Atomistry » Magnesium » PDB 3hwx-3i5f » 3i4d
Atomistry »
  Magnesium »
    PDB 3hwx-3i5f »
      3i4d »

Magnesium in PDB 3i4d: Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1

Protein crystallography data

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1, PDB code: 3i4d was solved by R.Fujii, S.Adachi, A.W.Roszak, A.T.Gardiner, R.J.Cogdell, N.W.Isaacs, S.Koshihara, H.Hashimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.25 / 2.01
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 138.800, 138.800, 184.569, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 20.7

Other elements in 3i4d:

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1 also contains other interesting chemical elements:

Potassium (K) 2 atoms
Iron (Fe) 1 atom
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1 (pdb code 3i4d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1, PDB code: 3i4d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3i4d

Go back to Magnesium Binding Sites List in 3i4d
Magnesium binding site 1 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg602

b:29.8
occ:1.00
MG L:BCL602 0.0 29.8 1.0
ND L:BCL602 2.0 28.1 1.0
NB L:BCL602 2.1 29.9 1.0
NC L:BCL602 2.1 28.4 1.0
NE2 L:HIS173 2.2 27.5 1.0
NA L:BCL602 2.2 26.4 1.0
C4D L:BCL602 3.0 28.1 1.0
C1B L:BCL602 3.1 29.7 1.0
C1C L:BCL602 3.1 29.0 1.0
C4A L:BCL602 3.1 30.1 1.0
CE1 L:HIS173 3.1 31.5 1.0
C4B L:BCL602 3.1 29.1 1.0
C4C L:BCL602 3.1 30.8 1.0
C1D L:BCL602 3.1 27.9 1.0
CD2 L:HIS173 3.2 29.5 1.0
C1A L:BCL602 3.2 28.9 1.0
CHB L:BCL602 3.4 28.5 1.0
CHC L:BCL602 3.5 29.6 1.0
CHD L:BCL602 3.5 30.1 1.0
CHA L:BCL602 3.5 30.2 1.0
CBB M:BCL603 3.7 28.0 1.0
CAB M:BCL603 3.9 34.6 1.0
OBB M:BCL603 4.1 34.3 1.0
C3D L:BCL602 4.2 28.6 1.0
ND1 L:HIS173 4.2 29.8 1.0
C3B L:BCL602 4.3 29.2 1.0
C2B L:BCL602 4.3 29.3 1.0
CG L:HIS173 4.3 29.7 1.0
C2D L:BCL602 4.3 30.4 1.0
C3A L:BCL602 4.4 31.1 1.0
C2C L:BCL602 4.4 30.3 1.0
C3C L:BCL602 4.4 29.6 1.0
C2A L:BCL602 4.5 31.3 1.0
C3B M:BCL603 4.6 29.3 1.0
CD2 L:PHE167 4.7 33.0 1.0
CMA L:BCL602 4.9 26.5 1.0
CBD L:BCL602 5.0 28.0 1.0

Magnesium binding site 2 out of 4 in 3i4d

Go back to Magnesium Binding Sites List in 3i4d
Magnesium binding site 2 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg604

b:28.3
occ:1.00
MG L:BCL604 0.0 28.3 1.0
ND L:BCL604 2.1 27.0 1.0
NC L:BCL604 2.1 28.6 1.0
NB L:BCL604 2.1 26.7 1.0
NA L:BCL604 2.1 29.1 1.0
NE2 L:HIS153 2.2 29.4 1.0
C4D L:BCL604 3.0 26.4 1.0
C1C L:BCL604 3.0 27.7 1.0
CD2 L:HIS153 3.0 32.2 1.0
C4B L:BCL604 3.1 30.0 1.0
C1B L:BCL604 3.1 28.6 1.0
C4A L:BCL604 3.1 27.2 1.0
C4C L:BCL604 3.1 26.1 1.0
C1D L:BCL604 3.1 27.5 1.0
C1A L:BCL604 3.2 27.4 1.0
CE1 L:HIS153 3.2 32.9 1.0
CHC L:BCL604 3.4 28.0 1.0
CHA L:BCL604 3.4 30.5 1.0
CHB L:BCL604 3.4 27.8 1.0
CHD L:BCL604 3.5 28.2 1.0
C3D L:BCL604 4.2 24.6 1.0
CG L:HIS153 4.2 31.6 1.0
C3B L:BCL604 4.3 27.1 1.0
ND1 L:HIS153 4.3 31.4 1.0
C2B L:BCL604 4.3 27.5 1.0
C2D L:BCL604 4.3 29.8 1.0
CBB L:BPH402 4.4 23.5 1.0
C2C L:BCL604 4.4 25.4 1.0
C3C L:BCL604 4.4 27.1 1.0
C3A L:BCL604 4.4 29.6 1.0
C2A L:BCL604 4.5 26.9 1.0
CBC L:BCL604 4.7 29.3 1.0
CE2 M:TYR210 4.7 28.3 1.0
CD1 L:LEU154 4.9 39.4 1.0
C19 L:BPH402 4.9 30.4 1.0
CBD L:BCL604 4.9 30.9 1.0
CBA L:BCL604 5.0 28.8 1.0
CMC L:BCL604 5.0 28.8 1.0

