Magnesium in PDB 3vdi: Structure of the Fmo Protein From Pelodictyon Phaeum

The structure of Structure of the Fmo Protein From Pelodictyon Phaeum, PDB code: 3vdi was solved by D.E.Tronrud, C.R.Larson, C.O.Seng, L.Lauman, H.J.Matthies, J.Wen, R.E.Blankenship, J.P.Allen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.99
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	83.967, 83.967, 115.724, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 19

The binding sites of Magnesium atom in the Structure of the Fmo Protein From Pelodictyon Phaeum (pdb code 3vdi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Structure of the Fmo Protein From Pelodictyon Phaeum, PDB code: 3vdi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Structure of the Fmo Protein From Pelodictyon Phaeum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Fmo Protein From Pelodictyon Phaeum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:17.4 occ:1.00 MG A:BCL401 0.0 17.4 1.0 ND A:BCL401 2.0 16.4 1.0 NB A:BCL401 2.1 17.2 1.0 NC A:BCL401 2.1 15.0 1.0 NA A:BCL401 2.2 18.4 1.0 NE2 A:HIS106 2.2 28.3 1.0 CE1 A:HIS106 2.9 28.1 1.0 C4D A:BCL401 3.0 18.0 1.0 C4B A:BCL401 3.1 17.0 1.0 C1B A:BCL401 3.1 17.9 1.0 C1C A:BCL401 3.1 15.9 1.0 C1D A:BCL401 3.2 15.9 1.0 C4A A:BCL401 3.2 18.4 1.0 C4C A:BCL401 3.2 15.0 1.0 C1A A:BCL401 3.2 18.7 1.0 CD2 A:HIS106 3.3 28.6 1.0 CHC A:BCL401 3.4 16.6 1.0 CHB A:BCL401 3.4 18.6 1.0 CHA A:BCL401 3.5 18.9 1.0 CHD A:BCL401 3.5 15.1 1.0 C3 A:BCL401 3.8 16.2 1.0 C2 A:BCL401 3.9 16.3 1.0 ND1 A:HIS106 4.1 28.4 1.0 C4 A:BCL401 4.2 14.8 1.0 C3D A:BCL401 4.2 17.5 1.0 C5 A:BCL401 4.2 15.9 1.0 CG A:HIS106 4.3 25.4 1.0 C1 A:BCL401 4.3 17.2 1.0 C2B A:BCL401 4.3 18.0 1.0 C2D A:BCL401 4.3 17.1 1.0 C3B A:BCL401 4.3 17.7 1.0 C2C A:BCL401 4.4 15.2 1.0 C3C A:BCL401 4.5 14.8 1.0 C3A A:BCL401 4.5 19.2 1.0 C2A A:BCL401 4.5 19.1 1.0 O2A A:BCL401 4.6 19.1 1.0 C6 A:BCL401 4.8 17.0 1.0 CBD A:BCL401 4.9 19.4 1.0

Magnesium binding site 2 out of 7 in the Structure of the Fmo Protein From Pelodictyon Phaeum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Fmo Protein From Pelodictyon Phaeum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:15.1 occ:1.00 MG A:BCL402 0.0 15.1 1.0 ND A:BCL402 2.0 14.2 1.0 O A:HOH1005 2.0 12.3 1.0 NB A:BCL402 2.1 14.5 1.0 NC A:BCL402 2.2 13.9 1.0 NA A:BCL402 2.2 15.2 1.0 C4D A:BCL402 3.0 14.7 1.0 C4B A:BCL402 3.1 15.2 1.0 C1B A:BCL402 3.1 15.2 1.0 C1C A:BCL402 3.1 13.9 1.0 C1D A:BCL402 3.1 14.1 1.0 C4A A:BCL402 3.2 15.7 1.0 C4C A:BCL402 3.2 14.2 1.0 C1A A:BCL402 3.2 15.1 1.0 CHC A:BCL402 3.4 14.6 1.0 CHB A:BCL402 3.4 15.5 1.0 CHA A:BCL402 3.5 14.7 1.0 CHD A:BCL402 3.5 14.6 1.0 O A:HOH1059 3.9 24.7 1.0 C12 A:BCL407 3.9 17.8 1.0 O A:HOH1069 4.0 23.8 1.0 C3D A:BCL402 4.2 14.0 1.0 C2B A:BCL402 4.3 15.2 1.0 C3B A:BCL402 4.3 15.7 1.0 C2D A:BCL402 4.3 13.4 1.0 ND2 A:ASN75 4.4 18.0 1.0 CG2 A:VAL70 4.5 20.1 1.0 C2C A:BCL402 4.5 14.6 1.0 C3A A:BCL402 4.5 16.0 1.0 C3C A:BCL402 4.5 15.2 1.0 C2A A:BCL402 4.5 15.1 1.0 C10 A:BCL407 4.5 15.5 1.0 C11 A:BCL407 4.6 16.1 1.0 CB A:VAL70 4.8 20.1 1.0 CG1 A:VAL70 4.8 19.8 1.0 C13 A:BCL407 4.9 21.0 1.0 C15 A:BCL407 4.9 23.9 1.0 CBD A:BCL402 5.0 16.5 1.0

