A:GLY18 2.6 22.8 1.0
C A:GLY18 3.4 23.9 1.0
C A:GLY15 3.4 23.0 1.0
N A:GLY18 3.7 26.6 1.0
CA A:GLY15 3.7 22.2 1.0
O A:HOH291 3.8 20.2 1.0
CA A:GLY18 3.9 25.8 1.0
O A:HOH869 3.9 49.9 1.0
OD2 A:ASP39 4.1 25.7 1.0
N A:GLY19 4.3 23.3 1.0
O A:HOH870 4.5 30.9 1.0
N A:GLY21 4.5 20.6 1.0
O A:ALA88 4.6 23.2 1.0
N A:GLY16 4.6 23.3 1.0
CA A:GLY19 4.7 22.0 1.0
N A:ALA17 4.7 26.1 1.0
C A:ALA17 4.8 27.8 1.0
N A:GLY90 4.8 29.9 1.0
CA A:GLY21 4.8 21.1 1.0
N A:LEU20 5.0 20.1 1.0

Magnesium binding site 3 out of 8 in 3ppi

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Magnesium binding site 3 out of 8 in the Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium


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 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg300

b:22.8
occ:1.00
 O B:ALA56 2.3 19.2 1.0
O B:HOH643 2.4 20.6 1.0
O B:GLY53 2.4 23.1 1.0
O B:HOH477 2.4 27.4 1.0
O B:ALA49 2.4 20.4 1.0
O B:HOH644 2.5 30.8 1.0
C B:ALA49 3.2 20.9 1.0
C B:GLY53 3.3 25.2 1.0
C B:ALA56 3.5 19.8 1.0
CB B:ALA49 3.9 19.7 1.0
CA B:ALA49 3.9 19.7 1.0
CA B:GLY53 4.0 24.9 1.0
N B:ASP50 4.0 22.3 1.0
N B:GLY53 4.0 24.8 1.0
N B:ASN54 4.1 26.0 1.0
CA B:ASP50 4.2 23.8 1.0
CA B:ASN54 4.2 26.6 0.6
CA B:ALA56 4.2 19.6 1.0
N B:ALA56 4.3 20.2 1.0
CB B:ALA56 4.4 18.5 1.0
CA B:ASN54 4.4 26.4 0.4
OE2 B:GLU57 4.4 32.1 1.0
O B:HOH338 4.4 20.7 1.0
N B:GLU57 4.5 19.4 1.0
OD1 B:ASP50 4.5 28.4 1.0
CA B:GLU57 4.7 20.3 1.0
C B:ASN54 4.7 25.9 1.0
CD B:GLU57 4.8 27.9 1.0
O B:HOH754 4.8 39.7 1.0
C B:ASP50 4.9 24.1 1.0

Magnesium binding site 4 out of 8 in 3ppi

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Magnesium binding site 4 out of 8 in the Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium


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 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:44.6
occ:1.00
 O B:HOH323 2.3 28.4 1.0
O B:HOH307 2.3 18.2 1.0
O B:GLY15 2.4 13.1 1.0
O B:HOH329 2.6 42.3 1.0
O B:GLY18 2.6 14.3 1.0
O B:HOH427 2.8 40.2 1.0
C B:GLY15 3.3 13.1 1.0
C B:GLY18 3.4 14.8 1.0
CA B:GLY15 3.6 12.7 1.0
N B:GLY18 3.7 15.8 1.0
O B:HOH872 3.9 40.6 1.0
CA B:GLY18 3.9 15.8 1.0
O B:HOH277 3.9 13.6 1.0
OD2 B:ASP39 4.1 16.1 1.0
O B:ALA88 4.3 16.2 1.0
N B:GLY21 4.4 11.4 1.0
N B:GLY19 4.4 14.4 1.0
N B:GLY16 4.6 12.7 1.0
CA B:GLY21 4.6 12.0 1.0
O B:HOH577 4.7 32.2 1.0
CA B:GLY19 4.7 14.0 1.0
N B:ALA17 4.7 15.1 1.0
N B:LEU20 4.9 12.7 1.0
C B:ALA17 4.9 16.3 1.0
C B:GLY19 5.0 13.1 1.0

Magnesium binding site 5 out of 8 in 3ppi

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Magnesium binding site 5 out of 8 in the Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg300

b:22.0
occ:1.00
 O C:ALA56 2.3 18.7 1.0
O C:GLY53 2.3 22.4 1.0
O C:HOH260 2.4 23.6 1.0
O C:HOH781 2.4 27.0 1.0
O C:HOH825 2.4 40.8 1.0
O C:ALA49 2.6 20.5 1.0
C C:GLY53 3.2 23.6 1.0
C C:ALA49 3.4 20.6 1.0
O C:HOH264 3.4 27.5 1.0
C C:ALA56 3.5 18.4 1.0
CA C:GLY53 3.9 23.2 1.0
N C:GLY53 4.0 22.7 1.0
CB C:ALA49 4.1 19.3 1.0
CA C:ALA49 4.1 19.9 1.0
N C:ASP50 4.2 22.1 1.0
N C:ASN54 4.2 24.2 1.0
N C:ALA56 4.2 17.6 1.0
CA C:ALA56 4.2 17.9 1.0
CB C:ALA56 4.3 18.2 1.0
CA C:ASP50 4.4 23.7 1.0
O C:HOH540 4.4 41.1 1.0
OE2 C:GLU57 4.5 37.2 1.0
O C:HOH599 4.5 20.3 1.0
CA C:ASN54 4.5 24.4 1.0
N C:GLU57 4.5 18.5 1.0
O C:HOH529 4.6 35.6 1.0
C C:ASN54 4.6 23.3 1.0
OD1 C:ASP50 4.7 29.7 1.0
CA C:GLU57 4.7 19.9 1.0
O C:HOH782 4.8 42.4 1.0
O C:ASN54 4.8 24.8 1.0

