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Magnesium in PDB 1k6n: E(L212)A,D(L213)A Double Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides

Protein crystallography data

The structure of E(L212)A,D(L213)A Double Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides, PDB code: 1k6n was solved by P.R.Pokkuluri, P.D.Laible, Y.-L.Deng, T.N.Wong, D.K.Hanson, M.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 3.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 141.500, 141.500, 187.400, 90.00, 90.00, 120.00
R / Rfree (%) 20.3 / 20.7

Other elements in 1k6n:

The structure of E(L212)A,D(L213)A Double Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides also contains other interesting chemical elements:

Iron (Fe) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E(L212)A,D(L213)A Double Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides (pdb code 1k6n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the E(L212)A,D(L213)A Double Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides, PDB code: 1k6n:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1k6n

Go back to Magnesium Binding Sites List in 1k6n
Magnesium binding site 1 out of 4 in the E(L212)A,D(L213)A Double Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E(L212)A,D(L213)A Double Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg302

b:17.6
occ:1.00
MG L:BCL302 0.0 17.6 1.0
ND L:BCL302 2.0 19.8 1.0
NB L:BCL302 2.1 15.3 1.0
NC L:BCL302 2.1 20.7 1.0
NA L:BCL302 2.2 14.4 1.0
NE2 L:HIS173 2.3 14.2 1.0
C4D L:BCL302 3.0 20.5 1.0
C1B L:BCL302 3.1 7.1 1.0
C4B L:BCL302 3.1 14.7 1.0
C1D L:BCL302 3.1 17.0 1.0
C4A L:BCL302 3.1 6.5 1.0
C1C L:BCL302 3.1 17.3 1.0
C4C L:BCL302 3.2 17.6 1.0
CD2 L:HIS173 3.2 14.9 1.0
C1A L:BCL302 3.2 16.3 1.0
CE1 L:HIS173 3.3 18.5 1.0
CHB L:BCL302 3.5 8.6 1.0
CHC L:BCL302 3.5 15.9 1.0
CHD L:BCL302 3.5 12.4 1.0
CHA L:BCL302 3.5 15.7 1.0
OBB M:BCL502 3.6 35.1 1.0
CAB M:BCL502 3.8 25.4 1.0
CBB M:BCL502 4.0 30.6 1.0
C3D L:BCL302 4.2 15.3 1.0
C2B L:BCL302 4.3 13.2 1.0
C2D L:BCL302 4.3 20.2 1.0
C3B L:BCL302 4.3 20.7 1.0
CG L:HIS173 4.3 20.2 1.0
ND1 L:HIS173 4.4 14.0 1.0
C3A L:BCL302 4.4 12.9 1.0
C2C L:BCL302 4.4 12.2 1.0
C3C L:BCL302 4.5 15.1 1.0
C2A L:BCL302 4.5 13.3 1.0
C3B M:BCL502 4.5 23.5 1.0
CD2 L:PHE167 4.7 23.1 1.0
CMA L:BCL302 4.9 5.1 1.0
CBD L:BCL302 5.0 15.8 1.0

Magnesium binding site 2 out of 4 in 1k6n

Go back to Magnesium Binding Sites List in 1k6n
Magnesium binding site 2 out of 4 in the E(L212)A,D(L213)A Double Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E(L212)A,D(L213)A Double Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg304

b:11.7
occ:1.00
MG L:BCL304 0.0 11.7 1.0
ND L:BCL304 2.0 2.0 1.0
NB L:BCL304 2.1 5.1 1.0
NC L:BCL304 2.1 2.0 1.0
NA L:BCL304 2.2 2.0 1.0
NE2 L:HIS153 2.3 18.5 1.0
C4D L:BCL304 3.0 2.0 1.0
C1D L:BCL304 3.0 9.3 1.0
C1B L:BCL304 3.1 3.1 1.0
C1C L:BCL304 3.1 8.6 1.0
C4B L:BCL304 3.1 2.0 1.0
C4C L:BCL304 3.1 5.7 1.0
C4A L:BCL304 3.1 2.0 1.0
C1A L:BCL304 3.2 4.1 1.0
CD2 L:HIS153 3.3 25.8 1.0
CE1 L:HIS153 3.3 24.6 1.0
CHC L:BCL304 3.4 7.7 1.0
CHB L:BCL304 3.4 2.0 1.0
CHD L:BCL304 3.4 3.6 1.0
CHA L:BCL304 3.5 2.8 1.0
C3D L:BCL304 4.2 2.1 1.0
C2D L:BCL304 4.3 7.1 1.0
C2B L:BCL304 4.3 2.0 1.0
CBB L:BPH402 4.3 29.4 1.0
C3B L:BCL304 4.3 7.2 1.0
C3C L:BCL304 4.3 7.3 1.0
C2C L:BCL304 4.4 10.1 1.0
CG L:HIS153 4.4 28.9 1.0
C3A L:BCL304 4.4 8.2 1.0
ND1 L:HIS153 4.4 25.9 1.0
C2A L:BCL304 4.5 9.2 1.0
CE2 M:TYR210 4.6 17.2 1.0
CBA L:BCL304 4.9 15.5 1.0
CD2 L:LEU154 4.9 21.1 1.0
CAC L:BCL304 4.9 17.3 1.0
CBD L:BCL304 5.0 11.5 1.0