Magnesium binding site 3 out of 7 in the Structure of the Fmo Protein From Pelodictyon Phaeum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Fmo Protein From Pelodictyon Phaeum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:14.3 occ:1.00 MG A:BCL403 0.0 14.3 1.0 ND A:BCL403 2.1 13.7 1.0 NB A:BCL403 2.1 15.0 1.0 NE2 A:HIS294 2.1 15.8 1.0 NC A:BCL403 2.1 15.0 1.0 NA A:BCL403 2.2 14.1 1.0 C4D A:BCL403 3.0 13.6 1.0 C4B A:BCL403 3.1 15.4 1.0 C1B A:BCL403 3.1 15.5 1.0 C1C A:BCL403 3.1 15.5 1.0 CE1 A:HIS294 3.1 15.3 1.0 CD2 A:HIS294 3.1 16.2 1.0 C4A A:BCL403 3.2 15.0 1.0 C4C A:BCL403 3.2 15.4 1.0 C1D A:BCL403 3.2 14.5 1.0 C1A A:BCL403 3.2 13.6 1.0 CHC A:BCL403 3.4 15.8 1.0 CHB A:BCL403 3.4 14.8 1.0 CHA A:BCL403 3.5 13.8 1.0 CHD A:BCL403 3.5 15.2 1.0 ND1 A:HIS294 4.2 16.0 1.0 CG A:HIS294 4.2 14.9 1.0 C3D A:BCL403 4.3 14.0 1.0 C2B A:BCL403 4.3 16.0 1.0 C3B A:BCL403 4.3 16.5 1.0 C2D A:BCL403 4.4 14.4 1.0 C2C A:BCL403 4.4 16.3 1.0 C3C A:BCL403 4.5 16.2 1.0 CBC A:BCL404 4.5 13.5 1.0 C3A A:BCL403 4.5 13.8 1.0 C2A A:BCL403 4.5 12.9 1.0 CD1 A:ILE261 4.8 15.4 1.0 CBD A:BCL403 5.0 14.6 1.0 CG2 A:VAL297 5.0 16.1 1.0

Magnesium binding site 4 out of 7 in the Structure of the Fmo Protein From Pelodictyon Phaeum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Fmo Protein From Pelodictyon Phaeum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:15.1 occ:1.00 MG A:BCL404 0.0 15.1 1.0 ND A:BCL404 2.0 14.6 1.0 NB A:BCL404 2.1 14.5 1.0 NC A:BCL404 2.1 13.8 1.0 NE2 A:HIS286 2.1 13.9 1.0 NA A:BCL404 2.2 15.1 1.0 C4D A:BCL404 3.0 15.1 1.0 CE1 A:HIS286 3.1 13.4 1.0 C1B A:BCL404 3.1 14.9 1.0 C4B A:BCL404 3.1 13.9 1.0 CD2 A:HIS286 3.1 14.3 1.0 C1C A:BCL404 3.1 13.2 1.0 C4A A:BCL404 3.1 15.8 1.0 C1D A:BCL404 3.2 14.9 1.0 C4C A:BCL404 3.2 14.0 1.0 C1A A:BCL404 3.2 15.2 1.0 CHB A:BCL404 3.4 15.2 1.0 CHC A:BCL404 3.4 12.9 1.0 CHA A:BCL404 3.5 15.3 1.0 CHD A:BCL404 3.5 13.7 1.0 CG A:HIS286 4.2 14.6 1.0 C4 A:BCL404 4.2 16.3 1.0 ND1 A:HIS286 4.2 15.3 1.0 C3D A:BCL404 4.2 15.5 1.0 C2B A:BCL404 4.3 15.3 1.0 C2D A:BCL404 4.3 15.3 1.0 C3B A:BCL404 4.4 14.5 1.0 C3A A:BCL404 4.4 16.5 1.0 C2C A:BCL404 4.4 13.2 1.0 C3C A:BCL404 4.5 13.7 1.0 C2A A:BCL404 4.5 16.6 1.0 O2A A:BCL404 4.6 19.8 1.0 C4 A:BCL405 4.7 12.7 1.0 C3 A:BCL404 4.8 17.4 1.0 CD2 A:LEU291 4.9 17.1 1.0 CMA A:BCL404 4.9 16.2 1.0 CBD A:BCL404 4.9 16.1 1.0

Magnesium binding site 5 out of 7 in the Structure of the Fmo Protein From Pelodictyon Phaeum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Fmo Protein From Pelodictyon Phaeum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:17.7 occ:1.00 MG A:BCL405 0.0 17.7 1.0 O A:LEU238 2.0 16.7 1.0 ND A:BCL405 2.0 16.5 1.0 NB A:BCL405 2.1 17.7 1.0 NA A:BCL405 2.2 18.0 1.0 NC A:BCL405 2.2 16.6 1.0 C4D A:BCL405 3.0 15.8 1.0 C1B A:BCL405 3.1 18.4 1.0 C4B A:BCL405 3.1 17.8 1.0 C A:LEU238 3.1 18.6 1.0 C4A A:BCL405 3.1 17.9 1.0 C1C A:BCL405 3.1 16.2 1.0 C1D A:BCL405 3.2 16.0 1.0 C4C A:BCL405 3.2 16.5 1.0 C1A A:BCL405 3.2 17.2 1.0 CHB A:BCL405 3.4 17.8 1.0 CHC A:BCL405 3.4 16.5 1.0 CHA A:BCL405 3.5 16.8 1.0 CHD A:BCL405 3.5 16.1 1.0 CA A:LEU238 3.8 17.2 1.0 C12 A:BCL406 3.9 27.4 1.0 CB A:LEU238 3.9 16.4 1.0 N A:PHE239 4.2 16.2 1.0 C3D A:BCL405 4.2 15.3 1.0 C2B A:BCL405 4.3 19.3 1.0 C3B A:BCL405 4.3 19.4 1.0 C2D A:BCL405 4.3 14.9 1.0 CD1 A:LEU238 4.4 19.6 1.0 C3A A:BCL405 4.4 17.6 1.0 C2C A:BCL405 4.5 15.6 1.0 C2A A:BCL405 4.5 16.8 1.0 C3C A:BCL405 4.5 16.4 1.0 CA A:PHE239 4.6 16.2 1.0 C15 A:BCL406 4.7 26.6 1.0 CG A:LEU238 4.8 20.3 1.0 C11 A:BCL406 4.8 27.4 1.0 C16 A:BCL406 4.8 26.4 1.0 CD A:PRO240 4.9 17.0 1.0 C13 A:BCL406 4.9 26.4 1.0 CBD A:BCL405 4.9 17.2 1.0

Magnesium binding site 6 out of 7 in the Structure of the Fmo Protein From Pelodictyon Phaeum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Fmo Protein From Pelodictyon Phaeum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:17.6 occ:1.00 MG A:BCL406 0.0 17.6 1.0 ND A:BCL406 2.0 18.0 1.0 NB A:BCL406 2.1 19.2 1.0 NC A:BCL406 2.1 17.1 1.0 NA A:BCL406 2.2 18.7 1.0 NE2 A:HIS141 2.2 15.4 1.0 C4D A:BCL406 3.0 18.2 1.0 CD2 A:HIS141 3.1 16.4 1.0 C4B A:BCL406 3.1 18.3 1.0 C1B A:BCL406 3.1 19.5 1.0 C1C A:BCL406 3.1 16.8 1.0 C4A A:BCL406 3.1 19.5 1.0 C1D A:BCL406 3.2 17.7 1.0 C4C A:BCL406 3.2 17.9 1.0 C1A A:BCL406 3.2 18.6 1.0 CE1 A:HIS141 3.2 15.1 1.0 CHB A:BCL406 3.4 19.4 1.0 CHC A:BCL406 3.4 16.8 1.0 CHA A:BCL406 3.5 18.4 1.0 CHD A:BCL406 3.5 17.0 1.0 C18 A:BCL403 4.0 36.1 1.0 C20 A:BCL403 4.2 36.1 1.0 C19 A:BCL403 4.2 37.1 1.0 C3D A:BCL406 4.2 18.1 1.0 CG A:HIS141 4.3 15.4 1.0 C2B A:BCL406 4.3 18.9 1.0 C3B A:BCL406 4.3 18.9 1.0 ND1 A:HIS141 4.3 16.3 1.0 C2D A:BCL406 4.3 17.8 1.0 C2C A:BCL406 4.5 17.3 1.0 C3A A:BCL406 4.5 19.0 1.0 C3C A:BCL406 4.5 18.2 1.0 C2A A:BCL406 4.5 19.5 1.0 CG2 A:VAL114 4.7 17.0 1.0 CBD A:BCL406 4.9 19.3 1.0

Magnesium binding site 7 out of 7 in the Structure of the Fmo Protein From Pelodictyon Phaeum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Fmo Protein From Pelodictyon Phaeum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:14.3 occ:1.00 MG A:BCL407 0.0 14.3 1.0 ND A:BCL407 2.0 14.3 1.0 NB A:BCL407 2.1 14.0 1.0 NC A:BCL407 2.1 14.7 1.0 NA A:BCL407 2.2 13.2 1.0 ND1 A:HIS293 2.2 15.2 1.0 C4D A:BCL407 3.0 13.6 1.0 C4B A:BCL407 3.1 15.3 1.0 C1B A:BCL407 3.1 13.9 1.0 C1C A:BCL407 3.1 16.1 1.0 CE1 A:HIS293 3.1 14.0 1.0 C1D A:BCL407 3.1 15.0 1.0 C4A A:BCL407 3.2 13.1 1.0 C4C A:BCL407 3.2 15.3 1.0 C1A A:BCL407 3.2 13.7 1.0 CG A:HIS293 3.2 14.1 1.0 CHC A:BCL407 3.4 15.5 1.0 C4 A:BCL403 3.4 17.9 1.0 CHB A:BCL407 3.4 12.8 1.0 CHA A:BCL407 3.4 13.2 1.0 CHD A:BCL407 3.5 14.4 1.0 CB A:HIS293 3.6 11.6 1.0 C3D A:BCL407 4.2 14.3 1.0 C2B A:BCL407 4.2 14.8 1.0 C3B A:BCL407 4.2 15.5 1.0 C2D A:BCL407 4.3 15.3 1.0 NE2 A:HIS293 4.3 14.4 1.0 CD2 A:HIS293 4.4 14.8 1.0 CG2 A:ILE289 4.4 11.9 1.0 C2C A:BCL407 4.5 16.2 1.0 C3C A:BCL407 4.5 14.9 1.0 C3A A:BCL407 4.5 13.5 1.0 C2A A:BCL407 4.5 13.2 1.0 C3 A:BCL403 4.7 18.4 1.0 CBD A:BCL407 4.9 13.9 1.0

D.E.Tronrud, J.P.Allen. Reinterpretation of the Electron Density at the Site of the Eighth Bacteriochlorophyll in the Fmo Protein From Pelodictyon Phaeum. Photosynth.Res. V. 112 71 2012.
ISSN: ISSN 0166-8595
PubMed: 22457093
DOI: 10.1007/S11120-012-9735-8