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Magnesium in PDB 2gnu: The Crystallization of Reaction Center From Rhodobacter Sphaeroides Occurs Via A New Route

Protein crystallography data

The structure of The Crystallization of Reaction Center From Rhodobacter Sphaeroides Occurs Via A New Route, PDB code: 2gnu was solved by P.Wadsten, A.B.Woehri, A.Snijder, G.Katona, A.T.Gardiner, R.J.Cogdell, R.Neutze, S.Engstroem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.80 / 2.20
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.422, 100.422, 235.412, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 24.6

Other elements in 2gnu:

The structure of The Crystallization of Reaction Center From Rhodobacter Sphaeroides Occurs Via A New Route also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystallization of Reaction Center From Rhodobacter Sphaeroides Occurs Via A New Route (pdb code 2gnu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Crystallization of Reaction Center From Rhodobacter Sphaeroides Occurs Via A New Route, PDB code: 2gnu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2gnu

Go back to Magnesium Binding Sites List in 2gnu
Magnesium binding site 1 out of 4 in the The Crystallization of Reaction Center From Rhodobacter Sphaeroides Occurs Via A New Route


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystallization of Reaction Center From Rhodobacter Sphaeroides Occurs Via A New Route within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1282

b:22.3
occ:1.00
MG L:BCL1282 0.0 22.3 1.0
ND L:BCL1282 2.1 23.4 1.0
NC L:BCL1282 2.1 22.5 1.0
NB L:BCL1282 2.1 22.9 1.0
NA L:BCL1282 2.2 23.1 1.0
NE2 L:HIS173 2.3 16.5 1.0
C4D L:BCL1282 3.0 23.6 1.0
C1B L:BCL1282 3.1 23.1 1.0
C4B L:BCL1282 3.1 22.9 1.0
CE1 L:HIS173 3.1 19.3 1.0
C4A L:BCL1282 3.2 23.1 1.0
C1D L:BCL1282 3.2 22.7 1.0
C1C L:BCL1282 3.2 22.9 1.0
C4C L:BCL1282 3.2 22.9 1.0
C1A L:BCL1282 3.3 22.5 1.0
CD2 L:HIS173 3.4 14.8 1.0
CHB L:BCL1282 3.4 22.4 1.0
CHC L:BCL1282 3.5 23.0 1.0
CBB M:BCL1303 3.5 17.9 1.0
OBB M:BCL1303 3.5 26.5 1.0
CAB M:BCL1303 3.6 20.1 1.0
CHA L:BCL1282 3.6 23.0 1.0
CHD L:BCL1282 3.6 23.4 1.0
C3D L:BCL1282 4.2 23.3 1.0
C3B L:BCL1282 4.3 23.1 1.0
C2B L:BCL1282 4.3 23.1 1.0
C2D L:BCL1282 4.3 23.1 1.0
C3B M:BCL1303 4.3 19.9 1.0
ND1 L:HIS173 4.3 17.8 1.0
C3A L:BCL1282 4.4 22.6 1.0
C3C L:BCL1282 4.5 22.7 1.0
C2C L:BCL1282 4.5 22.6 1.0
CG L:HIS173 4.5 19.3 1.0
C2A L:BCL1282 4.5 22.5 1.0
CD2 L:PHE167 4.9 32.7 1.0
C4B M:BCL1303 4.9 19.8 1.0
CMA L:BCL1282 5.0 16.9 1.0

Magnesium binding site 2 out of 4 in 2gnu

Go back to Magnesium Binding Sites List in 2gnu
Magnesium binding site 2 out of 4 in the The Crystallization of Reaction Center From Rhodobacter Sphaeroides Occurs Via A New Route


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystallization of Reaction Center From Rhodobacter Sphaeroides Occurs Via A New Route within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1283

b:21.8
occ:1.00
MG L:BCL1283 0.0 21.8 1.0
NC L:BCL1283 1.9 18.9 1.0
ND L:BCL1283 2.0 19.0 1.0
NB L:BCL1283 2.1 19.1 1.0
NA L:BCL1283 2.2 18.6 1.0
NE2 L:HIS153 2.4 24.4 1.0
C4D L:BCL1283 3.0 19.0 1.0
C1C L:BCL1283 3.0 19.3 1.0
C4C L:BCL1283 3.0 18.2 1.0
C4B L:BCL1283 3.1 19.1 1.0
C1D L:BCL1283 3.1 19.0 1.0
C1B L:BCL1283 3.2 18.6 1.0
CD2 L:HIS153 3.2 23.2 1.0
C1A L:BCL1283 3.2 18.8 1.0
C4A L:BCL1283 3.2 18.7 1.0
CHC L:BCL1283 3.4 18.8 1.0
CE1 L:HIS153 3.5 25.3 1.0
CHD L:BCL1283 3.5 18.6 1.0
CHA L:BCL1283 3.5 18.8 1.0
CHB L:BCL1283 3.6 18.6 1.0
C3D L:BCL1283 4.2 18.7 1.0
C3C L:BCL1283 4.2 18.7 1.0
CBB M:BPH1284 4.2 13.5 1.0
C2C L:BCL1283 4.2 19.0 1.0
C2D L:BCL1283 4.2 18.1 1.0
C3B L:BCL1283 4.3 19.1 1.0
C2B L:BCL1283 4.3 18.7 1.0
CG L:HIS153 4.4 27.0 1.0
ND1 L:HIS153 4.5 27.3 1.0
C3A L:BCL1283 4.5 19.0 1.0
C2A L:BCL1283 4.5 18.9 1.0
CE2 M:TYR210 4.6 14.2 1.0
CBC L:BCL1283 4.8 19.6 1.0
CBA L:BCL1283 4.8 18.3 1.0
CD2 L:LEU154 4.9 22.6 1.0
C19 M:BPH1284 5.0 19.3 1.0
CBD L:BCL1283 5.0 19.7 1.0

