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Iron in PDB 3d38: Crystal Structure of New Trigonal Form of Photosynthetic Reaction Center From Blastochloris Viridis. Crystals Grown in Microfluidics By Detergent Capture.

Protein crystallography data

The structure of Crystal Structure of New Trigonal Form of Photosynthetic Reaction Center From Blastochloris Viridis. Crystals Grown in Microfluidics By Detergent Capture., PDB code: 3d38 was solved by L.Li, S.H.M.Nachtergaele, A.M.Seddon, V.Tereshko, N.Ponomarenko, R.F.Ismagilov, Accelerated Technologies Center For Gene To 3Dstructure (Atcg3D), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.21
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 241.171, 241.171, 113.391, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 22.4

Other elements in 3d38:

The structure of Crystal Structure of New Trigonal Form of Photosynthetic Reaction Center From Blastochloris Viridis. Crystals Grown in Microfluidics By Detergent Capture. also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of New Trigonal Form of Photosynthetic Reaction Center From Blastochloris Viridis. Crystals Grown in Microfluidics By Detergent Capture. (pdb code 3d38). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of New Trigonal Form of Photosynthetic Reaction Center From Blastochloris Viridis. Crystals Grown in Microfluidics By Detergent Capture., PDB code: 3d38:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 3d38

Go back to Iron Binding Sites List in 3d38
Iron binding site 1 out of 5 in the Crystal Structure of New Trigonal Form of Photosynthetic Reaction Center From Blastochloris Viridis. Crystals Grown in Microfluidics By Detergent Capture.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of New Trigonal Form of Photosynthetic Reaction Center From Blastochloris Viridis. Crystals Grown in Microfluidics By Detergent Capture. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:0.1
occ:1.00
FE C:HEC401 0.0 0.1 1.0
NE2 C:HIS91 2.0 0.1 1.0
NA C:HEC401 2.0 0.4 1.0
NC C:HEC401 2.0 0.3 1.0
ND C:HEC401 2.1 0.5 1.0
NB C:HEC401 2.1 0.5 1.0
SD C:MET74 2.2 93.1 1.0
CE1 C:HIS91 2.7 0.2 1.0
C1A C:HEC401 3.0 0.4 1.0
C1D C:HEC401 3.0 0.3 1.0
C4D C:HEC401 3.0 0.4 1.0
C4C C:HEC401 3.0 0.8 1.0
C4A C:HEC401 3.1 0.2 1.0
C1C C:HEC401 3.1 0.2 1.0
C1B C:HEC401 3.1 0.9 1.0
C4B C:HEC401 3.1 0.3 1.0
CD2 C:HIS91 3.2 0.7 1.0
CE C:MET74 3.3 93.5 1.0
CHD C:HEC401 3.4 0.0 1.0
CHA C:HEC401 3.4 0.7 1.0
CHB C:HEC401 3.5 0.3 1.0
CHC C:HEC401 3.5 0.8 1.0
CG C:MET74 3.6 93.6 1.0
ND1 C:HIS91 3.9 0.2 1.0
CG C:HIS91 4.2 0.1 1.0
C2D C:HEC401 4.2 0.4 1.0
C3D C:HEC401 4.2 0.9 1.0
C2A C:HEC401 4.2 0.0 1.0
C3A C:HEC401 4.2 0.4 1.0
C3C C:HEC401 4.3 0.1 1.0
C2C C:HEC401 4.3 0.5 1.0
CB C:MET74 4.3 94.1 1.0
C2B C:HEC401 4.3 0.1 1.0
C3B C:HEC401 4.4 0.4 1.0

Iron binding site 2 out of 5 in 3d38

Go back to Iron Binding Sites List in 3d38
Iron binding site 2 out of 5 in the Crystal Structure of New Trigonal Form of Photosynthetic Reaction Center From Blastochloris Viridis. Crystals Grown in Microfluidics By Detergent Capture.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of New Trigonal Form of Photosynthetic Reaction Center From Blastochloris Viridis. Crystals Grown in Microfluidics By Detergent Capture. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe402

b:74.3
occ:1.00
FE C:HEC402 0.0 74.3 1.0
NE2 C:HIS136 1.9 68.1 1.0
NB C:HEC402 2.0 74.8 1.0
NC C:HEC402 2.1 75.0 1.0
ND C:HEC402 2.1 76.1 1.0
NA C:HEC402 2.1 77.0 1.0
SD C:MET110 2.3 85.3 1.0
CE1 C:HIS136 2.8 68.9 1.0
C4B C:HEC402 3.0 74.6 1.0
C1B C:HEC402 3.0 75.0 1.0
C1C C:HEC402 3.1 74.9 1.0
CD2 C:HIS136 3.1 70.2 1.0
C4A C:HEC402 3.1 77.0 1.0
C1D C:HEC402 3.1 76.3 1.0
C4D C:HEC402 3.1 76.7 1.0
C4C C:HEC402 3.1 74.3 1.0
C1A C:HEC402 3.1 77.5 1.0
CHC C:HEC402 3.4 75.1 1.0
CHB C:HEC402 3.4 75.6 1.0
CHD C:HEC402 3.4 74.9 1.0
CHA C:HEC402 3.5 77.1 1.0
CG C:MET110 3.5 89.3 1.0
CE C:MET110 3.5 85.0 1.0
ND1 C:HIS136 4.0 70.2 1.0
CG C:HIS136 4.1 71.3 1.0
C2B C:HEC402 4.2 74.9 1.0
C3B C:HEC402 4.2 74.9 1.0
CB C:MET110 4.2 91.2 1.0
C3A C:HEC402 4.3 77.6 1.0
C2C C:HEC402 4.3 74.2 1.0
C2D C:HEC402 4.3 76.8 1.0
C3D C:HEC402 4.3 77.5 1.0
C2A C:HEC402 4.3 77.6 1.0
C3C C:HEC402 4.3 73.8 1.0

Iron binding site 3 out of 5 in 3d38

Go back to Iron Binding Sites List in 3d38
Iron binding site 3 out of 5 in the Crystal Structure of New Trigonal Form of Photosynthetic Reaction Center From Blastochloris Viridis. Crystals Grown in Microfluidics By Detergent Capture.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of New Trigonal Form of Photosynthetic Reaction Center From Blastochloris Viridis. Crystals Grown in Microfluidics By Detergent Capture. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe403

b:47.7
occ:1.00
FE C:HEC403 0.0 47.7 1.0
NE2 C:HIS248 1.9 45.5 1.0
NA C:HEC403 2.0 48.1 1.0
ND C:HEC403 2.1 48.6 1.0
NC C:HEC403 2.1 49.0 1.0
NB C:HEC403 2.1 48.8 1.0
SD C:MET233 2.2 53.3 1.0
CD2 C:HIS248 2.8 46.1 1.0
CE1 C:HIS248 2.9 46.3 1.0
C1A C:HEC403 3.0 48.8 1.0
C4A C:HEC403 3.0 47.9 1.0
C4D C:HEC403 3.0 49.3 1.0
C1C C:HEC403 3.1 49.7 1.0
C1B C:HEC403 3.1 48.6 1.0
C4B C:HEC403 3.1 49.1 1.0
C4C C:HEC403 3.1 49.1 1.0
C1D C:HEC403 3.1 49.9 1.0
CG C:MET233 3.3 52.1 1.0
CHA C:HEC403 3.4 50.1 1.0
CE C:MET233 3.4 50.7 1.0
CHB C:HEC403 3.4 48.2 1.0
CHC C:HEC403 3.4 49.4 1.0
CHD C:HEC403 3.5 49.8 1.0
ND1 C:HIS248 4.0 47.6 1.0
CG C:HIS248 4.0 48.8 1.0
CB C:MET233 4.1 51.4 1.0
C3A C:HEC403 4.2 48.1 1.0
C2A C:HEC403 4.2 48.3 1.0
C3D C:HEC403 4.3 49.9 1.0
C2B C:HEC403 4.3 48.3 1.0
C2C C:HEC403 4.3 50.3 1.0
C3B C:HEC403 4.3 48.6 1.0
C3C C:HEC403 4.3 49.5 1.0
C2D C:HEC403 4.3 49.8 1.0

Iron binding site 4 out of 5 in 3d38

Go back to Iron Binding Sites List in 3d38
Iron binding site 4 out of 5 in the Crystal Structure of New Trigonal Form of Photosynthetic Reaction Center From Blastochloris Viridis. Crystals Grown in Microfluidics By Detergent Capture.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of New Trigonal Form of Photosynthetic Reaction Center From Blastochloris Viridis. Crystals Grown in Microfluidics By Detergent Capture. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe404

b:55.4
occ:1.00
FE C:HEC404 0.0 55.4 1.0
NE2 C:HIS124 1.9 72.9 1.0
NA C:HEC404 2.0 56.2 1.0
NB C:HEC404 2.0 54.3 1.0
ND C:HEC404 2.0 57.8 1.0
NE2 C:HIS309 2.1 57.2 1.0
NC C:HEC404 2.1 56.1 1.0
CE1 C:HIS124 2.8 73.3 1.0
CE1 C:HIS309 2.8 58.3 1.0
CD2 C:HIS124 3.0 73.8 1.0
C1A C:HEC404 3.0 56.5 1.0
C1B C:HEC404 3.0 53.9 1.0
C4A C:HEC404 3.0 55.2 1.0
C4D C:HEC404 3.0 58.8 1.0
C4B C:HEC404 3.1 53.7 1.0
C1D C:HEC404 3.1 59.3 1.0
C1C C:HEC404 3.1 55.5 1.0
C4C C:HEC404 3.1 56.5 1.0
CD2 C:HIS309 3.2 59.2 1.0
CHA C:HEC404 3.4 57.3 1.0
CHB C:HEC404 3.4 53.7 1.0
CHC C:HEC404 3.4 54.4 1.0
CHD C:HEC404 3.5 57.6 1.0
ND1 C:HIS124 3.9 73.7 1.0
ND1 C:HIS309 4.0 59.4 1.0
CG C:HIS124 4.1 74.8 1.0
C2A C:HEC404 4.2 55.8 1.0
CG C:HIS309 4.2 60.5 1.0
C2B C:HEC404 4.3 54.2 1.0
C3D C:HEC404 4.3 61.5 1.0
C3A C:HEC404 4.3 55.1 1.0
C2D C:HEC404 4.3 60.9 1.0
C3B C:HEC404 4.3 53.8 1.0
C2C C:HEC404 4.3 55.2 1.0
C3C C:HEC404 4.3 55.6 1.0
CG C:PRO315 4.9 64.2 1.0

Iron binding site 5 out of 5 in 3d38

Go back to Iron Binding Sites List in 3d38
Iron binding site 5 out of 5 in the Crystal Structure of New Trigonal Form of Photosynthetic Reaction Center From Blastochloris Viridis. Crystals Grown in Microfluidics By Detergent Capture.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of New Trigonal Form of Photosynthetic Reaction Center From Blastochloris Viridis. Crystals Grown in Microfluidics By Detergent Capture. within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe500

b:50.7
occ:1.00
NE2 L:HIS190 2.1 41.6 1.0
NE2 L:HIS230 2.1 57.4 1.0
NE2 M:HIS217 2.2 50.3 1.0
OE2 M:GLU232 2.2 59.0 1.0
NE2 M:HIS264 2.4 53.0 1.0
OE1 M:GLU232 2.4 58.6 1.0
CD M:GLU232 2.6 59.3 1.0
CE1 L:HIS190 2.8 42.0 1.0
CE1 L:HIS230 2.9 56.9 1.0
CE1 M:HIS217 3.0 51.0 1.0
CE1 M:HIS264 3.0 52.0 1.0
CD2 L:HIS230 3.2 55.6 1.0
CD2 M:HIS217 3.3 50.4 1.0
CD2 L:HIS190 3.3 43.0 1.0
CD2 M:HIS264 3.4 52.3 1.0
ND1 L:HIS190 4.0 43.0 1.0
ND1 L:HIS230 4.1 55.2 1.0
ND1 M:HIS264 4.2 52.0 1.0
CG M:GLU232 4.2 58.9 1.0
ND1 M:HIS217 4.2 50.6 1.0
CG L:HIS190 4.3 44.4 1.0
CG L:HIS230 4.3 52.8 1.0
CG1 M:ILE221 4.3 47.8 1.0
CG M:HIS217 4.3 49.5 1.0
CG M:HIS264 4.4 51.3 1.0
CG1 L:ILE194 4.8 54.5 1.0
CD1 M:ILE221 5.0 48.0 1.0

Reference:

L.Li, S.Nachtergaele, A.M.Seddon, V.Tereshko, N.Ponomarenko, R.F.Ismagilov. Simple Host-Guest Chemistry to Modulate the Process of Concentration and Crystallization of Membrane Proteins By Detergent Capture in A Microfluidic Device. J.Am.Chem.Soc. V. 130 14324 2008.
ISSN: ISSN 0002-7863
PubMed: 18831551
DOI: 10.1021/JA805361J
Page generated: Sun Dec 13 15:03:15 2020

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