Magnesium in PDB 2d5h: Crystal Structure of Recombinant Soybean Proglycinin A3B4 Subunit, Its Comparison with Mature Glycinin A3B4 Subunit, Responsible For Hexamer Assembly

The structure of Crystal Structure of Recombinant Soybean Proglycinin A3B4 Subunit, Its Comparison with Mature Glycinin A3B4 Subunit, Responsible For Hexamer Assembly, PDB code: 2d5h was solved by T.Itoh, M.Adachi, T.Masuda, B.Mikami, S.Utsumi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.378, 223.738, 88.660, 90.00, 119.85, 90.00
R / Rfree (%)	24.8 / 32.5

The binding sites of Magnesium atom in the Crystal Structure of Recombinant Soybean Proglycinin A3B4 Subunit, Its Comparison with Mature Glycinin A3B4 Subunit, Responsible For Hexamer Assembly (pdb code 2d5h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Recombinant Soybean Proglycinin A3B4 Subunit, Its Comparison with Mature Glycinin A3B4 Subunit, Responsible For Hexamer Assembly, PDB code: 2d5h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Recombinant Soybean Proglycinin A3B4 Subunit, Its Comparison with Mature Glycinin A3B4 Subunit, Responsible For Hexamer Assembly


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 Recombinant Soybean Proglycinin A3B4 Subunit, Its Comparison with Mature Glycinin A3B4 Subunit, Responsible For Hexamer Assembly within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:17.5 occ:1.00 OE1 A:GLU432 2.9 43.0 1.0 NE2 A:HIS383 3.0 26.3 1.0 OH A:TYR441 3.5 39.4 1.0 CE1 A:HIS383 3.6 36.1 1.0 CD A:GLU432 3.7 42.5 1.0 CD1 A:ILE392 3.8 32.2 1.0 OE2 A:GLU432 4.0 52.4 1.0 CG1 A:VAL430 4.1 10.9 1.0 CD2 A:HIS383 4.2 23.0 1.0 CE2 A:TYR380 4.3 38.5 1.0 CZ A:TYR441 4.4 45.4 1.0 CG2 A:VAL443 4.5 30.3 1.0 CG1 A:ILE392 4.7 34.9 1.0 CG A:GLU432 4.8 32.0 1.0 CZ A:TYR380 4.8 32.5 1.0 CD2 A:TYR380 4.8 28.3 1.0 ND1 A:HIS383 4.9 42.0 1.0 CG1 A:VAL443 4.9 24.8 1.0 OH A:TYR380 5.0 33.0 1.0 CE1 A:TYR441 5.0 32.2 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Recombinant Soybean Proglycinin A3B4 Subunit, Its Comparison with Mature Glycinin A3B4 Subunit, Responsible For Hexamer Assembly


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 Recombinant Soybean Proglycinin A3B4 Subunit, Its Comparison with Mature Glycinin A3B4 Subunit, Responsible For Hexamer Assembly within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:41.5 occ:1.00 OE1 B:GLU432 3.4 46.5 1.0 NE2 B:HIS383 3.5 39.4 1.0 CE1 B:TYR380 3.6 58.3 1.0 OH B:TYR441 3.8 63.3 1.0 CD1 B:ILE392 3.9 27.5 1.0 CE2 B:TYR441 4.0 55.0 1.0 CD1 B:TYR380 4.1 50.9 1.0 CE1 B:HIS383 4.1 41.8 1.0 CG1 B:VAL430 4.2 33.7 1.0 CG2 B:VAL443 4.4 42.5 1.0 CZ B:TYR441 4.4 59.9 1.0 CD B:GLU432 4.6 46.8 1.0 CZ B:TYR380 4.6 51.1 1.0 CG2 B:VAL430 4.6 25.0 1.0 CD2 B:HIS383 4.7 48.2 1.0 CG1 B:ILE392 4.8 40.5 1.0 OH B:TYR380 4.8 41.4 1.0 CG2 B:VAL372 4.9 52.6 1.0 CG1 B:VAL443 5.0 29.9 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Recombinant Soybean Proglycinin A3B4 Subunit, Its Comparison with Mature Glycinin A3B4 Subunit, Responsible For Hexamer Assembly


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 Recombinant Soybean Proglycinin A3B4 Subunit, Its Comparison with Mature Glycinin A3B4 Subunit, Responsible For Hexamer Assembly within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:21.5 occ:1.00 NE2 C:HIS383 3.0 29.8 1.0 OE1 C:GLU432 3.0 44.5 1.0 CD1 C:ILE392 3.2 25.8 1.0 OH C:TYR441 3.6 52.2 1.0 CD C:GLU432 3.6 41.2 1.0 CE1 C:HIS383 3.8 31.9 1.0 OE2 C:GLU432 3.8 23.2 1.0 CE2 C:TYR441 3.9 55.3 1.0 CD2 C:HIS383 4.0 35.5 1.0 CE2 C:TYR380 4.1 33.2 1.0 CG1 C:VAL430 4.1 21.8 1.0 CZ C:TYR441 4.2 54.3 1.0 CG1 C:ILE392 4.2 22.6 1.0 CD2 C:TYR380 4.2 38.0 1.0 CG2 C:VAL443 4.3 30.1 1.0 CG C:GLU432 4.8 40.0 1.0 CZ C:TYR380 4.9 40.9 1.0 ND1 C:HIS383 5.0 34.4 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Recombinant Soybean Proglycinin A3B4 Subunit, Its Comparison with Mature Glycinin A3B4 Subunit, Responsible For Hexamer Assembly