Magnesium binding site 3 out of 4 in 2gnu

Go back to Magnesium Binding Sites List in 2gnu
Magnesium binding site 3 out of 4 in the The Crystallization of Reaction Center From Rhodobacter Sphaeroides Occurs Via A New Route


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystallization of Reaction Center From Rhodobacter Sphaeroides Occurs Via A New Route within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1302

b:21.0
occ:1.00
MG M:BCL1302 0.0 21.0 1.0
ND M:BCL1302 2.0 20.0 1.0
NB M:BCL1302 2.1 19.4 1.0
NC M:BCL1302 2.1 19.7 1.0
NA M:BCL1302 2.1 19.3 1.0
NE2 M:HIS182 2.4 24.2 1.0
C4D M:BCL1302 2.9 19.3 1.0
C4B M:BCL1302 3.1 19.2 1.0
C1D M:BCL1302 3.1 19.0 1.0
C1B M:BCL1302 3.1 19.4 1.0
C1C M:BCL1302 3.2 19.9 1.0
C4A M:BCL1302 3.2 19.5 1.0
C4C M:BCL1302 3.2 19.0 1.0
C1A M:BCL1302 3.2 19.4 1.0
CD2 M:HIS182 3.3 19.0 1.0
CE1 M:HIS182 3.4 22.9 1.0
CHC M:BCL1302 3.5 19.1 1.0
CHB M:BCL1302 3.5 20.0 1.0
CHD M:BCL1302 3.5 20.0 1.0
CHA M:BCL1302 3.5 19.1 1.0
C3D M:BCL1302 4.1 19.6 1.0
C2D M:BCL1302 4.2 19.8 1.0
C3B M:BCL1302 4.2 19.8 1.0
C2B M:BCL1302 4.3 19.1 1.0
CBB M:BPH1304 4.4 17.0 1.0
C2A M:BCL1302 4.4 20.1 1.0
C3A M:BCL1302 4.4 19.8 1.0
C2C M:BCL1302 4.4 19.8 1.0
C3C M:BCL1302 4.5 19.6 1.0
CG M:HIS182 4.5 22.5 1.0
ND1 M:HIS182 4.5 21.8 1.0
CE2 L:PHE181 4.7 10.0 1.0
CBA M:BCL1302 4.9 27.8 1.0
CBD M:BCL1302 5.0 20.0 1.0

Magnesium binding site 4 out of 4 in 2gnu

Go back to Magnesium Binding Sites List in 2gnu
Magnesium binding site 4 out of 4 in the The Crystallization of Reaction Center From Rhodobacter Sphaeroides Occurs Via A New Route


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystallization of Reaction Center From Rhodobacter Sphaeroides Occurs Via A New Route within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1303

b:16.5
occ:1.00
MG M:BCL1303 0.0 16.5 1.0
ND M:BCL1303 1.9 19.7 1.0
NC M:BCL1303 2.1 19.8 1.0
NA M:BCL1303 2.2 19.3 1.0
NB M:BCL1303 2.2 19.3 1.0
NE2 M:HIS202 2.3 16.9 1.0
C4D M:BCL1303 2.9 19.8 1.0
C1D M:BCL1303 3.1 20.1 1.0
C1C M:BCL1303 3.1 19.6 1.0
C4C M:BCL1303 3.2 19.6 1.0
C4B M:BCL1303 3.2 19.8 1.0
C1B M:BCL1303 3.2 20.0 1.0
C1A M:BCL1303 3.2 19.8 1.0
C4A M:BCL1303 3.2 19.6 1.0
CE1 M:HIS202 3.3 14.4 1.0
CD2 M:HIS202 3.4 17.2 1.0
CHA M:BCL1303 3.5 19.1 1.0
CHC M:BCL1303 3.5 19.3 1.0
CHD M:BCL1303 3.5 19.1 1.0
CHB M:BCL1303 3.6 19.3 1.0
CBB L:BCL1282 3.6 16.6 1.0
CAB L:BCL1282 3.9 22.6 1.0
OBB L:BCL1282 4.0 22.3 1.0
C3D M:BCL1303 4.1 19.8 1.0
C2D M:BCL1303 4.2 19.9 1.0
C2C M:BCL1303 4.4 19.4 1.0
C3B M:BCL1303 4.4 19.9 1.0
C3C M:BCL1303 4.4 19.6 1.0
C2B M:BCL1303 4.4 19.7 1.0
ND1 M:HIS202 4.4 14.9 1.0
CG M:HIS202 4.5 15.0 1.0
C3A M:BCL1303 4.5 19.1 1.0
C2A M:BCL1303 4.6 19.3 1.0
C3B L:BCL1282 4.6 23.1 1.0
CMC M:BCL1303 4.8 12.8 1.0
CBD M:BCL1303 4.9 19.6 1.0

Reference:

P.Wadsten, A.B.Woehri, A.Snijder, G.Katona, A.T.Gardiner, R.J.Cogdell, R.Neutze, S.Engstroem. Lipidic Sponge Phase Crystallization of Membrane Proteins J.Mol.Biol. V. 364 44 2006.
ISSN: ISSN 0022-2836
PubMed: 17005199
DOI: 10.1016/J.JMB.2006.06.043
Page generated: Mon Dec 14 07:24:45 2020

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