Magnesium in PDB 3t6d: Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08

The structure of Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08, PDB code: 3t6d was solved by A.W.Roszak, A.T.Gardiner, N.W.Isaacs, R.J.Cogdell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.34 / 1.95
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	220.440, 220.440, 113.100, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.6

The structure of Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08 also contains other interesting chemical elements:

Iron

(Fe)

5 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08 (pdb code 3t6d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08, PDB code: 3t6d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08 within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg400 b:37.3 occ:1.00 MG L:BCB400 0.0 37.3 1.0 ND L:BCB400 2.0 32.3 1.0 NC L:BCB400 2.0 33.7 1.0 NB L:BCB400 2.0 32.6 1.0 NA L:BCB400 2.1 36.0 1.0 NE2 L:HIS173 2.3 35.7 1.0 C4D L:BCB400 2.9 34.6 1.0 C1D L:BCB400 3.0 37.0 1.0 C1C L:BCB400 3.0 32.5 1.0 C4B L:BCB400 3.1 30.8 1.0 C4C L:BCB400 3.1 33.3 1.0 C4A L:BCB400 3.1 34.3 1.0 C1B L:BCB400 3.1 32.3 1.0 C1A L:BCB400 3.1 33.8 1.0 CD2 L:HIS173 3.2 32.2 1.0 CE1 L:HIS173 3.3 37.7 1.0 CBB M:BCB401 3.3 29.2 1.0 CHD L:BCB400 3.4 35.1 1.0 CHC L:BCB400 3.4 30.8 1.0 CHA L:BCB400 3.4 36.1 1.0 CHB L:BCB400 3.4 33.1 1.0 CAB M:BCB401 3.5 30.9 1.0 OBB M:BCB401 3.7 34.0 1.0 C3D L:BCB400 4.1 30.8 1.0 C2D L:BCB400 4.2 37.4 1.0 C3B L:BCB400 4.2 28.2 1.0 C2B L:BCB400 4.3 30.7 1.0 C3C L:BCB400 4.3 32.0 1.0 CD1 L:TRP167 4.3 38.1 1.0 C3B M:BCB401 4.3 28.3 1.0 C2C L:BCB400 4.3 34.6 1.0 ND1 L:HIS173 4.4 33.3 1.0 CG L:HIS173 4.4 33.4 1.0 C2A L:BCB400 4.4 37.2 1.0 C3A L:BCB400 4.4 36.9 1.0 NE1 L:TRP167 4.4 35.5 1.0 CBD L:BCB400 4.9 36.2 1.0 C2B M:BCB401 5.0 29.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08 within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg401 b:34.9 occ:1.00 MG L:BCB401 0.0 34.9 1.0 NB L:BCB401 2.0 30.7 1.0 ND L:BCB401 2.0 30.9 1.0 NC L:BCB401 2.0 30.8 1.0 NA L:BCB401 2.1 30.6 1.0 NE2 L:HIS153 2.2 32.9 1.0 C4D L:BCB401 2.9 32.6 1.0 C4B L:BCB401 3.0 31.3 1.0 C1C L:BCB401 3.1 33.3 1.0 C1D L:BCB401 3.1 29.8 1.0 C1B L:BCB401 3.1 32.0 1.0 C4A L:BCB401 3.1 32.7 1.0 C1A L:BCB401 3.1 33.4 1.0 C4C L:BCB401 3.2 31.7 1.0 CE1 L:HIS153 3.2 32.6 1.0 CD2 L:HIS153 3.3 35.3 1.0 CHC L:BCB401 3.4 30.3 1.0 CHA L:BCB401 3.5 35.3 1.0 CHB L:BCB401 3.5 30.5 1.0 CHD L:BCB401 3.5 30.1 1.0 CBB L:BPB402 3.9 40.9 1.0 C3D L:BCB401 4.2 32.6 1.0 C3B L:BCB401 4.2 32.4 1.0 C2D L:BCB401 4.2 31.0 1.0 C2B L:BCB401 4.3 34.0 1.0 ND1 L:HIS153 4.4 31.7 1.0 C2C L:BCB401 4.4 35.3 1.0 C3C L:BCB401 4.4 30.6 1.0 CG L:HIS153 4.4 30.4 1.0 CE2 M:TYR208 4.4 31.5 1.0 C2A L:BCB401 4.5 33.4 1.0 C3A L:BCB401 4.5 33.2 1.0 CBA L:BCB401 4.8 38.0 1.0 CBD L:BCB401 4.9 36.0 1.0 CD2 L:LEU154 4.9 32.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08 within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg400 b:38.5 occ:1.00 MG M:BCB400 0.0 38.5 1.0 NB M:BCB400 2.0 38.5 1.0 ND M:BCB400 2.0 35.6 1.0 NC M:BCB400 2.1 35.3 1.0 NA M:BCB400 2.1 37.8 1.0 NE2 M:HIS180 2.3 39.1 1.0 C4D M:BCB400 2.9 38.3 1.0 C4B M:BCB400 3.1 42.8 1.0 C1D M:BCB400 3.1 40.0 1.0 C1B M:BCB400 3.1 40.3 1.0 C4A M:BCB400 3.1 39.5 1.0 C1C M:BCB400 3.1 34.7 1.0 C1A M:BCB400 3.1 37.6 1.0 C4C M:BCB400 3.1 34.2 1.0 CD2 M:HIS180 3.2 40.7 1.0 CE1 M:HIS180 3.3 40.6 1.0 CHC M:BCB400 3.4 36.4 1.0 CHA M:BCB400 3.5 39.0 1.0 CHD M:BCB400 3.5 36.6 1.0 CHB M:BCB400 3.5 37.9 1.0 C3D M:BCB400 4.1 38.4 1.0 CBB M:BPB402 4.1 48.6 1.0 C2D M:BCB400 4.2 38.0 1.0 C3B M:BCB400 4.3 39.2 1.0 C2B M:BCB400 4.3 38.8 1.0 CG M:HIS180 4.4 38.0 1.0 C3C M:BCB400 4.4 34.3 1.0 ND1 M:HIS180 4.4 36.5 1.0 C2C M:BCB400 4.4 36.3 1.0 C3A M:BCB400 4.4 40.2 1.0 C2A M:BCB400 4.4 41.2 1.0 CE2 L:PHE181 4.6 39.3 1.0 CBA M:BCB400 4.7 47.2 1.0 CBD M:BCB400 4.9 40.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08 within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg401 b:33.0 occ:1.00 MG M:BCB401 0.0 33.0 1.0 NB M:BCB401 2.0 31.0 1.0 ND M:BCB401 2.0 30.9 1.0 NC M:BCB401 2.0 29.5 1.0 NA M:BCB401 2.1 32.1 1.0 NE2 M:HIS200 2.3 34.9 1.0 C4D M:BCB401 2.9 34.5 1.0 C1D M:BCB401 3.0 34.5 1.0 C4B M:BCB401 3.1 31.1 1.0 C4A M:BCB401 3.1 31.5 1.0 C1B M:BCB401 3.1 32.7 1.0 C1C M:BCB401 3.1 32.0 1.0 C4C M:BCB401 3.1 32.3 1.0 C1A M:BCB401 3.1 33.2 1.0 CBB L:BCB400 3.2 28.5 1.0 CD2 M:HIS200 3.2 35.2 1.0 CE1 M:HIS200 3.3 33.8 1.0 CHC M:BCB401 3.4 31.0 1.0 CHD M:BCB401 3.4 34.0 1.0 CHB M:BCB401 3.4 31.9 1.0 CHA M:BCB401 3.4 33.5 1.0 CAB L:BCB400 3.6 31.3 1.0 OBB L:BCB400 3.9 31.9 1.0 C3D M:BCB401 4.2 32.3 1.0 C2D M:BCB401 4.2 33.2 1.0 C3B M:BCB401 4.3 28.3 1.0 C2B M:BCB401 4.3 29.7 1.0 C2C M:BCB401 4.3 32.8 1.0 C3C M:BCB401 4.4 31.4 1.0 C3B L:BCB400 4.4 28.2 1.0 ND1 M:HIS200 4.4 37.2 1.0 CG M:HIS200 4.4 32.1 1.0 C3A M:BCB401 4.4 35.3 1.0 C2A M:BCB401 4.4 36.6 1.0 CBD M:BCB401 4.9 34.7 1.0 CMC M:BCB401 4.9 30.4 1.0 CD1 M:ILE204 5.0 33.9 1.0 C4B L:BCB400 5.0 30.8 1.0

A.W.Roszak, V.Moulisova, A.D.Reksodipuro, A.T.Gardiner, R.Fujii, H.Hashimoto, N.W.Isaacs, R.J.Cogdell. New Insights Into the Structure of the Reaction Centre From Blastochloris Viridis: Evolution in the Laboratory. Biochem.J. V. 442 27 2012.
ISSN: ISSN 0264-6021
PubMed: 22054235
DOI: 10.1042/BJ20111540