Magnesium binding site 3 out of 4 in 3i4d

Go back to Magnesium Binding Sites List in 3i4d
Magnesium binding site 3 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg601

b:33.1
occ:1.00
MG M:BCL601 0.0 33.1 1.0
ND M:BCL601 2.0 29.1 1.0
NB M:BCL601 2.1 32.8 1.0
NC M:BCL601 2.1 30.9 1.0
NA M:BCL601 2.2 33.1 1.0
NE2 M:HIS182 2.3 29.3 1.0
C4D M:BCL601 2.9 31.1 1.0
C4B M:BCL601 3.1 31.6 1.0
C1D M:BCL601 3.1 29.4 1.0
CD2 M:HIS182 3.1 32.0 1.0
C1C M:BCL601 3.1 30.8 1.0
C1B M:BCL601 3.1 31.1 1.0
C4A M:BCL601 3.1 33.6 1.0
C4C M:BCL601 3.1 33.2 1.0
C1A M:BCL601 3.2 33.5 1.0
CE1 M:HIS182 3.3 34.4 1.0
CHC M:BCL601 3.4 30.6 1.0
CHB M:BCL601 3.4 33.5 1.0
CHA M:BCL601 3.4 33.1 1.0
CHD M:BCL601 3.5 29.9 1.0
C3D M:BCL601 4.1 29.2 1.0
C2D M:BCL601 4.2 29.0 1.0
C3B M:BCL601 4.3 32.8 1.0
C2B M:BCL601 4.3 33.3 1.0
CG M:HIS182 4.3 33.1 1.0
ND1 M:HIS182 4.4 35.9 1.0
C3A M:BCL601 4.4 33.4 1.0
C2C M:BCL601 4.4 34.5 1.0
C3C M:BCL601 4.4 34.1 1.0
C2A M:BCL601 4.5 34.2 1.0
CBB M:BPH401 4.5 31.4 1.0
CE2 L:PHE181 4.8 28.2 1.0
CBD M:BCL601 4.9 32.5 1.0
CMA M:BCL601 5.0 32.1 1.0

Magnesium binding site 4 out of 4 in 3i4d

Go back to Magnesium Binding Sites List in 3i4d
Magnesium binding site 4 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg603

b:30.6
occ:1.00
MG M:BCL603 0.0 30.6 1.0
ND M:BCL603 2.0 28.3 1.0
NB M:BCL603 2.1 30.6 1.0
NC M:BCL603 2.1 29.1 1.0
NA M:BCL603 2.2 28.9 1.0
NE2 M:HIS202 2.3 30.6 1.0
C4D M:BCL603 2.9 33.5 1.0
C1C M:BCL603 3.0 30.7 1.0
C1B M:BCL603 3.1 29.8 1.0
C4B M:BCL603 3.1 31.4 1.0
C4C M:BCL603 3.1 31.0 1.0
C1D M:BCL603 3.1 31.7 1.0
C4A M:BCL603 3.1 30.4 1.0
CE1 M:HIS202 3.2 27.5 1.0
C1A M:BCL603 3.2 30.2 1.0
CD2 M:HIS202 3.3 31.2 1.0
CHC M:BCL603 3.4 30.1 1.0
CHB M:BCL603 3.4 28.1 1.0
CHA M:BCL603 3.4 29.5 1.0
CHD M:BCL603 3.4 29.1 1.0
CBB L:BCL602 3.6 28.0 1.0
CAB L:BCL602 3.8 33.0 1.0
OBB L:BCL602 4.0 31.9 1.0
C3D M:BCL603 4.2 29.2 1.0
C2D M:BCL603 4.3 31.8 1.0
C2B M:BCL603 4.3 28.1 1.0
ND1 M:HIS202 4.3 29.6 1.0
C3B M:BCL603 4.3 29.3 1.0
C2C M:BCL603 4.3 31.6 1.0
C3C M:BCL603 4.4 30.4 1.0
CG M:HIS202 4.4 27.6 1.0
C3A M:BCL603 4.5 28.7 1.0
C2A M:BCL603 4.5 29.6 1.0
C3B L:BCL602 4.6 29.2 1.0
CBD M:BCL603 4.9 29.0 1.0
CMC M:BCL603 4.9 29.8 1.0

Reference:

R.Fujii, S.Adachi, A.W.Roszak, A.T.Gardiner, R.J.Cogdell, N.W.Isaacs, S.Koshihara, H.Hashimoto. Structure of the Carotenoid Bound to the Reaction Centre From Rhodobacter Sphaeroides 2.4.1 Revealed By Time-Resolved X-Ray Crystallography To Be Published.
Page generated: Mon Dec 14 08:15:33 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy