Magnesium in PDB 9evv: HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate

Enzymatic activity of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate

All present enzymatic activity of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate:
4.2.1.25; 4.2.1.6; 4.2.1.67;

Protein crystallography data

The structure of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate, PDB code: 9evv was solved by Y.Ren, J.Rouvinen, N.Hakulinen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.48 / 2.44
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 107.947, 148.211, 165.025, 90, 90, 90
R / Rfree (%) 18.5 / 23.7

Other elements in 9evv:

The structure of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate (pdb code 9evv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate, PDB code: 9evv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 9evv

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Magnesium binding site 1 out of 4 in the HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:40.1
occ:1.00
 OQ2 A:KCX129 2.0 40.3 1.0
O A:HOH743 2.1 37.3 1.0
OE2 A:GLU453 2.1 37.6 1.0
OE2 A:GLU91 2.2 35.7 1.0
O A:HOH745 2.2 27.1 1.0
OD2 A:ASP128 2.2 37.5 1.0
CD A:GLU453 3.1 38.3 1.0
CX A:KCX129 3.2 43.9 1.0
CD A:GLU91 3.3 43.0 1.0
CG A:ASP128 3.4 39.0 1.0
OG1 A:THR205 3.4 27.5 1.0
OE1 A:GLU453 3.4 43.2 1.0
O A:HOH763 3.7 37.4 1.0
NZ A:KCX129 3.9 45.3 1.0
ND2 A:ASN278 3.9 37.3 1.0
CB A:THR205 4.0 38.6 1.0
OQ1 A:KCX129 4.1 44.0 1.0
CB A:ASP128 4.1 39.5 1.0
OE1 A:GLU91 4.2 45.6 1.0
CG A:GLU91 4.2 43.0 1.0
OD1 A:ASP128 4.2 45.5 1.0
OG A:SER480 4.3 35.8 1.0
N A:GLY481 4.3 33.0 1.0
CA A:SER480 4.4 34.0 1.0
CG A:GLU453 4.5 34.0 1.0
CB A:SER480 4.6 39.5 1.0
NH1 A:ARG478 4.8 38.6 1.0
CG2 A:THR205 4.8 32.3 1.0
O A:HOH723 4.8 39.2 1.0
C A:SER480 4.9 36.0 1.0
O B:HOH791 4.9 46.0 1.0

Magnesium binding site 2 out of 4 in 9evv

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Magnesium binding site 2 out of 4 in the HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:40.5
occ:1.00
 OE2 B:GLU453 2.1 42.0 1.0
OE2 B:GLU91 2.2 42.2 1.0
OD2 B:ASP128 2.2 42.1 1.0
OQ2 B:KCX129 2.3 41.5 1.0
O B:HOH730 2.4 41.1 1.0
O B:HOH717 2.7 33.7 1.0
CD B:GLU453 3.1 43.1 1.0
CD B:GLU91 3.1 45.2 1.0
CG B:ASP128 3.3 36.5 1.0
OE1 B:GLU453 3.4 40.9 1.0
CX B:KCX129 3.4 42.1 1.0
OG1 B:THR205 3.5 41.0 1.0
O B:HOH727 3.8 45.4 1.0
CG B:GLU91 3.9 42.6 1.0
NZ B:KCX129 3.9 37.0 1.0
OE1 B:GLU91 3.9 46.3 1.0
CB B:ASP128 4.0 34.9 1.0
CB B:THR205 4.1 36.2 1.0
ND2 B:ASN278 4.1 33.2 1.0
OD1 B:ASP128 4.2 36.6 1.0
OQ1 B:KCX129 4.4 32.0 1.0
CG B:GLU453 4.4 41.9 1.0
NH1 B:ARG478 4.5 34.3 1.0
OG B:SER480 4.5 44.6 1.0
CA B:SER480 4.7 39.9 1.0
N B:GLY481 4.7 36.7 1.0
CG2 B:THR205 4.7 37.5 1.0

