Magnesium in PDB 3vys: Crystal Structure of the Hypc-Hypd-Hype Complex (Form I)

The structure of Crystal Structure of the Hypc-Hypd-Hype Complex (Form I), PDB code: 3vys was solved by S.Watanabe, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.93 / 2.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.567, 99.201, 104.025, 90.00, 97.69, 90.00
R / Rfree (%)	21.8 / 26.1

The structure of Crystal Structure of the Hypc-Hypd-Hype Complex (Form I) also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I) (pdb code 3vys). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I), PDB code: 3vys:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I)


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 the Hypc-Hypd-Hype Complex (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:71.6 occ:1.00 OD2 C:ASP59 2.4 75.9 1.0 OD2 C:ASP84 2.4 59.6 1.0 O C:HOH701 2.9 59.8 1.0 O C:HOH721 3.3 68.3 1.0 CG C:ASP84 3.3 56.5 1.0 MG C:MG602 3.4 52.3 1.0 OD1 C:ASP84 3.4 55.6 1.0 CG C:ASP59 3.5 71.4 1.0 OD2 C:ASP221 3.9 74.2 1.0 OD1 C:ASP59 4.0 78.2 1.0 OG1 C:THR223 4.1 66.0 1.0 CG2 C:THR223 4.6 51.4 1.0 CB C:ASP84 4.7 54.4 1.0 CG C:ASP221 4.7 63.7 1.0 CB C:ASP59 4.7 64.0 1.0 OD1 C:ASP221 4.7 62.7 1.0 O C:GLY80 4.8 53.1 1.0 CB C:THR223 4.8 53.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I)


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 the Hypc-Hypd-Hype Complex (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:52.3 occ:1.00 OD1 C:ASP43 2.0 69.8 1.0 OD1 C:ASP84 2.0 55.6 1.0 OD1 C:ASP221 2.3 62.7 1.0 CG C:ASP43 3.1 64.0 1.0 CG C:ASP84 3.1 56.5 1.0 CG C:ASP221 3.2 63.7 1.0 MG C:MG601 3.4 71.6 1.0 OD2 C:ASP221 3.4 74.2 1.0 CB C:ASP43 3.5 64.0 1.0 OD2 C:ASP84 3.5 59.6 1.0 CA C:ASP43 3.9 65.0 1.0 O C:ASP221 4.1 52.7 1.0 OD2 C:ASP43 4.2 72.2 1.0 CB C:ASP84 4.4 54.4 1.0 NZ C:LYS220 4.5 52.9 1.0 OG1 C:THR223 4.6 66.0 1.0 N C:ASP221 4.6 58.9 1.0 CB C:ASP221 4.6 60.8 1.0 CA C:ASP84 4.7 53.8 1.0 O C:ASP43 4.8 67.2 1.0 C C:ASP43 4.9 66.5 1.0 N C:ASP43 4.9 66.2 1.0 CG2 C:VAL87 5.0 43.5 1.0 C C:ASP221 5.0 52.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I)


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 the Hypc-Hypd-Hype Complex (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:71.3 occ:1.00 OD1 C:ASP158 2.3 82.4 1.0 O C:MET219 2.6 63.1 1.0 OD2 C:ASP42 2.7 84.3 1.0 OD2 C:ASP43 2.7 72.2 1.0 CG C:ASP158 3.5 78.1 1.0 O C:VAL87 3.6 48.9 1.0 C C:MET219 3.6 60.1 1.0 CG C:ASP42 3.7 79.6 1.0 SD C:MET88 3.9 59.4 1.0 CG C:ASP43 3.9 64.0 1.0 OD1 C:ASP42 3.9 81.5 1.0 N C:ASP158 4.0 60.0 1.0 C C:SER157 4.0 59.3 1.0 O C:VAL156 4.1 66.7 1.0 OD2 C:ASP158 4.2 79.6 1.0 CA C:SER157 4.3 62.2 1.0 CB C:ASP43 4.3 64.0 1.0 C C:VAL87 4.3 48.3 1.0 N C:MET219 4.4 65.1 1.0 CG2 C:VAL87 4.4 43.5 1.0 N C:LYS220 4.4 61.3 1.0 CA C:MET219 4.5 60.1 1.0 CA C:LYS220 4.5 59.8 1.0 CA C:ASP158 4.5 65.6 1.0 O C:SER157 4.5 59.1 1.0 CB C:VAL87 4.5 51.6 1.0 N C:ASP43 4.5 66.2 1.0 CE C:LYS220 4.6 70.0 1.0 CB C:LYS220 4.6 64.2 1.0 CB C:ASP158 4.6 70.5 1.0 NZ C:LYS220 4.6 52.9 1.0 C C:VAL156 4.7 63.2 1.0 CB C:MET219 4.8 61.2 1.0 N C:SER157 4.9 60.6 1.0 OD1 C:ASP43 4.9 69.8 1.0 N C:MET88 5.0 53.4 1.0 CB C:ASP42 5.0 73.4 1.0

S.Watanabe, R.Matsumi, H.Atomi, T.Imanaka, K.Miki. Crystal Structures of the Hypcd Complex and the Hypcde Ternary Complex: Transient Intermediate Complexes During [Nife] Hydrogenase Maturation Structure V. 20 2124 2012.
ISSN: ISSN 0969-2126
PubMed: 23123111
DOI: 10.1016/J.STR.2012.09.018