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Magnesium in PDB 5j84: Crystal Structure of L-Arabinonate Dehydratase in Holo-Form

Enzymatic activity of Crystal Structure of L-Arabinonate Dehydratase in Holo-Form

All present enzymatic activity of Crystal Structure of L-Arabinonate Dehydratase in Holo-Form:
4.2.1.9;

Protein crystallography data

The structure of Crystal Structure of L-Arabinonate Dehydratase in Holo-Form, PDB code: 5j84 was solved by M.M.Rahman, J.Rouvinen, N.Hakulinen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.89 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 106.070, 208.610, 147.090, 90.00, 90.43, 90.00
R / Rfree (%) 15.6 / 18.5

Other elements in 5j84:

The structure of Crystal Structure of L-Arabinonate Dehydratase in Holo-Form also contains other interesting chemical elements:

Iron (Fe) 16 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form (pdb code 5j84). 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 L-Arabinonate Dehydratase in Holo-Form, PDB code: 5j84:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5j84

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Magnesium binding site 1 out of 8 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


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 L-Arabinonate Dehydratase in Holo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:43.5
occ:1.00
 O A:HOH769 2.1 31.7 1.0
OE2 A:GLU453 2.2 34.9 1.0
OD2 A:ASP128 2.2 42.6 1.0
OE1 A:GLU91 2.3 70.7 1.0
OQ1 A:KCX129 2.4 35.0 1.0
CD A:GLU91 2.6 52.7 1.0
CD A:GLU453 2.9 33.4 1.0
OE1 A:GLU453 3.0 67.1 1.0
CG A:GLU91 3.2 40.3 1.0
OE2 A:GLU91 3.3 44.1 1.0
CG A:ASP128 3.3 51.7 1.0
CX A:KCX129 3.4 39.3 1.0
NZ A:KCX129 3.8 66.8 1.0
O A:HOH816 4.0 30.4 1.0
CB A:ASP128 4.0 38.2 1.0
OG1 A:THR205 4.2 27.5 1.0
OD1 A:ASP128 4.3 53.3 1.0
CB A:GLU91 4.3 44.1 1.0
CG A:GLU453 4.3 29.8 1.0
OQ2 A:KCX129 4.5 65.4 1.0
OG A:SER480 4.5 37.7 1.0
ND2 A:ASN278 4.5 44.0 1.0
CA A:SER480 4.6 32.5 1.0
CB A:THR205 4.6 23.8 1.0
CB A:SER480 4.8 20.1 1.0
NH1 A:ARG478 4.8 33.5 1.0
N A:GLY481 4.9 48.0 1.0

Magnesium binding site 2 out of 8 in 5j84

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Magnesium binding site 2 out of 8 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


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 L-Arabinonate Dehydratase in Holo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:45.0
occ:1.00
 O B:HOH814 2.1 39.5 1.0
OE1 B:GLU91 2.1 54.1 1.0
OE2 B:GLU453 2.1 41.6 1.0
OD2 B:ASP128 2.2 41.9 1.0
OQ1 B:KCX129 2.3 57.7 1.0
CD B:GLU453 3.1 43.6 1.0
CG B:ASP128 3.1 48.6 1.0
CD B:GLU91 3.2 66.0 1.0
OE1 B:GLU453 3.4 61.4 1.0
CX B:KCX129 3.5 36.7 1.0
OG1 B:THR205 3.6 25.9 1.0
ND2 B:ASN278 3.7 50.1 1.0
CG B:GLU91 3.8 51.9 1.0
CB B:ASP128 3.8 41.5 1.0
OD1 B:ASP128 4.0 51.2 1.0
CB B:THR205 4.0 31.1 1.0
O B:HOH838 4.1 49.1 1.0
OE2 B:GLU91 4.3 61.8 1.0
NZ B:KCX129 4.3 50.4 1.0
OQ2 B:KCX129 4.3 46.6 1.0
CG B:GLU453 4.5 35.6 1.0
CA B:SER480 4.5 34.4 1.0
NH1 B:ARG478 4.5 36.3 1.0
OG B:SER480 4.7 47.4 1.0
CB B:GLU91 4.7 41.6 1.0
CG2 B:THR205 4.7 33.6 1.0
N B:GLY481 4.7 42.4 1.0
O B:HOH702 4.7 30.7 1.0
CG B:ASN278 4.8 28.7 1.0
CB B:SER480 4.9 40.4 1.0
O B:HOH868 5.0 33.4 1.0