Magnesium binding site 3 out of 4 in 9evv

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Magnesium binding site 3 out of 4 in the HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:41.6
occ:1.00
 O C:HOH738 2.1 47.4 1.0
OD2 C:ASP128 2.2 49.7 1.0
OE2 C:GLU91 2.2 51.5 1.0
OE2 C:GLU453 2.3 43.5 1.0
OQ2 C:KCX129 2.3 38.7 1.0
O C:HOH711 2.7 30.8 1.0
CD C:GLU453 3.1 46.6 1.0
OE1 C:GLU453 3.1 45.7 1.0
OG1 C:THR205 3.2 37.4 1.0
CG C:ASP128 3.3 45.1 1.0
CD C:GLU91 3.4 54.3 1.0
CX C:KCX129 3.4 42.8 1.0
NZ C:KCX129 3.9 39.7 1.0
ND2 C:ASN278 4.0 47.5 1.0
O C:HOH812 4.0 43.3 1.0
CG C:GLU91 4.1 45.0 1.0
CB C:THR205 4.1 42.9 1.0
CB C:ASP128 4.1 42.8 1.0
OD1 C:ASP128 4.2 40.5 1.0
OE1 C:GLU91 4.4 56.1 1.0
CA C:SER480 4.4 44.9 1.0
OQ1 C:KCX129 4.5 41.7 1.0
N C:GLY481 4.5 42.0 1.0
CG C:GLU453 4.5 49.1 1.0
OG C:SER480 4.6 51.7 1.0
NH1 C:ARG478 4.6 33.7 1.0
CB C:SER480 4.8 49.7 1.0
CG2 C:THR205 4.8 43.6 1.0
O C:HOH809 4.9 41.3 1.0
CB C:GLU91 4.9 41.7 1.0

Magnesium binding site 4 out of 4 in 9evv

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Magnesium binding site 4 out of 4 in the HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of HIS579LEU Variant of L-Arabinonate Dehydratase Co-Crystallized with 2- Oxobutyrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:34.0
occ:1.00
 O3 D:2KT603 2.0 45.1 1.0
OXT D:2KT603 2.1 38.2 1.0
OD2 D:ASP128 2.1 39.1 1.0
OE2 D:GLU91 2.1 41.7 1.0
OQ2 D:KCX129 2.1 39.9 1.0
OE2 D:GLU453 2.2 39.1 1.0
C D:2KT603 2.6 48.1 1.0
C2 D:2KT603 2.6 55.2 1.0
CD D:GLU91 2.9 42.8 1.0
CD D:GLU453 3.1 38.3 1.0
CG D:ASP128 3.2 42.0 1.0
CX D:KCX129 3.2 40.3 1.0
OE1 D:GLU453 3.3 39.5 1.0
OG1 D:THR205 3.6 32.3 1.0
NZ D:KCX129 3.6 42.1 1.0
CG D:GLU91 3.7 34.8 1.0
O D:2KT603 3.7 32.1 1.0
OE1 D:GLU91 3.7 41.2 1.0
CB D:ASP128 3.9 40.2 1.0
CB D:THR205 4.1 34.4 1.0
OD1 D:ASP128 4.1 45.5 1.0
C3 D:2KT603 4.1 48.9 1.0
OQ1 D:KCX129 4.3 33.1 1.0
ND2 D:ASN278 4.5 31.9 1.0
CG D:GLU453 4.5 34.2 1.0
H32 D:2KT603 4.6 58.7 1.0
H43 D:2KT603 4.6 54.5 1.0
H31 D:2KT603 4.7 58.7 1.0
NH1 D:ARG478 4.7 38.1 1.0
O D:HOH718 4.8 35.9 1.0
O D:HOH707 4.8 39.6 1.0
CG2 D:THR205 4.8 34.9 1.0
C4 D:2KT603 4.9 45.4 1.0
CB D:GLU91 4.9 34.2 1.0
CA D:SER480 4.9 35.3 1.0
H42 D:2KT603 5.0 54.5 1.0

Reference:

Y.Ren, E.Vettenranta, L.Penttinen, M.Blomster Andberg, A.Koivula, J.Rouvinen, N.Hakulinen. Unveiling the Importance of the C-Terminus in the Sugar Acid Dehydratase of the Ilvd/Edd Superfamily. Appl.Microbiol.Biotechnol. V. 108 436 2024.
ISSN: ESSN 1432-0614
PubMed: 39126499
DOI: 10.1007/S00253-024-13270-8
Page generated: Sat Oct 5 08:59:30 2024

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