Magnesium in PDB 5t4y: Crystal Structure of BT1762-1763

The structure of Crystal Structure of BT1762-1763, PDB code: 5t4y was solved by B.Van Den Berg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	130.35 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	110.826, 152.085, 253.005, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 27

The binding sites of Magnesium atom in the Crystal Structure of BT1762-1763 (pdb code 5t4y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of BT1762-1763, PDB code: 5t4y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of BT1762-1763


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 BT1762-1763 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:28.4 occ:1.00 OD1 D:ASN664 1.9 75.9 1.0 O A:TYR273 2.0 70.1 1.0 OD1 A:ASN401 2.2 73.3 1.0 OE2 A:GLU262 2.5 64.7 1.0 OE1 A:GLU262 2.6 76.9 1.0 O A:SER399 2.7 55.5 1.0 CD A:GLU262 2.9 68.0 1.0 CG D:ASN664 3.1 58.4 1.0 C A:TYR273 3.2 66.4 1.0 CG A:ASN401 3.3 64.8 1.0 N A:TYR273 3.9 55.7 1.0 C A:SER399 3.9 70.5 1.0 ND2 A:ASN401 4.0 58.5 1.0 CA A:TYR273 4.0 54.8 1.0 ND2 D:ASN664 4.1 61.1 1.0 CB D:ASN664 4.1 46.2 1.0 N A:SER274 4.2 65.2 1.0 CA D:ASN664 4.2 53.5 1.0 C A:GLN272 4.2 62.4 1.0 OE1 A:GLN272 4.3 74.1 1.0 CA A:SER274 4.4 60.0 1.0 N A:ASN401 4.4 58.0 1.0 CG A:GLU262 4.4 61.8 1.0 CB A:SER399 4.4 53.5 1.0 CB A:TYR273 4.5 55.0 1.0 CB A:ASN401 4.5 69.3 1.0 CA A:GLN272 4.6 67.3 1.0 CA A:ASN401 4.6 58.5 1.0 CA A:SER399 4.7 54.0 1.0 O A:GLN272 4.7 71.1 1.0 N D:ASN664 4.8 56.5 1.0 OD2 D:ASP659 4.8 0.4 1.0 C A:LEU400 4.9 85.7 1.0 N A:LEU400 5.0 55.8 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of BT1762-1763


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 BT1762-1763 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:84.5 occ:1.00 OH A:TYR519 1.9 0.3 1.0 O A:SER55 2.3 73.6 1.0 O A:VAL53 2.8 95.9 1.0 CZ A:TYR519 3.0 91.5 1.0 O A:CYS58 3.1 74.3 1.0 C A:SER55 3.4 88.5 1.0 CE1 A:TYR519 3.4 86.6 1.0 O A:ARG54 3.5 87.1 1.0 CE2 A:TYR508 3.6 85.3 1.0 C A:VAL53 3.7 92.9 1.0 C A:ARG54 3.7 87.8 1.0 CG A:GLU75 3.8 84.4 1.0 OH A:TYR508 4.0 99.0 1.0 N A:SER55 4.0 81.5 1.0 O A:GLU75 4.2 0.6 1.0 CE2 A:TYR519 4.2 73.5 1.0 OE2 A:GLU75 4.2 95.9 1.0 CZ A:TYR508 4.2 93.9 1.0 N A:ASP56 4.3 89.9 1.0 CA A:SER55 4.3 81.3 1.0 C A:CYS58 4.3 77.3 1.0 CA A:ARG54 4.4 85.8 1.0 CA A:ASP56 4.4 87.8 1.0 N A:ARG54 4.5 90.7 1.0 CD A:GLU75 4.5 93.4 1.0 CA A:VAL53 4.5 89.4 1.0 CD2 A:TYR508 4.6 85.2 1.0 N A:CYS58 4.7 84.6 1.0 CD1 A:TYR519 4.8 81.3 1.0 C A:ASP56 4.9 84.4 1.0 CB A:GLU75 5.0 79.1 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of BT1762-1763


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 BT1762-1763 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:4.7 occ:1.00 OD1 C:ASN664 2.0 54.7 1.0 OD1 B:ASN401 2.1 60.6 1.0 O B:TYR273 2.3 62.5 1.0 OE1 B:GLU262 2.4 68.8 1.0 OE2 B:GLU262 2.4 50.4 1.0 CD B:GLU262 2.7 58.8 1.0 O B:SER399 2.8 55.2 1.0 CG C:ASN664 3.2 43.9 1.0 CG B:ASN401 3.2 60.9 1.0 C B:TYR273 3.5 49.3 1.0 ND2 B:ASN401 3.9 59.1 1.0 CB C:ASN664 3.9 43.5 1.0 N B:TYR273 4.0 42.3 1.0 CA C:ASN664 4.0 51.2 1.0 C B:SER399 4.1 51.1 1.0 CG B:GLU262 4.1 53.1 1.0 N B:ASN401 4.1 42.8 1.0 ND2 C:ASN664 4.2 43.9 1.0 CA B:TYR273 4.2 47.6 1.0 OE1 B:GLN272 4.2 42.9 1.0 C B:GLN272 4.3 53.4 1.0 CB B:ASN401 4.3 55.4 1.0 CA B:ASN401 4.4 42.8 1.0 CA B:GLN272 4.5 49.7 1.0 N B:SER274 4.5 43.5 1.0 N C:ASN664 4.5 55.7 1.0 CB B:TYR273 4.6 40.4 1.0 CB B:SER399 4.6 45.4 1.0 CA B:SER274 4.7 40.3 1.0 O B:GLN272 4.8 64.7 1.0 C B:LEU400 4.8 55.2 1.0 OD2 C:ASP659 4.8 61.3 1.0 CA B:SER399 4.9 42.1 1.0 CB B:GLU262 4.9 56.3 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of BT1762-1763


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 BT1762-1763 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:0.3 occ:1.00 O B:VAL53 2.2 60.9 1.0 O B:SER55 2.2 53.1 1.0 OH B:TYR519 2.3 57.2 1.0 C B:SER55 3.3 68.9 1.0 O B:CYS58 3.3 59.1 1.0 CZ B:TYR519 3.4 66.4 1.0 C B:VAL53 3.4 57.4 1.0 CE2 B:TYR508 3.4 74.3 1.0 C B:ARG54 3.5 61.0 1.0 O B:ARG54 3.6 60.0 1.0 CE1 B:TYR519 3.6 71.0 1.0 N B:SER55 3.7 64.4 1.0 CG B:GLU75 3.8 86.0 1.0 OH B:TYR508 3.9 55.4 1.0 CA B:ARG54 4.0 57.2 1.0 CA B:SER55 4.1 66.2 1.0 N B:ARG54 4.1 54.3 1.0 CZ B:TYR508 4.2 56.2 1.0 N B:ASP56 4.3 79.4 1.0 O B:GLU75 4.3 78.7 1.0 CD2 B:TYR508 4.3 77.6 1.0 CA B:VAL53 4.4 58.2 1.0 CA B:ASP56 4.5 80.3 1.0 OE2 B:GLU75 4.5 0.0 1.0 C B:CYS58 4.5 60.2 1.0 CE2 B:TYR519 4.6 65.5 1.0 CD B:GLU75 4.7 0.0 1.0 CA B:GLU75 4.9 67.6 1.0 N B:CYS58 4.9 59.0 1.0 CB B:GLU75 4.9 69.5 1.0 C B:GLU75 5.0 75.3 1.0 C B:ASP56 5.0 84.8 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of BT1762-1763


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 BT1762-1763 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1101 b:47.8 occ:1.00 O C:VAL843 2.1 0.6 1.0 OD1 C:ASP837 2.8 71.2 1.0 CB C:ASP839 2.8 82.5 1.0 OD1 C:ASN841 2.9 86.0 1.0 OD2 C:ASP839 2.9 99.0 1.0 C C:VAL843 3.1 0.2 1.0 CG C:ASP839 3.3 85.0 1.0 OD2 C:ASP848 3.5 0.6 1.0 CA C:ILE844 3.6 82.9 1.0 CG C:ASN841 3.7 83.5 1.0 N C:ILE844 3.7 0.1 1.0 N C:ASP845 3.7 79.4 1.0 ND2 C:ASN841 3.9 74.9 1.0 CB C:ASP848 3.9 0.2 1.0 CG C:ASP837 4.0 81.2 1.0 CG2 C:VAL843 4.1 0.5 1.0 CA C:ASP839 4.1 87.2 1.0 C C:ILE844 4.2 76.6 1.0 CG C:ASP848 4.2 0.8 1.0 N C:ASP839 4.3 81.8 1.0 CA C:VAL843 4.3 0.7 1.0 CA C:ASP848 4.5 84.5 1.0 OD1 C:ASP839 4.5 62.8 1.0 OD2 C:ASP845 4.5 0.7 1.0 N C:VAL843 4.5 0.2 1.0 CG C:ASP845 4.6 0.7 1.0 OD1 C:ASP845 4.7 0.9 1.0 CB C:ILE844 4.8 75.3 1.0 CB C:VAL843 4.8 0.3 1.0 OD2 C:ASP837 4.8 76.3 1.0 CG1 C:ILE844 4.8 78.1 1.0 CA C:ASP837 4.8 79.8 1.0 N C:ASP848 4.9 72.0 1.0 CA C:ASP845 4.9 89.1 1.0 CB C:ASP837 4.9 81.6 1.0

A.J.Glenwright, K.R.Pothula, S.P.Bhamidimarri, D.S.Chorev, A.Basle, S.J.Firbank, H.Zheng, C.V.Robinson, M.Winterhalter, U.Kleinekathofer, D.N.Bolam, B.Van Den Berg. Structural Basis For Nutrient Acquisition By Dominant Members of the Human Gut Microbiota. Nature V. 541 407 2017.
ISSN: ESSN 1476-4687
PubMed: 28077872
DOI: 10.1038/NATURE20828