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Iron in PDB 5m7k: Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL

Protein crystallography data

The structure of Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL, PDB code: 5m7k 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) 55.44 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.900, 84.800, 384.300, 90.00, 90.00, 90.00
R / Rfree (%) 25.3 / 27.4

Other elements in 5m7k:

The structure of Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL (pdb code 5m7k). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL, PDB code: 5m7k:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 5m7k

Go back to Iron Binding Sites List in 5m7k
Iron binding site 1 out of 5 in the Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:47.8
occ:1.00
FE A:HEC401 0.0 47.8 1.0
NC A:HEC401 2.0 49.1 1.0
ND A:HEC401 2.1 49.4 1.0
NA A:HEC401 2.1 45.3 1.0
NB A:HEC401 2.1 49.7 1.0
NE2 A:HIS91 2.5 46.5 1.0
SD A:MET74 2.8 52.7 1.0
C1C A:HEC401 3.0 51.2 1.0
C4C A:HEC401 3.0 48.9 1.0
C1D A:HEC401 3.0 51.4 1.0
C4B A:HEC401 3.1 50.2 1.0
C1B A:HEC401 3.1 50.5 1.0
C4A A:HEC401 3.1 48.5 1.0
C4D A:HEC401 3.1 46.0 1.0
C1A A:HEC401 3.1 48.6 1.0
CD2 A:HIS91 3.2 47.8 1.0
CHD A:HEC401 3.4 49.7 1.0
CHC A:HEC401 3.4 51.7 1.0
CHB A:HEC401 3.5 48.2 1.0
CHA A:HEC401 3.5 46.6 1.0
CE1 A:HIS91 3.6 47.8 1.0
CG A:MET74 3.7 49.9 1.0
CE A:MET74 3.8 47.0 1.0
C2C A:HEC401 4.2 54.6 1.0
C3C A:HEC401 4.2 49.7 1.0
C2B A:HEC401 4.2 51.4 1.0
C3B A:HEC401 4.2 50.5 1.0
C2D A:HEC401 4.3 45.2 1.0
C3D A:HEC401 4.3 43.4 1.0
C3A A:HEC401 4.3 51.8 1.0
C2A A:HEC401 4.3 50.7 1.0
CG A:HIS91 4.4 47.4 1.0
CB A:MET74 4.5 49.8 1.0
ND1 A:HIS91 4.6 48.4 1.0

Iron binding site 2 out of 5 in 5m7k

Go back to Iron Binding Sites List in 5m7k
Iron binding site 2 out of 5 in the Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:62.5
occ:1.00
FE A:HEC402 0.0 62.5 1.0
NC A:HEC402 2.0 47.0 1.0
NA A:HEC402 2.1 48.2 1.0
ND A:HEC402 2.1 43.6 1.0
NB A:HEC402 2.1 43.7 1.0
NE2 A:HIS136 2.5 44.5 1.0
SD A:MET110 2.9 43.6 1.0
C1B A:HEC402 3.0 45.0 1.0
C4B A:HEC402 3.0 45.7 1.0
C4C A:HEC402 3.0 46.3 1.0
C1C A:HEC402 3.0 44.6 1.0
C4A A:HEC402 3.1 45.9 1.0
C1D A:HEC402 3.1 42.1 1.0
C1A A:HEC402 3.1 46.5 1.0
C4D A:HEC402 3.1 48.8 1.0
CE A:MET110 3.4 44.7 1.0
CHB A:HEC402 3.4 43.0 1.0
CHC A:HEC402 3.4 43.1 1.0
CHD A:HEC402 3.4 44.7 1.0
CE1 A:HIS136 3.5 44.2 1.0
CHA A:HEC402 3.5 47.1 1.0
CG A:MET110 3.5 40.7 1.0
CD2 A:HIS136 3.5 42.6 1.0
C3B A:HEC402 4.1 46.4 1.0
C2B A:HEC402 4.2 46.0 1.0
CB A:MET110 4.2 37.7 1.0
C3C A:HEC402 4.2 44.7 1.0
C2C A:HEC402 4.2 43.5 1.0
C3A A:HEC402 4.3 43.8 1.0
C2D A:HEC402 4.3 46.4 1.0
C2A A:HEC402 4.3 43.0 1.0
C3D A:HEC402 4.3 52.8 1.0
ND1 A:HIS136 4.6 41.7 1.0
CG A:HIS136 4.6 41.3 1.0

Iron binding site 3 out of 5 in 5m7k

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Iron binding site 3 out of 5 in the Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:24.5
occ:1.00
FE A:HEC403 0.0 24.5 1.0
NC A:HEC403 2.0 33.3 1.0
NB A:HEC403 2.0 33.8 1.0
NA A:HEC403 2.0 35.6 1.0
ND A:HEC403 2.1 36.1 1.0
NE2 A:HIS248 2.5 33.2 1.0
SD A:MET233 2.7 35.2 1.0
C1B A:HEC403 3.0 33.9 1.0
C4C A:HEC403 3.0 37.3 1.0
C4B A:HEC403 3.0 36.9 1.0
C4A A:HEC403 3.0 39.6 1.0
C1C A:HEC403 3.0 30.0 1.0
C1D A:HEC403 3.1 37.5 1.0
CD2 A:HIS248 3.1 35.0 1.0
C1A A:HEC403 3.1 35.4 1.0
C4D A:HEC403 3.1 37.8 1.0
CG A:MET233 3.3 33.4 1.0
CHB A:HEC403 3.4 39.3 1.0
CHD A:HEC403 3.4 38.9 1.0
CHC A:HEC403 3.4 33.2 1.0
CHA A:HEC403 3.5 37.2 1.0
CE1 A:HIS248 3.6 38.4 1.0
CE A:MET233 3.8 35.1 1.0
CB A:MET233 4.1 32.1 1.0
C2B A:HEC403 4.2 33.2 1.0
C3B A:HEC403 4.2 37.4 1.0
C3C A:HEC403 4.2 37.1 1.0
C2C A:HEC403 4.3 32.7 1.0
C3A A:HEC403 4.3 34.8 1.0
C2D A:HEC403 4.3 36.4 1.0
C2A A:HEC403 4.3 32.0 1.0
C3D A:HEC403 4.3 35.6 1.0
CG A:HIS248 4.3 37.6 1.0
ND1 A:HIS248 4.6 39.8 1.0

Iron binding site 4 out of 5 in 5m7k

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Iron binding site 4 out of 5 in the Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe404

b:43.1
occ:1.00
FE A:HEC404 0.0 43.1 1.0
ND A:HEC404 2.0 42.0 1.0
NA A:HEC404 2.0 42.6 1.0
NC A:HEC404 2.1 45.6 1.0
NB A:HEC404 2.1 40.7 1.0
NE2 A:HIS309 2.3 43.6 1.0
NE2 A:HIS124 2.4 42.7 1.0
C4B A:HEC404 3.0 42.8 1.0
C4D A:HEC404 3.0 44.0 1.0
C1B A:HEC404 3.0 39.2 1.0
C1A A:HEC404 3.0 43.3 1.0
C1D A:HEC404 3.1 45.5 1.0
C1C A:HEC404 3.1 45.2 1.0
C4A A:HEC404 3.1 40.1 1.0
C4C A:HEC404 3.1 47.9 1.0
CE1 A:HIS309 3.1 43.8 1.0
CE1 A:HIS124 3.1 42.1 1.0
CHA A:HEC404 3.4 44.1 1.0
CHC A:HEC404 3.4 44.7 1.0
CHB A:HEC404 3.4 40.0 1.0
CD2 A:HIS309 3.4 43.8 1.0
CHD A:HEC404 3.4 46.1 1.0
CD2 A:HIS124 3.5 39.1 1.0
C2B A:HEC404 4.2 42.4 1.0
C3B A:HEC404 4.2 41.4 1.0
C3D A:HEC404 4.3 46.0 1.0
C2D A:HEC404 4.3 45.7 1.0
C2A A:HEC404 4.3 41.1 1.0
C3A A:HEC404 4.3 40.1 1.0
C2C A:HEC404 4.3 46.8 1.0
ND1 A:HIS124 4.3 39.5 1.0
C3C A:HEC404 4.3 50.4 1.0
ND1 A:HIS309 4.3 50.9 1.0
CG A:HIS124 4.5 41.2 1.0
CG A:HIS309 4.5 44.0 1.0
CD A:PRO315 4.9 41.6 1.0
CG A:PRO315 4.9 43.0 1.0

Iron binding site 5 out of 5 in 5m7k

Go back to Iron Binding Sites List in 5m7k
Iron binding site 5 out of 5 in the Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe403

b:67.9
occ:1.00
NE2 C:HIS217 2.5 67.4 1.0
NE2 B:HIS190 2.5 74.2 1.0
NE2 C:HIS264 2.5 75.7 1.0
OE1 C:GLU232 2.5 76.4 1.0
OE2 C:GLU232 2.5 70.5 1.0
NE2 B:HIS230 2.6 64.3 1.0
CD C:GLU232 2.9 74.7 1.0
CE1 C:HIS264 3.2 78.6 1.0
CE1 C:HIS217 3.2 67.1 1.0
CE1 B:HIS230 3.3 64.7 1.0
CE1 B:HIS190 3.4 74.8 1.0
CD2 B:HIS190 3.4 73.4 1.0
CD2 C:HIS264 3.5 73.5 1.0
CD2 C:HIS217 3.6 68.2 1.0
CD2 B:HIS230 3.6 66.5 1.0
ND1 C:HIS264 4.4 75.8 1.0
CG C:GLU232 4.4 75.7 1.0
ND1 C:HIS217 4.5 65.3 1.0
CG1 B:ILE194 4.5 66.9 1.0
ND1 B:HIS230 4.5 67.3 1.0
ND1 B:HIS190 4.5 74.4 1.0
CG C:HIS264 4.5 73.7 1.0
CG B:HIS190 4.6 76.2 1.0
CG C:HIS217 4.6 66.3 1.0
CG B:HIS230 4.7 65.7 1.0
CG1 C:ILE221 4.8 63.3 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: Sun Dec 13 16:08:10 2020

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