Magnesium binding site 3 out of 8 in 5j84

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Magnesium binding site 3 out of 8 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


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 L-Arabinonate Dehydratase in Holo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:29.9
occ:1.00
 O C:HOH719 2.1 17.3 1.0
OE1 C:GLU91 2.1 54.7 1.0
OQ2 C:KCX129 2.2 29.7 1.0
OD2 C:ASP128 2.3 40.6 1.0
OE2 C:GLU453 2.3 42.9 1.0
OG1 C:THR205 2.3 31.4 1.0
CD C:GLU91 3.0 72.9 1.0
CB C:THR205 3.1 25.9 1.0
CG C:ASP128 3.3 44.1 1.0
CD C:GLU453 3.3 49.1 1.0
ND2 C:ASN278 3.3 50.2 1.0
CX C:KCX129 3.4 36.3 1.0
OE2 C:GLU91 3.5 73.2 1.0
OE1 C:GLU453 3.6 61.3 1.0
CG2 C:THR205 3.9 28.9 1.0
OD1 C:ASP128 4.0 52.1 1.0
CB C:ASP128 4.0 36.9 1.0
OQ1 C:KCX129 4.2 34.5 1.0
CG C:GLU91 4.3 40.4 1.0
NZ C:KCX129 4.3 41.1 1.0
N C:GLY481 4.3 37.4 1.0
CA C:SER480 4.3 37.0 1.0
CA C:THR205 4.4 21.6 1.0
N C:THR205 4.4 27.3 1.0
OG C:SER480 4.5 46.9 1.0
CG C:ASN278 4.5 31.0 1.0
CG C:GLU453 4.6 29.3 1.0
NH1 C:ARG478 4.7 37.4 1.0
CB C:SER480 4.8 32.7 1.0
C C:SER480 4.9 35.2 1.0

Magnesium binding site 4 out of 8 in 5j84

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Magnesium binding site 4 out of 8 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


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 L-Arabinonate Dehydratase in Holo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:45.2
occ:1.00
 OQ2 D:KCX129 2.1 39.9 1.0
OE2 D:GLU453 2.1 35.7 1.0
O D:HOH816 2.1 21.7 1.0
OD2 D:ASP128 2.2 49.1 1.0
OE1 D:GLU91 2.3 57.4 1.0
CD D:GLU453 3.0 45.1 1.0
CD D:GLU91 3.0 54.5 1.0
OE1 D:GLU453 3.1 58.1 1.0
CX D:KCX129 3.2 37.6 1.0
CG D:ASP128 3.3 37.8 1.0
OG1 D:THR205 3.4 26.6 1.0
OE2 D:GLU91 3.7 57.6 1.0
CG D:GLU91 3.8 35.5 1.0
NZ D:KCX129 3.8 34.8 1.0
ND2 D:ASN278 4.0 40.7 1.0
CB D:THR205 4.1 24.9 1.0
CB D:ASP128 4.1 40.4 1.0
OD1 D:ASP128 4.1 58.5 1.0
OQ1 D:KCX129 4.2 41.6 1.0
CA D:SER480 4.4 34.4 1.0
CG D:GLU453 4.4 30.7 1.0
OG D:SER480 4.5 35.1 1.0
N D:GLY481 4.6 27.9 1.0
NH1 D:ARG478 4.6 33.7 1.0
CB D:SER480 4.7 26.7 1.0
O D:HOH783 4.8 20.3 1.0
CG2 D:THR205 4.9 29.2 1.0

Magnesium binding site 5 out of 8 in 5j84

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Magnesium binding site 5 out of 8 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


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 L-Arabinonate Dehydratase in Holo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:33.5
occ:1.00
 O E:HOH785 2.1 37.0 1.0
O E:HOH790 2.1 23.1 1.0
OE1 E:GLU91 2.2 68.4 1.0
OE2 E:GLU453 2.2 37.4 1.0
OD2 E:ASP128 2.2 40.0 1.0
OQ2 E:KCX129 2.3 41.9 1.0
CG E:ASP128 3.1 43.6 1.0
CD E:GLU453 3.2 35.9 1.0
CD E:GLU91 3.3 55.9 1.0
CX E:KCX129 3.5 23.9 1.0
OG1 E:THR205 3.5 30.3 1.0
OE1 E:GLU453 3.5 59.8 1.0
CB E:ASP128 3.8 34.1 1.0
ND2 E:ASN278 3.8 52.3 1.0
CG E:GLU91 3.9 43.0 1.0
OD1 E:ASP128 3.9 59.1 1.0
NZ E:KCX129 3.9 25.3 1.0
CB E:THR205 4.0 36.0 1.0
OE2 E:GLU91 4.4 47.9 1.0
OQ1 E:KCX129 4.5 31.2 1.0
CA E:SER480 4.5 33.8 1.0
CG E:GLU453 4.5 31.0 1.0
NH1 E:ARG478 4.6 37.0 1.0
OG E:SER480 4.6 41.4 1.0
N E:GLY481 4.7 32.0 1.0
CG2 E:THR205 4.7 28.0 1.0
CB E:GLU91 4.8 43.7 1.0
CB E:SER480 4.9 29.6 1.0
CG E:ASN278 5.0 34.1 1.0
O E:HOH707 5.0 32.5 1.0

Magnesium binding site 6 out of 8 in 5j84

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Magnesium binding site 6 out of 8 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


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 L-Arabinonate Dehydratase in Holo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:47.2
occ:1.00
 O F:HOH729 2.1 40.1 1.0
OE2 F:GLU453 2.1 44.1 1.0
O F:HOH758 2.1 43.1 1.0
OD2 F:ASP128 2.1 41.0 1.0
OE1 F:GLU91 2.1 65.3 1.0
OQ2 F:KCX129 2.3 50.1 1.0
CD F:GLU453 3.0 54.8 1.0
CD F:GLU91 3.0 59.4 1.0
OE1 F:GLU453 3.2 62.1 1.0
CG F:ASP128 3.2 51.6 1.0
CG F:GLU91 3.3 49.2 1.0
CX F:KCX129 3.3 34.0 1.0
NZ F:KCX129 3.7 32.1 1.0
O F:HOH812 3.8 21.2 1.0
CB F:ASP128 3.8 40.7 1.0
CB F:GLU91 4.0 38.5 1.0
OG1 F:THR205 4.1 39.4 1.0
OD1 F:ASP128 4.1 50.8 1.0
OE2 F:GLU91 4.1 43.7 1.0
CG F:GLU453 4.4 34.5 1.0
OQ1 F:KCX129 4.4 55.4 1.0
CB F:THR205 4.6 39.8 1.0
ND2 F:ASN278 4.7 49.0 1.0
OG F:SER480 4.7 44.4 1.0
NH1 F:ARG478 4.8 38.7 1.0
CA F:SER480 4.8 24.4 1.0

Magnesium binding site 7 out of 8 in 5j84

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Magnesium binding site 7 out of 8 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