Magnesium binding site 6 out of 8 in 3ppi

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Magnesium binding site 6 out of 8 in the Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:26.8
occ:1.00
 O C:HOH673 2.3 17.2 1.0
O C:GLY15 2.3 15.4 1.0
O C:HOH775 2.4 29.7 1.0
O C:HOH671 2.5 25.6 1.0
O C:GLY18 2.5 16.8 1.0
O C:HOH419 2.5 28.4 1.0
C C:GLY15 3.3 15.6 1.0
C C:GLY18 3.4 17.8 1.0
CA C:GLY15 3.6 15.8 1.0
N C:GLY18 3.8 18.8 1.0
CA C:GLY18 4.0 18.7 1.0
O C:HOH270 4.0 12.2 1.0
OD2 C:ASP39 4.2 17.3 1.0
N C:GLY21 4.2 15.9 1.0
N C:GLY19 4.3 17.5 1.0
O C:HOH774 4.3 40.2 1.0
O C:ALA88 4.4 19.7 1.0
CA C:GLY21 4.5 15.7 1.0
O C:HOH670 4.5 28.3 1.0
N C:GLY16 4.5 15.2 1.0
CA C:GLY19 4.5 17.2 1.0
N C:LEU20 4.7 16.3 1.0
N C:ALA17 4.7 17.0 1.0
C C:GLY19 4.8 16.8 1.0
N C:GLY90 4.8 28.1 1.0
N C:GLU22 4.9 15.6 1.0
C C:ALA17 5.0 19.1 1.0

Magnesium binding site 7 out of 8 in 3ppi

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Magnesium binding site 7 out of 8 in the Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg300

b:25.0
occ:1.00
 O D:ALA56 2.3 17.0 1.0
O D:GLY53 2.4 20.0 1.0
O D:HOH690 2.4 26.5 1.0
O D:HOH689 2.4 28.5 1.0
O D:ALA49 2.5 17.7 1.0
O D:HOH691 2.6 21.2 1.0
C D:GLY53 3.2 21.5 1.0
C D:ALA49 3.2 17.8 1.0
C D:ALA56 3.5 17.3 1.0
CB D:ALA49 3.8 17.0 1.0
CA D:GLY53 3.9 21.1 1.0
CA D:ALA49 3.9 17.1 1.0
N D:GLY53 4.0 20.3 1.0
N D:ASP50 4.0 18.2 1.0
N D:ASN54 4.1 22.6 1.0
CA D:ASN54 4.2 23.6 1.0
CA D:ALA56 4.3 17.2 1.0
N D:ALA56 4.3 18.4 1.0
CA D:ASP50 4.3 19.6 1.0
CB D:ALA56 4.4 17.2 1.0
N D:GLU57 4.5 16.2 1.0
O D:HOH327 4.5 25.8 1.0
OE2 D:GLU57 4.6 28.3 1.0
CA D:GLU57 4.7 16.9 1.0
OD1 D:ASP50 4.8 18.7 1.0
O D:HOH263 4.8 22.3 1.0
CD D:GLU57 4.8 23.1 1.0
C D:ASN54 4.8 23.0 1.0
C D:ASP50 5.0 19.8 1.0

Magnesium binding site 8 out of 8 in 3ppi

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Magnesium binding site 8 out of 8 in the Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of 3-Hydroxyacyl-Coa Dehydrogenase Type-2 From Mycobacterium Avium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:24.0
occ:1.00
 O D:HOH860 2.3 28.8 1.0
O D:HOH681 2.3 14.6 1.0
O D:GLY18 2.4 14.0 1.0
O D:GLY15 2.4 14.6 1.0
O D:HOH679 2.5 19.1 1.0
O D:HOH682 2.5 21.2 1.0
C D:GLY18 3.2 15.8 1.0
C D:GLY15 3.4 14.3 1.0
N D:GLY18 3.7 17.0 1.0
CA D:GLY15 3.7 14.4 1.0
CA D:GLY18 3.9 16.7 1.0
O D:HOH261 4.0 14.6 1.0
N D:GLY21 4.1 13.6 1.0
N D:GLY19 4.2 15.4 1.0
O D:HOH299 4.2 33.8 1.0
OD2 D:ASP39 4.3 15.8 1.0
CA D:GLY19 4.4 14.5 1.0
O D:ALA88 4.5 17.7 1.0
CA D:GLY21 4.5 13.2 1.0
N D:GLY16 4.6 14.1 1.0
O D:HOH683 4.6 21.3 1.0
O D:HOH610 4.6 37.3 1.0
N D:LEU20 4.6 14.1 1.0
C D:GLY19 4.7 14.5 1.0
N D:ALA17 4.7 15.7 1.0
N D:GLY90 4.8 23.9 1.0
N D:GLU22 4.8 14.2 1.0
C D:ALA17 4.9 17.6 1.0
C D:GLY16 5.0 14.9 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: Mon Dec 14 08:40:39 2020

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