Magnesium in PDB 5nj4: From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography

The structure of From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography, PDB code: 5nj4 was solved by R.Dods, P.Baath, G.Branden, R.Neutze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.70 / 2.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	226.500, 226.500, 113.900, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 18.6

The structure of From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography also contains other interesting chemical elements:

Iron

(Fe)

5 atoms

The binding sites of Magnesium atom in the From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography (pdb code 5nj4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography, PDB code: 5nj4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg301 b:61.9 occ:1.00 MG L:BCB301 0.0 61.9 1.0 NA L:BCB301 2.0 57.8 1.0 ND L:BCB301 2.0 56.1 1.0 NC L:BCB301 2.0 59.4 1.0 NB L:BCB301 2.1 59.4 1.0 NE2 L:HIS173 2.4 63.3 1.0 C1A L:BCB301 3.0 57.9 1.0 C4A L:BCB301 3.0 58.3 1.0 C4D L:BCB301 3.0 56.1 1.0 C4B L:BCB301 3.1 56.4 1.0 C1D L:BCB301 3.1 60.2 1.0 C4C L:BCB301 3.1 58.4 1.0 C1B L:BCB301 3.1 59.1 1.0 C1C L:BCB301 3.1 59.1 1.0 CBB M:BCB403 3.3 58.9 1.0 CD2 L:HIS173 3.4 61.5 1.0 CHB L:BCB301 3.4 59.1 1.0 CHA L:BCB301 3.4 58.6 1.0 CHC L:BCB301 3.4 55.1 1.0 CE1 L:HIS173 3.4 63.2 1.0 CAB M:BCB403 3.4 56.1 1.0 CHD L:BCB301 3.5 57.9 1.0 OBB M:BCB403 3.6 59.3 1.0 C3B M:BCB403 4.2 57.0 1.0 C3D L:BCB301 4.3 58.4 1.0 C2D L:BCB301 4.3 58.6 1.0 C3A L:BCB301 4.3 57.4 1.0 C2A L:BCB301 4.3 57.8 1.0 C3C L:BCB301 4.3 56.8 1.0 C3B L:BCB301 4.4 58.0 1.0 C2B L:BCB301 4.4 58.9 1.0 C2C L:BCB301 4.5 60.8 1.0 CD1 L:TRP167 4.5 59.6 1.0 CG L:HIS173 4.5 63.3 1.0 ND1 L:HIS173 4.5 60.2 1.0 NE1 L:TRP167 4.6 59.7 1.0 CBD L:BCB301 4.9 59.2 1.0 C2B M:BCB403 4.9 55.5 1.0 C4B M:BCB403 5.0 54.0 1.0

Magnesium binding site 2 out of 4 in the From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg302 b:63.3 occ:1.00 MG L:BCB302 0.0 63.3 1.0 ND L:BCB302 2.0 64.1 1.0 NA L:BCB302 2.0 65.8 1.0 NC L:BCB302 2.0 64.0 1.0 NB L:BCB302 2.1 64.4 1.0 NE2 L:HIS153 2.5 64.9 1.0 C1A L:BCB302 3.0 65.2 1.0 C4A L:BCB302 3.0 63.5 1.0 C4D L:BCB302 3.0 64.8 1.0 C4B L:BCB302 3.1 60.2 1.0 C1D L:BCB302 3.1 64.7 1.0 C1C L:BCB302 3.1 59.8 1.0 C4C L:BCB302 3.1 63.1 1.0 C1B L:BCB302 3.1 60.4 1.0 CD2 L:HIS153 3.4 66.5 1.0 CHB L:BCB302 3.4 63.4 1.0 CHC L:BCB302 3.4 60.1 1.0 CHA L:BCB302 3.4 63.1 1.0 CHD L:BCB302 3.5 63.3 1.0 CE1 L:HIS153 3.5 65.0 1.0 CBB L:BPB303 4.0 66.5 1.0 C3D L:BCB302 4.3 65.4 1.0 C2D L:BCB302 4.3 62.5 1.0 C3C L:BCB302 4.3 63.9 1.0 CE2 M:TYR208 4.3 63.5 1.0 C2A L:BCB302 4.4 65.5 1.0 C3A L:BCB302 4.4 66.0 1.0 C3B L:BCB302 4.4 62.2 1.0 C2B L:BCB302 4.4 62.2 1.0 C2C L:BCB302 4.4 62.8 1.0 CG L:HIS153 4.6 63.3 1.0 ND1 L:HIS153 4.6 63.1 1.0 CBA L:BCB302 4.8 64.2 1.0 CBD L:BCB302 4.9 64.0 1.0 CD2 M:TYR208 4.9 58.6 1.0

Magnesium binding site 3 out of 4 in the From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg402 b:69.2 occ:1.00 MG M:BCB402 0.0 69.2 1.0 NA M:BCB402 2.0 69.2 1.0 ND M:BCB402 2.0 65.2 1.0 NB M:BCB402 2.0 70.3 1.0 NC M:BCB402 2.0 72.1 1.0 NE2 M:HIS180 2.4 63.4 1.0 C1A M:BCB402 3.0 65.5 1.0 C4D M:BCB402 3.0 64.1 1.0 C4A M:BCB402 3.0 69.7 1.0 C4B M:BCB402 3.0 69.5 1.0 C1B M:BCB402 3.1 69.8 1.0 C4C M:BCB402 3.1 67.3 1.0 C1D M:BCB402 3.1 69.7 1.0 C1C M:BCB402 3.1 64.8 1.0 CD2 M:HIS180 3.3 64.2 1.0 CE1 M:HIS180 3.4 64.8 1.0 CHC M:BCB402 3.4 69.5 1.0 CHA M:BCB402 3.4 66.0 1.0 CHB M:BCB402 3.4 67.8 1.0 CHD M:BCB402 3.5 68.0 1.0 OBB M:BPB404 4.2 84.0 1.0 C3D M:BCB402 4.3 66.5 1.0 C2D M:BCB402 4.3 67.7 1.0 C2A M:BCB402 4.3 68.3 1.0 C3B M:BCB402 4.3 72.2 1.0 C3C M:BCB402 4.3 66.3 1.0 C3A M:BCB402 4.4 68.4 1.0 C2B M:BCB402 4.4 70.1 1.0 C2C M:BCB402 4.4 63.9 1.0 CG M:HIS180 4.5 63.6 1.0 ND1 M:HIS180 4.5 62.6 1.0 CE2 L:PHE181 4.7 65.3 1.0 CBA M:BCB402 4.8 76.9 1.0 CBD M:BCB402 4.9 68.4 1.0

Magnesium binding site 4 out of 4 in the From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg403 b:61.1 occ:1.00 MG M:BCB403 0.0 61.1 1.0 NC M:BCB403 2.0 57.8 1.0 ND M:BCB403 2.0 57.5 1.0 NA M:BCB403 2.0 61.9 1.0 NB M:BCB403 2.0 55.1 1.0 NE2 M:HIS200 2.4 65.2 1.0 C1A M:BCB403 3.0 60.7 1.0 C4D M:BCB403 3.0 59.5 1.0 C4A M:BCB403 3.0 58.6 1.0 C4B M:BCB403 3.0 54.0 1.0 C4C M:BCB403 3.1 57.6 1.0 C1C M:BCB403 3.1 54.7 1.0 C1D M:BCB403 3.1 62.9 1.0 C1B M:BCB403 3.1 54.1 1.0 CBB L:BCB301 3.3 60.6 1.0 CE1 M:HIS200 3.3 67.8 1.0 CD2 M:HIS200 3.4 64.5 1.0 CHC M:BCB403 3.4 54.3 1.0 CHA M:BCB403 3.4 59.9 1.0 CHB M:BCB403 3.4 55.8 1.0 CAB L:BCB301 3.5 58.7 1.0 CHD M:BCB403 3.5 61.1 1.0 OBB L:BCB301 3.7 62.0 1.0 C3B L:BCB301 4.2 58.0 1.0 C3C M:BCB403 4.3 59.9 1.0 C3D M:BCB403 4.3 60.9 1.0 C2D M:BCB403 4.3 60.2 1.0 C3A M:BCB403 4.3 62.1 1.0 C3B M:BCB403 4.4 57.0 1.0 C2A M:BCB403 4.4 63.4 1.0 C2B M:BCB403 4.4 55.5 1.0 C2C M:BCB403 4.4 59.7 1.0 ND1 M:HIS200 4.5 61.0 1.0 CG M:HIS200 4.5 61.5 1.0 CBD M:BCB403 4.9 64.8 1.0 C4B L:BCB301 5.0 56.4 1.0 C2B L:BCB301 5.0 58.9 1.0 CMC M:BCB403 5.0 61.9 1.0

R.Dods, P.Bath, D.Arnlund, K.R.Beyerlein, G.Nelson, M.Liang, R.Harimoorthy, P.Berntsen, E.Malmerberg, L.Johansson, R.Andersson, R.Bosman, S.Carbajo, E.Claesson, C.E.Conrad, P.Dahl, G.Hammarin, M.S.Hunter, C.Li, S.Lisova, D.Milathianaki, J.Robinson, C.Safari, A.Sharma, G.Williams, C.Wickstrand, O.Yefanov, J.Davidsson, D.P.Deponte, A.Barty, G.Branden, R.Neutze. From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography. Structure V. 25 1461 2017.
ISSN: ISSN 1878-4186
PubMed: 28781082
DOI: 10.1016/J.STR.2017.07.002