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 Recombinant Soybean Proglycinin A3B4 Subunit, Its Comparison with Mature Glycinin A3B4 Subunit, Responsible For Hexamer Assembly within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg604 b:17.8 occ:1.00 OE1 D:GLU432 2.7 5.5 1.0 NE2 D:HIS383 3.2 12.1 1.0 OH D:TYR441 3.5 27.7 1.0 CD D:GLU432 3.7 22.5 1.0 CE1 D:HIS383 3.9 10.7 1.0 CE2 D:TYR380 4.0 17.5 1.0 OE2 D:GLU432 4.0 5.5 1.0 CE2 D:TYR441 4.1 47.4 1.0 CZ D:TYR441 4.2 37.2 1.0 CG2 D:VAL443 4.3 28.1 1.0 CD2 D:TYR380 4.3 15.1 1.0 CD2 D:HIS383 4.3 11.9 1.0 CD1 D:ILE392 4.3 8.3 1.0 CG1 D:VAL430 4.3 7.8 1.0 CZ D:TYR380 4.6 10.0 1.0 OH D:TYR380 5.0 25.5 1.0 CG D:GLU432 5.0 27.1 1.0 CG1 D:ILE392 5.0 18.9 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Recombinant Soybean Proglycinin A3B4 Subunit, Its Comparison with Mature Glycinin A3B4 Subunit, Responsible For Hexamer Assembly


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 Recombinant Soybean Proglycinin A3B4 Subunit, Its Comparison with Mature Glycinin A3B4 Subunit, Responsible For Hexamer Assembly within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg605 b:5.5 occ:1.00 OE1 E:GLU432 2.9 16.3 1.0 OH E:TYR441 3.2 5.5 1.0 NE2 E:HIS383 3.4 6.7 1.0 CD E:GLU432 3.8 7.6 1.0 CE2 E:TYR441 3.8 5.6 1.0 CE2 E:TYR380 4.0 5.5 1.0 CZ E:TYR441 4.0 5.5 1.0 OE2 E:GLU432 4.0 14.2 1.0 CG2 E:VAL443 4.1 5.5 1.0 CD1 E:ILE392 4.1 5.5 1.0 CE1 E:HIS383 4.3 5.5 1.0 CG1 E:VAL430 4.3 5.5 1.0 CD2 E:HIS383 4.4 5.5 1.0 CD2 E:TYR380 4.4 13.4 1.0 CG1 E:ILE392 4.7 5.5 1.0 CZ E:TYR380 4.8 8.0 1.0 CG2 E:VAL372 4.9 5.5 1.0 CG1 E:VAL443 4.9 5.5 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Recombinant Soybean Proglycinin A3B4 Subunit, Its Comparison with Mature Glycinin A3B4 Subunit, Responsible For Hexamer Assembly


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 Recombinant Soybean Proglycinin A3B4 Subunit, Its Comparison with Mature Glycinin A3B4 Subunit, Responsible For Hexamer Assembly within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg606 b:8.1 occ:1.00 OH F:TYR441 2.8 5.5 1.0 NE2 F:HIS383 3.1 7.6 1.0 OE1 F:GLU432 3.4 29.6 1.0 CE2 F:TYR441 3.7 11.3 1.0 CZ F:TYR441 3.7 14.3 1.0 CE1 F:HIS383 3.9 17.1 1.0 CE2 F:TYR380 4.0 22.3 1.0 CD F:GLU432 4.0 17.4 1.0 OE2 F:GLU432 4.0 25.0 1.0 CD2 F:HIS383 4.1 7.3 1.0 CG2 F:VAL443 4.3 5.5 1.0 CD1 F:ILE392 4.3 7.4 1.0 CD2 F:TYR380 4.4 22.3 1.0 CZ F:TYR380 4.4 11.7 1.0 CG1 F:VAL430 4.6 5.5 1.0 OH F:TYR380 4.7 18.8 1.0

M.R.Tandang-Silvas, T.Fukuda, C.Fukuda, K.Prak, C.Cabanos, A.Kimura, T.Itoh, B.Mikami, S.Utsumi, N.Maruyama. Conservation and Divergence on Plant Seed 11S Globulins Based on Crystal Structures. Biochim.Biophys.Acta 2010.
ISSN: ISSN 0006-3002
PubMed: 20215054
DOI: 10.1016/J.BBAPAP.2010.02.016