Magnesium in PDB 5uds: Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Mgatp

The structure of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Mgatp, PDB code: 5uds was solved by M.Fellner, B.Desguin, R.P.Hausinger, J.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.63 / 2.37
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	107.724, 107.724, 318.054, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 25.7

The binding sites of Magnesium atom in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Mgatp (pdb code 5uds). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Mgatp, PDB code: 5uds:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Mgatp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Mgatp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:50.3 occ:1.00 O2B A:ATP501 1.9 30.4 0.8 O3G A:ATP501 2.3 32.5 0.8 PB A:ATP501 3.3 34.8 0.8 PG A:ATP501 3.5 34.8 0.8 O2A A:ATP501 3.5 43.9 0.8 O3B A:ATP501 3.7 40.9 0.8 OG A:SER26 3.9 39.6 1.0 O3A A:ATP501 4.1 44.2 0.8 O2G A:ATP501 4.2 36.4 0.8 PA A:ATP501 4.3 42.0 0.8 O1B A:ATP501 4.4 40.7 0.8 CA A:GLY28 4.6 32.6 1.0 O1G A:ATP501 4.7 40.1 0.8 CB A:SER26 4.7 37.4 1.0 O5' A:ATP501 4.9 44.4 0.8 N A:GLY28 5.0 42.5 1.0

Magnesium binding site 2 out of 6 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Mgatp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Mgatp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:36.4 occ:1.00 O B:HOH658 1.9 40.0 1.0 O3G B:ATP501 2.3 32.0 0.8 O B:HOH645 2.4 36.2 1.0 O2B B:ATP501 2.5 36.2 0.8 O2A B:ATP501 2.7 34.0 0.8 OG B:SER26 3.6 25.5 1.0 PG B:ATP501 3.6 29.8 0.8 PB B:ATP501 3.7 33.5 0.8 O3B B:ATP501 3.9 33.7 0.8 PA B:ATP501 3.9 37.8 0.8 CB B:SER26 4.0 23.6 1.0 O B:HOH669 4.2 38.5 1.0 O3A B:ATP501 4.2 37.5 0.8 O1G B:ATP501 4.3 34.4 0.8 O B:HOH664 4.4 34.3 1.0 O5' B:ATP501 4.5 36.3 0.8 O2G B:ATP501 4.7 31.5 0.8 CA B:GLY28 4.7 33.1 1.0 N B:SER175 4.7 45.2 1.0 CB B:SER175 4.8 45.6 1.0 N B:GLY28 4.8 32.5 1.0 O1B B:ATP501 4.9 36.9 0.8

Magnesium binding site 3 out of 6 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Mgatp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Mgatp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:51.6 occ:1.00 O1B C:ATP501 2.3 44.9 0.9 O1A C:ATP501 2.6 41.8 0.9 O1G C:ATP501 2.6 30.4 0.9 O C:HOH617 2.8 38.8 1.0 O C:HOH662 3.3 36.4 1.0 PB C:ATP501 3.4 46.8 0.9 OG C:SER26 3.4 32.8 1.0 PA C:ATP501 3.6 51.0 0.9 PG C:ATP501 3.7 26.9 0.9 O3B C:ATP501 3.8 32.6 0.9 O3A C:ATP501 3.9 48.1 0.9 CB C:SER26 3.9 25.1 1.0 O5' C:ATP501 4.1 41.1 0.9 OG C:SER175 4.3 62.3 1.0 O2B C:ATP501 4.7 54.6 0.9 O2G C:ATP501 4.7 34.1 0.9 O3G C:ATP501 4.7 31.0 0.9 C8 C:ATP501 4.8 33.0 0.9 O2A C:ATP501 5.0 45.1 0.9

Magnesium binding site 4 out of 6 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Mgatp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Mgatp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:54.2 occ:1.00 O3G D:ATP501 2.1 45.1 0.8 O1B D:ATP501 2.5 41.0 0.8 O1A D:ATP501 3.1 40.6 0.8 PG D:ATP501 3.5 48.9 0.8 OG D:SER26 3.6 46.2 1.0 PB D:ATP501 3.8 47.7 0.8 O D:HOH626 3.9 41.2 1.0 O1G D:ATP501 4.0 54.6 0.8 O3B D:ATP501 4.1 49.5 0.8 CA D:GLY28 4.2 53.3 1.0 CB D:SER26 4.2 40.4 1.0 PA D:ATP501 4.4 50.5 0.8 N D:GLY28 4.5 50.2 1.0 O3A D:ATP501 4.6 47.6 0.8 O2G D:ATP501 4.6 52.4 0.8 N D:SER175 4.9 61.0 1.0 O2B D:ATP501 4.9 53.5 0.8 CA D:ALA174 5.0 72.8 1.0

Magnesium binding site 5 out of 6 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Mgatp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Mgatp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:45.9 occ:1.00 O2B E:ATP501 2.2 43.8 0.8 O3G E:ATP501 2.7 35.8 0.8 O2A E:ATP501 3.5 39.1 0.8 PB E:ATP501 3.6 41.9 0.8 PG E:ATP501 3.7 35.2 0.8 OG E:SER26 3.9 39.8 1.0 O3B E:ATP501 3.9 36.5 0.8 O1G E:ATP501 4.2 32.8 0.8 N E:SER175 4.2 51.1 1.0 CA E:GLY28 4.3 33.0 1.0 O E:HOH688 4.4 45.8 1.0 CB E:SER175 4.4 53.7 1.0 PA E:ATP501 4.4 44.0 0.8 O3A E:ATP501 4.5 36.6 0.8 O1B E:ATP501 4.6 38.3 0.8 N E:GLY28 4.6 34.3 1.0 O E:SER175 4.6 55.8 1.0 CB E:SER26 4.6 39.8 1.0 O5' E:ATP501 4.8 42.5 0.8 CA E:SER175 4.8 46.8 1.0

Magnesium binding site 6 out of 6 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Mgatp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Mgatp within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg502 b:42.4 occ:1.00 O F:HOH604 2.5 37.9 1.0 O1B F:ATP501 2.6 37.9 0.8 O1G F:ATP501 2.9 33.8 0.8 O3G F:ATP501 3.7 35.9 0.8 PG F:ATP501 3.7 32.7 0.8 PB F:ATP501 4.0 39.8 0.8 CA F:GLY28 4.1 33.6 1.0 O3B F:ATP501 4.3 36.7 0.8 CA F:ALA174 4.3 67.8 1.0 CB F:ALA174 4.4 58.4 1.0 O2A F:ATP501 4.4 43.5 0.8 OG F:SER26 4.7 30.1 1.0 O2B F:ATP501 4.8 39.5 0.8 N F:GLY28 4.8 33.6 1.0 O F:ASN171 4.8 49.5 1.0

M.Fellner, B.Desguin, R.P.Hausinger, J.Hu. Structural Insights Into the Catalytic Mechanism of A Sacrificial Sulfur Insertase of the N-Type Atp Pyrophosphatase Family, Lare. Proc. Natl. Acad. Sci. V. 114 9074 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28784764
DOI: 10.1073/PNAS.1704967114