Atomistry » Magnesium » PDB 5m3f-5mdl » 5m7l
Atomistry »
  Magnesium »
    PDB 5m3f-5mdl »
      5m7l »

Magnesium in PDB 5m7l: Blastochloris Viridis Photosynthetic Reaction Center Synchrotron Structure

Protein crystallography data

The structure of Blastochloris Viridis Photosynthetic Reaction Center Synchrotron Structure, PDB code: 5m7l was solved by A.S.Sharma, L.Johansson, E.Dunevall, W.Y.Wahlgren, R.Neutze, G.Katona, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.50 / 3.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.600, 82.900, 382.100, 90.00, 90.00, 90.00
R / Rfree (%) 24.2 / 28

Other elements in 5m7l:

The structure of Blastochloris Viridis Photosynthetic Reaction Center Synchrotron Structure also contains other interesting chemical elements:

Iron (Fe) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Blastochloris Viridis Photosynthetic Reaction Center Synchrotron Structure (pdb code 5m7l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Blastochloris Viridis Photosynthetic Reaction Center Synchrotron Structure, PDB code: 5m7l:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5m7l

Go back to Magnesium Binding Sites List in 5m7l
Magnesium binding site 1 out of 4 in the Blastochloris Viridis Photosynthetic Reaction Center Synchrotron Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Blastochloris Viridis Photosynthetic Reaction Center Synchrotron Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:37.5
occ:1.00
MG B:BCL301 0.0 37.5 1.0
ND B:BCL301 2.0 56.7 1.0
NB B:BCL301 2.1 61.4 1.0
NC B:BCL301 2.1 55.3 1.0
NA B:BCL301 2.2 66.0 1.0
NE2 C:HIS180 2.7 62.8 1.0
C4D B:BCL301 3.0 58.7 1.0
C4B B:BCL301 3.1 60.2 1.0
C1B B:BCL301 3.1 62.7 1.0
C1C B:BCL301 3.1 55.4 1.0
C1D B:BCL301 3.1 55.0 1.0
C4A B:BCL301 3.1 66.4 1.0
C4C B:BCL301 3.2 53.7 1.0
C1A B:BCL301 3.2 66.3 1.0
CHC B:BCL301 3.4 57.8 1.0
CHB B:BCL301 3.4 64.8 1.0
CHA B:BCL301 3.5 62.0 1.0
CD2 C:HIS180 3.5 62.9 1.0
CHD B:BCL301 3.5 53.7 1.0
CE1 C:HIS180 3.8 63.4 1.0
C3D B:BCL301 4.2 57.0 1.0
C2D B:BCL301 4.3 55.8 1.0
C2B B:BCL301 4.3 62.5 1.0
C3B B:BCL301 4.3 61.4 1.0
C2C B:BCL301 4.4 52.6 1.0
C3C B:BCL301 4.4 52.4 1.0
C3A B:BCL301 4.5 68.6 1.0
C2A B:BCL301 4.5 71.6 1.0
OBB C:BPB402 4.5 75.4 1.0
CG C:HIS180 4.7 63.0 1.0
CE2 B:PHE181 4.8 63.1 1.0
ND1 C:HIS180 4.8 63.5 1.0
C22 C:NS5405 4.9 67.5 1.0
CBD B:BCL301 4.9 60.6 1.0
CBA B:BCL301 4.9 89.1 1.0

Magnesium binding site 2 out of 4 in 5m7l

Go back to Magnesium Binding Sites List in 5m7l
Magnesium binding site 2 out of 4 in the Blastochloris Viridis Photosynthetic Reaction Center Synchrotron Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Blastochloris Viridis Photosynthetic Reaction Center Synchrotron Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:48.2
occ:1.00
MG B:BCL302 0.0 48.2 1.0
ND B:BCL302 2.0 60.9 1.0
NB B:BCL302 2.1 64.3 1.0
NC B:BCL302 2.1 61.0 1.0
NA B:BCL302 2.2 63.4 1.0
NE2 B:HIS173 3.0 52.0 1.0
C4D B:BCL302 3.0 61.7 1.0
C1B B:BCL302 3.1 64.8 1.0
C4B B:BCL302 3.1 64.1 1.0
C1C B:BCL302 3.1 60.2 1.0
C1D B:BCL302 3.1 60.7 1.0
C4A B:BCL302 3.1 63.8 1.0
C4C B:BCL302 3.2 60.0 1.0
CAB C:BCL401 3.2 58.6 1.0
C1A B:BCL302 3.2 63.0 1.0
CBB C:BCL401 3.2 58.3 1.0
OBB C:BCL401 3.2 58.0 1.0
CHB B:BCL302 3.4 64.5 1.0
CHC B:BCL302 3.4 62.0 1.0
CHA B:BCL302 3.5 62.5 1.0
CHD B:BCL302 3.5 60.3 1.0
CD2 B:HIS173 3.7 53.8 1.0
C3B C:BCL401 3.9 60.5 1.0
CE1 B:HIS173 4.0 52.2 1.0
C3D B:BCL302 4.2 62.0 1.0
C2B B:BCL302 4.3 65.7 1.0
C2D B:BCL302 4.3 60.9 1.0
C3B B:BCL302 4.3 65.5 1.0
C3A B:BCL302 4.4 63.5 1.0
C2C B:BCL302 4.4 58.0 1.0
C3C B:BCL302 4.5 58.1 1.0
C2A B:BCL302 4.5 62.9 1.0
C2B C:BCL401 4.6 61.9 1.0
C4B C:BCL401 4.7 60.9 1.0
CD1 B:TRP167 4.8 62.2 1.0
NE1 B:TRP167 4.8 63.5 1.0
CMB C:BCL401 4.9 62.3 1.0
CBD B:BCL302 4.9 63.0 1.0
CG B:HIS173 5.0 55.4 1.0

