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

The structure of Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward), PDB code: 3vyt 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)	34.79 / 2.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.333, 99.412, 103.923, 90.00, 97.79, 90.00
R / Rfree (%)	20.7 / 25.3

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

Iron	(Fe)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward) (pdb code 3vyt). 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 the Hypc-Hypd-Hype Complex (Form I Inward), PDB code: 3vyt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward)


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 Inward) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:34.5 occ:1.00 O C:HOH783 2.1 58.3 1.0 O C:HOH701 2.1 36.7 1.0 OD2 C:ASP59 2.1 44.8 1.0 OD2 C:ASP84 2.3 35.3 1.0 CL C:CL604 3.0 58.9 1.0 CG C:ASP59 3.2 54.1 1.0 MG C:MG606 3.2 60.4 1.0 CG C:ASP84 3.3 40.7 1.0 MG C:MG605 3.3 69.5 1.0 OD1 C:ASP59 3.5 51.3 1.0 OD1 C:ASP84 3.6 42.0 1.0 MG C:MG602 3.7 29.6 1.0 O C:HOH720 3.7 39.6 1.0 O C:HOH721 3.7 49.3 1.0 OG1 C:THR223 4.2 38.7 1.0 OD2 C:ASP221 4.3 49.5 1.0 CB C:ASP59 4.5 42.6 1.0 O C:HOH719 4.6 47.7 1.0 CG2 C:THR223 4.7 31.6 1.0 CB C:ASP84 4.7 39.7 1.0 O C:GLY80 4.7 38.5 1.0 O C:HOH713 4.8 39.7 1.0 CB C:THR223 4.9 34.1 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward)


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 Inward) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:29.6 occ:1.00 OD1 C:ASP43 1.9 46.7 1.0 OD1 C:ASP84 1.9 42.0 1.0 O C:HOH719 2.0 47.7 1.0 O C:HOH721 2.4 49.3 1.0 O C:HOH701 2.4 36.7 1.0 OD1 C:ASP221 2.7 51.7 1.0 CG C:ASP43 2.9 44.7 1.0 CG C:ASP84 3.0 40.7 1.0 CB C:ASP43 3.3 41.7 1.0 OD2 C:ASP84 3.5 35.3 1.0 CG C:ASP221 3.5 50.0 1.0 MG C:MG601 3.7 34.5 1.0 OD2 C:ASP221 3.7 49.5 1.0 MG C:MG605 3.7 69.5 1.0 CA C:ASP43 3.7 48.8 1.0 OD2 C:ASP43 4.0 57.4 1.0 O C:HOH761 4.1 57.9 1.0 O C:ASP221 4.2 36.1 1.0 CB C:ASP84 4.3 39.7 1.0 O C:HOH783 4.4 58.3 1.0 NZ C:LYS220 4.4 38.5 1.0 O C:ASP43 4.6 51.1 1.0 CA C:ASP84 4.6 39.4 1.0 C C:ASP43 4.7 50.3 1.0 N C:ASP221 4.7 41.9 1.0 OG1 C:THR223 4.7 38.7 1.0 N C:ASP43 4.7 51.8 1.0 CG2 C:VAL87 4.9 21.9 1.0 CG C:LYS220 4.9 59.1 1.0 CB C:ASP221 4.9 42.2 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward)


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 Inward) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:57.6 occ:1.00 O C:HOH722 2.3 39.0 1.0 OD2 C:ASP42 2.4 65.0 1.0 OD1 C:ASP158 2.4 67.7 1.0 O C:MET219 2.5 52.7 1.0 OD2 C:ASP43 2.6 57.4 1.0 CG C:ASP158 3.4 61.0 1.0 CG C:ASP42 3.4 62.1 1.0 C C:MET219 3.7 48.5 1.0 SD C:MET88 3.7 40.7 1.0 CG C:ASP43 3.8 44.7 1.0 N C:ASP158 3.8 39.4 1.0 OD1 C:ASP42 3.8 67.7 1.0 O C:VAL87 3.9 33.3 1.0 OD2 C:ASP158 3.9 63.3 1.0 C C:SER157 4.1 47.2 1.0 CA C:SER157 4.2 46.0 1.0 CB C:ASP43 4.3 41.7 1.0 NZ C:LYS220 4.3 38.5 1.0 N C:ASP43 4.3 51.8 1.0 O C:VAL156 4.3 49.3 1.0 CA C:ASP158 4.3 48.3 1.0 CB C:ASP158 4.4 54.9 1.0 CA C:LYS220 4.5 49.7 1.0 CE C:LYS220 4.5 54.2 1.0 CB C:LYS220 4.5 53.6 1.0 N C:LYS220 4.5 47.9 1.0 N C:MET219 4.6 55.9 1.0 C C:VAL87 4.6 36.8 1.0 CG2 C:VAL87 4.6 21.9 1.0 CA C:MET219 4.6 46.4 1.0 O C:SER157 4.7 46.6 1.0 CB C:ASP42 4.7 55.8 1.0 OD1 C:ASP43 4.8 46.7 1.0 CB C:VAL87 4.8 40.2 1.0 CE C:MET88 4.9 46.9 1.0 C C:VAL156 4.9 43.9 1.0 N C:SER157 4.9 42.8 1.0 CA C:ASP43 5.0 48.8 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward)


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 the Hypc-Hypd-Hype Complex (Form I Inward) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg605 b:69.5 occ:1.00 O C:HOH721 2.2 49.3 1.0 O C:HOH713 2.8 39.7 1.0 OD2 C:ASP84 3.1 35.3 1.0 MG C:MG606 3.1 60.4 1.0 MG C:MG601 3.3 34.5 1.0 O C:ASP43 3.5 51.1 1.0 CG C:ASP84 3.5 40.7 1.0 OD1 C:ASP84 3.6 42.0 1.0 MG C:MG602 3.7 29.6 1.0 OD2 C:ASP59 4.0 44.8 1.0 C C:ASP43 4.0 50.3 1.0 CA C:ASP43 4.1 48.8 1.0 OG1 C:THR57 4.2 55.3 1.0 O C:HOH701 4.3 36.7 1.0 OD1 C:ASP59 4.3 51.3 1.0 O C:ILE58 4.4 30.9 1.0 CG C:ASP59 4.4 54.1 1.0 CB C:ASP84 4.5 39.7 1.0 O C:HOH761 4.6 57.9 1.0 O C:ASP42 4.6 47.3 1.0 CB C:ASP43 4.8 41.7 1.0 OD1 C:ASP43 4.9 46.7 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward)


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 the Hypc-Hypd-Hype Complex (Form I Inward) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg606 b:60.4 occ:1.00 OD1 C:ASP59 2.2 51.3 1.0 O C:HOH713 2.6 39.7 1.0 CG C:ASP59 3.0 54.1 1.0 MG C:MG605 3.1 69.5 1.0 CL C:CL604 3.2 58.9 1.0 MG C:MG601 3.2 34.5 1.0 OD2 C:ASP59 3.3 44.8 1.0 NH2 C:ARG224 3.8 42.8 1.0 O C:HOH721 4.0 49.3 1.0 O C:ILE58 4.3 30.9 1.0 CB C:ASP59 4.4 42.6 1.0 OD2 C:ASP84 4.6 35.3 1.0 CA C:ASP59 4.7 37.9 1.0 O C:HOH701 4.7 36.7 1.0 CZ C:ARG224 5.0 58.7 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