Iron in PDB 3vto: The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike

The structure of The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike, PDB code: 3vto was solved by K.Harada, E.Yamashita, A.Nakagawa, S.Takeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.52 / 1.44
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.403, 152.399, 53.062, 90.00, 91.01, 90.00
R / Rfree (%)	16.2 / 19.5

The structure of The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	2 atoms

The binding sites of Iron atom in the The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike (pdb code 3vto). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike, PDB code: 3vto:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:12.7 occ:1.00 NE2 C:HIS185 2.2 12.8 1.0 NE2 A:HIS183 2.2 12.5 1.0 NE2 A:HIS185 2.2 12.2 1.0 NE2 B:HIS185 2.2 12.5 1.0 NE2 B:HIS183 2.2 14.9 1.0 NE2 C:HIS183 2.2 13.8 1.0 CE1 C:HIS185 3.1 12.2 1.0 CE1 B:HIS185 3.1 13.1 1.0 CD2 A:HIS185 3.1 14.6 1.0 CE1 B:HIS183 3.1 14.2 1.0 CE1 A:HIS183 3.1 14.4 1.0 CE1 C:HIS183 3.2 13.5 1.0 CD2 A:HIS183 3.2 13.4 1.0 CD2 B:HIS185 3.2 12.3 1.0 CE1 A:HIS185 3.2 12.3 1.0 CD2 C:HIS183 3.2 13.7 1.0 CD2 C:HIS185 3.2 14.6 1.0 CD2 B:HIS183 3.2 14.2 1.0 ND1 C:HIS185 4.2 12.9 1.0 ND1 B:HIS185 4.3 13.7 1.0 ND1 A:HIS185 4.3 13.3 1.0 ND1 A:HIS183 4.3 13.7 1.0 ND1 B:HIS183 4.3 12.7 1.0 ND1 C:HIS183 4.3 13.0 1.0 CG A:HIS185 4.3 13.1 1.0 CG B:HIS185 4.3 13.3 1.0 CG C:HIS185 4.3 12.1 1.0 CG A:HIS183 4.3 13.6 1.0 CG C:HIS183 4.3 13.8 1.0 CG B:HIS183 4.3 13.7 1.0

Iron binding site 2 out of 2 in the The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike within 5.0Å range: probe atom residue distance (Å) B Occ P:Fe301 b:13.2 occ:1.00 NE2 P:HIS183 2.2 14.0 1.0 NE2 Q:HIS183 2.2 14.4 1.0 NE2 R:HIS185 2.2 13.5 1.0 NE2 R:HIS183 2.2 12.9 1.0 NE2 Q:HIS185 2.2 13.4 1.0 NE2 P:HIS185 2.2 14.1 1.0 CE1 P:HIS183 3.1 15.1 1.0 CE1 Q:HIS183 3.1 14.2 1.0 CE1 Q:HIS185 3.1 13.4 1.0 CE1 R:HIS185 3.1 12.8 1.0 CE1 R:HIS183 3.2 15.3 1.0 CD2 P:HIS185 3.2 12.6 1.0 CD2 R:HIS185 3.2 15.1 1.0 CD2 R:HIS183 3.2 14.6 1.0 CD2 Q:HIS183 3.2 14.0 1.0 CD2 P:HIS183 3.2 13.4 1.0 CD2 Q:HIS185 3.2 14.3 1.0 CE1 P:HIS185 3.2 14.3 1.0 ND1 P:HIS183 4.2 12.8 1.0 ND1 Q:HIS183 4.3 15.0 1.0 ND1 R:HIS185 4.3 13.9 1.0 ND1 Q:HIS185 4.3 13.9 1.0 ND1 R:HIS183 4.3 13.6 1.0 ND1 P:HIS185 4.3 14.5 1.0 CG Q:HIS183 4.3 14.4 1.0 CG R:HIS185 4.3 13.7 1.0 CG P:HIS183 4.3 13.2 1.0 CG R:HIS183 4.3 15.3 1.0 CG P:HIS185 4.3 13.6 1.0 CG Q:HIS185 4.3 12.7 1.0

K.Harada, E.Yamashita, A.Nakagawa, T.Miyafusa, K.Tsumoto, T.Ueno, Y.Toyama, S.Takeda. Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike and Functions of Bound Calcium Ion Biochim.Biophys.Acta V.1834 284 2013.
ISSN: ISSN 0006-3002
PubMed: 22922659
DOI: 10.1016/J.BBAPAP.2012.08.015