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

Protein crystallography data

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

Other elements in 5nj4:

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

Iron (Fe) 5 atoms

Magnesium Binding Sites:

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 5nj4

Go back to Magnesium Binding Sites List in 5nj4
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 5nj4

Go back to Magnesium Binding Sites List in 5nj4
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 5nj4

Go back to Magnesium Binding Sites List in 5nj4
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 5nj4

Go back to Magnesium Binding Sites List in 5nj4
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

Reference:

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
Page generated: Sun Sep 29 23:18:36 2024

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