Indium in PDB 3vtm: Structure of Heme Transport Protein Isdh-NEAT3 From S. Aureus in Complex with Indium-Porphyrin

The structure of Structure of Heme Transport Protein Isdh-NEAT3 From S. Aureus in Complex with Indium-Porphyrin, PDB code: 3vtm was solved by N.T.Vu, J.M.M.Caaveiro, Y.Moriwaki, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.82 / 2.80
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.460, 71.010, 75.800, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 29.2

The binding sites of Indium atom in the Structure of Heme Transport Protein Isdh-NEAT3 From S. Aureus in Complex with Indium-Porphyrin (pdb code 3vtm). This binding sites where shown within 5.0 Angstroms radius around Indium atom.
In total 2 binding sites of Indium where determined in the Structure of Heme Transport Protein Isdh-NEAT3 From S. Aureus in Complex with Indium-Porphyrin, PDB code: 3vtm:
Jump to Indium binding site number: 1; 2;

Indium binding site 1 out of 2 in the Structure of Heme Transport Protein Isdh-NEAT3 From S. Aureus in Complex with Indium-Porphyrin


Mono view


Stereo pair view

A full contact list of Indium with other atoms in the In binding site number 1 of Structure of Heme Transport Protein Isdh-NEAT3 From S. Aureus in Complex with Indium-Porphyrin within 5.0Å range: probe atom residue distance (Å) B Occ A:In701 b:23.3 occ:1.00 IN A:3ZZ701 0.0 23.3 1.0 NB A:3ZZ701 2.0 19.6 1.0 NA A:3ZZ701 2.0 21.8 1.0 OH A:TYR642 2.1 16.4 1.0 ND A:3ZZ701 2.1 20.7 1.0 NC A:3ZZ701 2.2 20.0 1.0 C4B A:3ZZ701 3.0 18.4 1.0 CZ A:TYR642 3.0 18.2 1.0 C4A A:3ZZ701 3.0 22.1 1.0 C1B A:3ZZ701 3.0 19.6 1.0 C1A A:3ZZ701 3.1 22.3 1.0 C4D A:3ZZ701 3.1 20.9 1.0 C1D A:3ZZ701 3.1 20.5 1.0 C1C A:3ZZ701 3.1 18.1 1.0 C4C A:3ZZ701 3.2 19.9 1.0 CHB A:3ZZ701 3.4 20.9 1.0 CHC A:3ZZ701 3.4 17.9 1.0 CHA A:3ZZ701 3.4 20.7 1.0 CHD A:3ZZ701 3.5 20.2 1.0 CE2 A:TYR642 3.8 18.6 1.0 CE1 A:TYR642 3.8 18.2 1.0 CG1 A:VAL564 4.0 19.1 1.0 C3B A:3ZZ701 4.2 18.0 1.0 C3A A:3ZZ701 4.3 24.3 1.0 C2B A:3ZZ701 4.3 18.0 1.0 C2A A:3ZZ701 4.3 24.5 1.0 OH A:TYR646 4.3 20.9 1.0 C3D A:3ZZ701 4.3 20.3 1.0 C2D A:3ZZ701 4.3 20.7 1.0 C2C A:3ZZ701 4.4 18.7 1.0 C3C A:3ZZ701 4.4 18.8 1.0 CZ A:TYR646 4.6 20.7 1.0 CE1 A:TYR646 4.6 21.0 1.0 CB A:VAL564 4.7 18.7 1.0 CMB B:3ZZ701 4.8 17.5 1.0 CD2 A:TYR642 5.0 18.3 1.0

Indium binding site 2 out of 2 in the Structure of Heme Transport Protein Isdh-NEAT3 From S. Aureus in Complex with Indium-Porphyrin


Mono view


Stereo pair view

A full contact list of Indium with other atoms in the In binding site number 2 of Structure of Heme Transport Protein Isdh-NEAT3 From S. Aureus in Complex with Indium-Porphyrin within 5.0Å range: probe atom residue distance (Å) B Occ B:In701 b:22.3 occ:1.00 IN B:3ZZ701 0.0 22.3 1.0 NB B:3ZZ701 2.1 19.1 1.0 NA B:3ZZ701 2.1 20.4 1.0 OH B:TYR642 2.1 23.2 1.0 ND B:3ZZ701 2.1 20.9 1.0 NC B:3ZZ701 2.2 19.9 1.0 CZ B:TYR642 3.0 25.7 1.0 C1B B:3ZZ701 3.0 18.4 1.0 C4A B:3ZZ701 3.0 20.3 1.0 C1D B:3ZZ701 3.0 21.1 1.0 C4C B:3ZZ701 3.1 19.8 1.0 C4B B:3ZZ701 3.1 17.8 1.0 C1A B:3ZZ701 3.1 18.9 1.0 C4D B:3ZZ701 3.1 20.1 1.0 C1C B:3ZZ701 3.2 18.2 1.0 CHB B:3ZZ701 3.3 19.2 1.0 CHD B:3ZZ701 3.4 20.6 1.0 CHA B:3ZZ701 3.5 18.3 1.0 CHC B:3ZZ701 3.5 17.2 1.0 CE2 B:TYR642 3.7 25.0 1.0 CE1 B:TYR642 3.8 27.2 1.0 CG1 B:VAL564 4.0 21.8 1.0 OH B:TYR646 4.1 24.7 1.0 C2B B:3ZZ701 4.2 17.6 1.0 C3A B:3ZZ701 4.3 21.3 1.0 C2D B:3ZZ701 4.3 21.8 1.0 C3B B:3ZZ701 4.3 17.2 1.0 C3C B:3ZZ701 4.3 19.3 1.0 C2A B:3ZZ701 4.3 20.9 1.0 C3D B:3ZZ701 4.3 21.4 1.0 C2C B:3ZZ701 4.4 19.2 1.0 CZ B:TYR646 4.5 25.8 1.0 CE1 B:TYR646 4.5 26.0 1.0 CB B:VAL564 4.6 23.1 1.0 CMB A:3ZZ701 4.6 17.2 1.0 CD2 B:TYR642 4.9 25.9 1.0 CG2 B:VAL564 4.9 21.8 1.0 CG2 B:VAL635 5.0 24.9 1.0 CD1 B:TYR642 5.0 26.9 1.0

N.T.Vu, Y.Moriwaki, J.M.M.Caaveiro, T.Terada, H.Tsutsumi, I.Hamachi, K.Shimizu, K.Tsumoto. