Magnesium in PDB 1od5: Crystal Structure of Glycinin A3B4 Subunit Homohexamer

The structure of Crystal Structure of Glycinin A3B4 Subunit Homohexamer, PDB code: 1od5 was solved by M.Adachi, J.Kanamori, T.Masuda, K.Yagasaki, K.Kitamura, B.Mikami, S.Utsumi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.10
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	114.842, 114.842, 191.572, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 25.4

The binding sites of Magnesium atom in the Crystal Structure of Glycinin A3B4 Subunit Homohexamer (pdb code 1od5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Glycinin A3B4 Subunit Homohexamer, PDB code: 1od5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Glycinin A3B4 Subunit Homohexamer


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 Glycinin A3B4 Subunit Homohexamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg498 b:7.0 occ:1.00 O B:HOH2083 2.9 38.2 1.0 NE2 B:HIS383 2.9 11.9 1.0 OE1 B:GLU432 3.2 14.2 1.0 OH B:TYR441 3.4 7.2 1.0 CE1 B:HIS383 3.6 9.0 1.0 OE2 B:GLU432 3.9 14.6 1.0 CD B:GLU432 3.9 11.7 1.0 CE2 B:TYR380 3.9 4.9 1.0 CD2 B:HIS383 4.0 8.4 1.0 CE2 B:TYR441 4.1 5.2 1.0 CZ B:TYR441 4.2 4.1 1.0 CG2 B:VAL443 4.2 13.1 1.0 CD1 B:ILE392 4.2 5.4 1.0 O B:HOH2081 4.3 35.2 1.0 CG2 B:VAL430 4.4 16.2 1.0 CD2 B:TYR380 4.4 5.4 1.0 CZ B:TYR380 4.7 6.3 1.0 CB B:VAL430 4.8 14.7 1.0 ND1 B:HIS383 4.8 9.8 1.0 CG1 B:VAL443 4.8 10.9 1.0 OH B:TYR380 4.9 11.4 1.0 CG1 B:ILE392 4.9 7.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Glycinin A3B4 Subunit Homohexamer


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 Glycinin A3B4 Subunit Homohexamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg499 b:10.3 occ:1.00 OE1 A:GLU432 2.9 13.8 1.0 NE2 A:HIS383 3.0 7.3 1.0 OH A:TYR441 3.2 8.1 1.0 CD A:GLU432 3.7 13.7 1.0 CE1 A:HIS383 3.7 6.1 1.0 OE2 A:GLU432 3.8 13.4 1.0 CE2 A:TYR441 4.0 6.7 1.0 CD2 A:HIS383 4.0 7.8 1.0 CZ A:TYR441 4.1 7.2 1.0 CE2 A:TYR380 4.2 7.9 1.0 CD1 A:ILE392 4.3 13.9 1.0 CG2 A:VAL430 4.4 14.3 1.0 CG2 A:VAL443 4.4 14.0 1.0 CD2 A:TYR380 4.5 9.9 1.0 O A:HOH2074 4.6 42.2 1.0 CB A:VAL430 4.8 14.5 1.0 CG1 A:ILE392 4.8 10.2 1.0 CZ A:TYR380 4.9 7.9 1.0 CG1 A:VAL443 4.9 14.2 1.0 ND1 A:HIS383 4.9 5.9 1.0

M.Adachi, J.Kanamori, T.Masuda, K.Yagasaki, K.Kitamura, B.Mikami, S.Utsumi. Crystal Structure of Soybean 11S Globulin: Glycinin A3B4 Homohexamer Proc.Natl.Acad.Sci.Usa V. 100 7395 2003.
ISSN: ISSN 0027-8424
PubMed: 12771376
DOI: 10.1073/PNAS.0832158100