Magnesium binding site 3 out of 4 in 5m7l

Go back to Magnesium Binding Sites List in 5m7l
Magnesium binding site 3 out of 4 in the Blastochloris Viridis Photosynthetic Reaction Center Synchrotron Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Blastochloris Viridis Photosynthetic Reaction Center Synchrotron Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:79.9
occ:1.00
MG B:BCL303 0.0 79.9 1.0
ND B:BCL303 2.0 58.4 1.0
NB B:BCL303 2.1 64.5 1.0
NC B:BCL303 2.1 59.6 1.0
NA B:BCL303 2.2 62.6 1.0
NE2 B:HIS153 2.8 58.7 1.0
C4D B:BCL303 3.0 58.9 1.0
C1B B:BCL303 3.1 65.0 1.0
C4B B:BCL303 3.1 64.2 1.0
C1C B:BCL303 3.1 59.8 1.0
C1D B:BCL303 3.1 58.1 1.0
C4A B:BCL303 3.1 63.8 1.0
C4C B:BCL303 3.2 58.4 1.0
C1A B:BCL303 3.2 62.1 1.0
CHB B:BCL303 3.4 64.6 1.0
CHC B:BCL303 3.4 62.4 1.0
CHA B:BCL303 3.5 60.2 1.0
CHD B:BCL303 3.5 58.1 1.0
CD2 B:HIS153 3.6 58.8 1.0
CE1 B:HIS153 3.9 58.9 1.0
C3D B:BCL303 4.2 58.2 1.0
C2D B:BCL303 4.3 58.0 1.0
C2B B:BCL303 4.3 66.0 1.0
C3B B:BCL303 4.3 65.2 1.0
OBB B:BPB304 4.3 66.0 1.0
C2C B:BCL303 4.4 57.5 1.0
C3C B:BCL303 4.4 57.3 1.0
C3A B:BCL303 4.5 64.0 1.0
C2A B:BCL303 4.5 63.8 1.0
CG B:HIS153 4.8 59.8 1.0
CE2 C:TYR208 4.8 66.5 1.0
CD2 B:LEU154 4.9 58.9 1.0
CBD B:BCL303 4.9 59.5 1.0
C19 B:BPB304 4.9 57.5 1.0
ND1 B:HIS153 5.0 58.9 1.0

Magnesium binding site 4 out of 4 in 5m7l

Go back to Magnesium Binding Sites List in 5m7l
Magnesium binding site 4 out of 4 in the Blastochloris Viridis Photosynthetic Reaction Center Synchrotron Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Blastochloris Viridis Photosynthetic Reaction Center Synchrotron Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:55.4
occ:1.00
MG C:BCL401 0.0 55.4 1.0
ND C:BCL401 2.0 62.6 1.0
NB C:BCL401 2.1 62.2 1.0
NC C:BCL401 2.1 57.8 1.0
NA C:BCL401 2.2 66.2 1.0
CE1 C:HIS200 2.8 59.7 1.0
C4D C:BCL401 3.0 63.7 1.0
C4B C:BCL401 3.1 60.9 1.0
C1C C:BCL401 3.1 57.8 1.0
C1B C:BCL401 3.1 62.8 1.0
C1D C:BCL401 3.1 61.5 1.0
C4A C:BCL401 3.2 65.7 1.0
C4C C:BCL401 3.2 58.1 1.0
C1A C:BCL401 3.2 66.2 1.0
CHC C:BCL401 3.3 59.1 1.0
CHA C:BCL401 3.4 64.8 1.0
CHB C:BCL401 3.4 64.2 1.0
CHD C:BCL401 3.5 59.7 1.0
CBB B:BCL302 3.6 66.2 1.0
ND1 C:HIS200 3.7 60.6 1.0
NE2 C:HIS200 3.7 59.8 1.0
CAB B:BCL302 4.0 66.1 1.0
C3D C:BCL401 4.2 63.9 1.0
C2B C:BCL401 4.3 61.9 1.0
C2D C:BCL401 4.3 62.1 1.0
C3B C:BCL401 4.3 60.5 1.0
C2C C:BCL401 4.3 56.7 1.0
OBB B:BCL302 4.3 66.3 1.0
C3C C:BCL401 4.4 57.1 1.0
C3A C:BCL401 4.5 66.4 1.0
C2A C:BCL401 4.5 66.9 1.0
C3B B:BCL302 4.5 65.5 1.0
CMC C:BCL401 4.8 55.7 1.0
CBD C:BCL401 4.8 64.7 1.0
CG C:HIS200 4.9 61.4 1.0
CD2 C:HIS200 4.9 60.5 1.0

Reference:

A.Sharma, L.Johansson, E.Dunevall, W.Y.Wahlgren, R.Neutze, G.Katona. Asymmetry in Serial Femtosecond Crystallography Data. Acta Crystallogr A Found Adv V. 73 93 2017.
ISSN: ESSN 2053-2733
PubMed: 28248658
DOI: 10.1107/S2053273316018696
Page generated: Mon Dec 14 20:50:47 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