Magnesium binding site 3 out of 4 in 1k6n

Go back to Magnesium Binding Sites List in 1k6n
Magnesium binding site 3 out of 4 in the E(L212)A,D(L213)A Double Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E(L212)A,D(L213)A Double Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg501

b:29.3
occ:1.00
MG M:BCL501 0.0 29.3 1.0
ND M:BCL501 2.0 27.8 1.0
NB M:BCL501 2.1 29.9 1.0
NC M:BCL501 2.1 27.9 1.0
NA M:BCL501 2.2 29.0 1.0
NE2 M:HIS182 2.2 24.7 1.0
C4D M:BCL501 3.0 27.9 1.0
C1B M:BCL501 3.1 29.5 1.0
CD2 M:HIS182 3.1 20.6 1.0
C1D M:BCL501 3.1 27.2 1.0
C4B M:BCL501 3.1 29.9 1.0
C4C M:BCL501 3.1 28.8 1.0
C1C M:BCL501 3.1 29.1 1.0
C4A M:BCL501 3.2 30.7 1.0
C1A M:BCL501 3.2 29.7 1.0
CE1 M:HIS182 3.2 22.8 1.0
CHB M:BCL501 3.5 30.6 1.0
CHA M:BCL501 3.5 28.7 1.0
CHD M:BCL501 3.5 27.8 1.0
CHC M:BCL501 3.5 29.1 1.0
C3D M:BCL501 4.2 27.7 1.0
CG M:HIS182 4.3 13.9 1.0
C2B M:BCL501 4.3 30.6 1.0
C2D M:BCL501 4.3 28.8 1.0
ND1 M:HIS182 4.3 15.0 1.0
C3B M:BCL501 4.3 30.4 1.0
C3C M:BCL501 4.4 29.9 1.0
C2C M:BCL501 4.4 30.1 1.0
C3A M:BCL501 4.5 32.0 1.0
C2A M:BCL501 4.5 32.2 1.0
CBB M:BPH401 4.8 32.8 1.0
CE2 L:PHE181 4.8 23.8 1.0
CBD M:BCL501 5.0 30.2 1.0
CBA M:BCL501 5.0 40.7 1.0

Magnesium binding site 4 out of 4 in 1k6n

Go back to Magnesium Binding Sites List in 1k6n
Magnesium binding site 4 out of 4 in the E(L212)A,D(L213)A Double Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E(L212)A,D(L213)A Double Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg502

b:17.8
occ:1.00
MG M:BCL502 0.0 17.8 1.0
ND M:BCL502 2.0 16.8 1.0
NB M:BCL502 2.1 18.5 1.0
NC M:BCL502 2.1 21.8 1.0
NA M:BCL502 2.2 13.3 1.0
NE2 M:HIS202 2.2 17.2 1.0
C4D M:BCL502 3.0 19.3 1.0
C1B M:BCL502 3.1 20.9 1.0
C4B M:BCL502 3.1 18.4 1.0
C1C M:BCL502 3.1 21.4 1.0
C1D M:BCL502 3.1 16.6 1.0
CE1 M:HIS202 3.1 26.6 1.0
C4C M:BCL502 3.1 21.3 1.0
CD2 M:HIS202 3.1 19.0 1.0
C4A M:BCL502 3.1 15.2 1.0
C1A M:BCL502 3.2 12.6 1.0
CHC M:BCL502 3.4 17.9 1.0
CHB M:BCL502 3.5 11.0 1.0
CHA M:BCL502 3.5 13.4 1.0
CHD M:BCL502 3.5 17.6 1.0
CBB L:BCL302 3.7 16.1 1.0
CAB L:BCL302 4.0 18.5 1.0
OBB L:BCL302 4.2 27.2 1.0
C3D M:BCL502 4.2 20.1 1.0
ND1 M:HIS202 4.3 18.8 1.0
CG M:HIS202 4.3 18.1 1.0
C2B M:BCL502 4.3 24.1 1.0
C3B M:BCL502 4.3 23.5 1.0
C2D M:BCL502 4.3 21.4 1.0
C2C M:BCL502 4.3 23.6 1.0
C3C M:BCL502 4.4 21.0 1.0
C2A M:BCL502 4.4 15.7 1.0
C3A M:BCL502 4.4 13.7 1.0
C3B L:BCL302 4.5 20.7 1.0
CBD M:BCL502 4.9 18.2 1.0
O2D M:BCL502 4.9 28.3 1.0
CMC M:BCL502 5.0 15.6 1.0

Reference:

P.R.Pokkuluri, P.D.Laible, Y.L.Deng, T.N.Wong, D.K.Hanson, M.Schiffer. The Structure of A Mutant Photosynthetic Reaction Center Shows Unexpected Changes in Main Chain Orientations and Quinone Position. Biochemistry V. 41 5998 2002.
ISSN: ISSN 0006-2960
PubMed: 11993994
DOI: 10.1021/BI0118963
Page generated: Mon Dec 14 06:14:56 2020

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