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 L-Arabinonate Dehydratase in Holo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg601

b:58.4
occ:1.00
 O G:HOH788 2.1 34.0 1.0
OE2 G:GLU91 2.1 75.0 1.0
OE2 G:GLU453 2.1 49.8 1.0
OD2 G:ASP128 2.2 42.8 1.0
OQ1 G:KCX129 2.5 71.6 1.0
CD G:GLU453 3.0 58.3 1.0
CD G:GLU91 3.1 62.5 1.0
OE1 G:GLU453 3.2 55.2 1.0
CG G:ASP128 3.3 53.2 1.0
O G:HOH810 3.4 31.7 1.0
CX G:KCX129 3.7 72.7 1.0
CG G:GLU91 3.8 43.9 1.0
OG1 G:THR205 3.9 45.1 1.0
OE1 G:GLU91 4.1 69.8 1.0
OG G:SER480 4.1 52.8 1.0
OD1 G:ASP128 4.1 65.3 1.0
CB G:ASP128 4.2 32.4 1.0
NZ G:KCX129 4.3 75.3 1.0
CB G:THR205 4.4 30.5 1.0
CB G:GLU91 4.4 50.7 1.0
CG G:GLU453 4.4 37.4 1.0
CA G:SER480 4.5 38.6 1.0
O G:HOH725 4.5 25.3 1.0
CB G:SER480 4.5 33.3 1.0
OQ2 G:KCX129 4.6 38.0 1.0
ND2 G:ASN278 4.7 48.8 1.0
N G:GLY481 4.7 41.1 1.0
FE2 G:FES602 4.8 62.6 1.0

Magnesium binding site 8 out of 8 in 5j84

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Magnesium binding site 8 out of 8 in the Crystal Structure of L-Arabinonate Dehydratase in Holo-Form


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 L-Arabinonate Dehydratase in Holo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg601

b:37.8
occ:1.00
 OE2 H:GLU453 2.0 42.0 1.0
O H:HOH715 2.1 41.2 1.0
O H:HOH787 2.1 28.2 1.0
OE1 H:GLU91 2.2 66.3 1.0
OD2 H:ASP128 2.2 44.6 1.0
OQ1 H:KCX129 2.4 75.5 1.0
CD H:GLU453 2.9 41.9 1.0
CD H:GLU91 2.9 62.6 1.0
OE1 H:GLU453 3.1 59.4 1.0
CG H:ASP128 3.2 42.5 1.0
CG H:GLU91 3.2 46.9 1.0
CX H:KCX129 3.5 58.9 1.0
CB H:ASP128 3.9 32.7 1.0
OG1 H:THR205 3.9 40.1 1.0
O H:HOH797 3.9 22.9 1.0
OE2 H:GLU91 4.0 58.7 1.0
NZ H:KCX129 4.1 25.7 1.0
CB H:GLU91 4.2 37.9 1.0
OD1 H:ASP128 4.2 57.5 1.0
CG H:GLU453 4.3 24.6 1.0
ND2 H:ASN278 4.4 42.2 1.0
CB H:THR205 4.4 31.4 1.0
OG H:SER480 4.4 41.6 1.0
CA H:SER480 4.5 27.8 1.0
OQ2 H:KCX129 4.5 31.9 1.0
CB H:SER480 4.7 30.9 1.0
NH1 H:ARG478 4.7 40.3 1.0
N H:GLY481 4.8 37.8 1.0
O H:HOH753 4.9 20.9 1.0

Reference:

M.M.Rahman, M.Andberg, S.K.Thangaraj, T.Parkkinen, M.Penttila, J.Janis, A.Koivula, J.Rouvinen, N.Hakulinen. The Crystal Structure of A Bacterial L-Arabinonate Dehydratase Contains A [2FE-2S] Cluster. Acs Chem. Biol. V. 12 1919 2017.
ISSN: ESSN 1554-8937
PubMed: 28574691
DOI: 10.1021/ACSCHEMBIO.7B00304
Page generated: Sun Sep 29 17:37:28 2024

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