Iron in PDB 8tgb: Crystal Structure of Root Lateral Formation Protein (Rlf) B5-Domain From Oryza Sativa

The structure of Crystal Structure of Root Lateral Formation Protein (Rlf) B5-Domain From Oryza Sativa, PDB code: 8tgb was solved by S.Lovell, M.M.Kashipathy, K.P.Battaile, D.R.Benson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.25 / 1.55
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	58.951, 26.138, 82.873, 90, 95.5, 90
R / Rfree (%)	17.5 / 20

The binding sites of Iron atom in the Crystal Structure of Root Lateral Formation Protein (Rlf) B5-Domain From Oryza Sativa (pdb code 8tgb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Root Lateral Formation Protein (Rlf) B5-Domain From Oryza Sativa, PDB code: 8tgb:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Root Lateral Formation Protein (Rlf) B5-Domain From Oryza Sativa


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 Root Lateral Formation Protein (Rlf) B5-Domain From Oryza Sativa within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:12.4 occ:1.00 FE A:HEM301 0.0 12.4 1.0 ND A:HEM301 2.0 12.8 1.0 NC A:HEM301 2.0 12.5 1.0 NA A:HEM301 2.0 11.5 1.0 NB A:HEM301 2.0 10.6 1.0 NE2 A:HIS197 2.0 12.2 1.0 NE2 A:HIS174 2.1 11.4 1.0 CD2 A:HIS197 3.0 12.1 1.0 C1D A:HEM301 3.0 11.8 1.0 CE1 A:HIS197 3.0 12.2 1.0 CD2 A:HIS174 3.0 11.3 1.0 C4C A:HEM301 3.0 12.8 1.0 C4D A:HEM301 3.0 15.6 1.0 C4A A:HEM301 3.0 11.9 1.0 C1A A:HEM301 3.0 14.3 1.0 C1C A:HEM301 3.1 12.6 1.0 C4B A:HEM301 3.1 14.3 1.0 C1B A:HEM301 3.1 9.9 1.0 CE1 A:HIS174 3.1 13.2 1.0 CHD A:HEM301 3.4 15.7 1.0 CHA A:HEM301 3.4 13.6 1.0 CHC A:HEM301 3.4 13.2 1.0 CHB A:HEM301 3.4 13.9 1.0 ND1 A:HIS197 4.1 12.4 1.0 CG A:HIS197 4.1 11.8 1.0 CG A:HIS174 4.2 11.8 1.0 ND1 A:HIS174 4.2 11.8 1.0 C3D A:HEM301 4.2 12.2 1.0 C2D A:HEM301 4.2 15.5 1.0 C3A A:HEM301 4.2 13.7 1.0 C2A A:HEM301 4.2 15.0 1.0 C3C A:HEM301 4.2 12.7 1.0 C2C A:HEM301 4.3 12.6 1.0 C3B A:HEM301 4.3 14.9 1.0 C2B A:HEM301 4.3 14.4 1.0 N A:GLY176 4.8 13.7 1.0 CA A:GLY176 4.9 13.9 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Root Lateral Formation Protein (Rlf) B5-Domain From Oryza Sativa


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 Root Lateral Formation Protein (Rlf) B5-Domain From Oryza Sativa within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:17.6 occ:1.00 FE B:HEM301 0.0 17.6 1.0 ND B:HEM301 2.0 18.8 1.0 NA B:HEM301 2.0 21.8 1.0 NC B:HEM301 2.0 23.7 1.0 NB B:HEM301 2.0 15.2 1.0 NE2 B:HIS174 2.1 16.0 1.0 NE2 B:HIS197 2.1 16.6 1.0 C1D B:HEM301 3.0 18.5 1.0 CD2 B:HIS174 3.0 16.5 1.0 C4A B:HEM301 3.0 12.8 1.0 C4C B:HEM301 3.1 15.8 1.0 C4D B:HEM301 3.1 22.3 1.0 C1A B:HEM301 3.1 20.6 1.0 C1B B:HEM301 3.1 13.7 1.0 CD2 B:HIS197 3.1 17.9 1.0 C4B B:HEM301 3.1 19.1 1.0 C1C B:HEM301 3.1 17.5 1.0 CE1 B:HIS197 3.1 16.3 1.0 CE1 B:HIS174 3.1 17.7 1.0 CHD B:HEM301 3.4 17.1 1.0 CHB B:HEM301 3.4 19.4 1.0 CHC B:HEM301 3.4 17.9 1.0 CHA B:HEM301 3.4 19.6 1.0 ND1 B:HIS197 4.2 15.6 1.0 CG B:HIS174 4.2 18.0 1.0 ND1 B:HIS174 4.2 20.4 1.0 CG B:HIS197 4.2 15.7 1.0 C2D B:HEM301 4.2 24.8 1.0 C3D B:HEM301 4.3 28.1 1.0 C2A B:HEM301 4.3 20.9 1.0 C3A B:HEM301 4.3 17.2 1.0 C3B B:HEM301 4.3 18.8 1.0 C2B B:HEM301 4.3 15.6 1.0 C3C B:HEM301 4.3 20.5 1.0 C2C B:HEM301 4.3 18.2 1.0 N B:GLY176 4.7 19.8 1.0 CA B:GLY176 4.9 23.0 1.0

D.R.Benson, B.Deng, M.M.Kashipathy, S.Lovell, K.P.Battaile, A.Cooper, P.Gao, A.W.Fenton, H.Zhu. The N-Terminal Intrinsically Disordered Region of NCB5OR Docks with the Cytochrome B 5 Core to Form A Helical Motif That Is of Ancient Origin. Proteins 2023.
ISSN: ESSN 1097-0134
PubMed: 38041394
DOI: 10.1002/PROT.26647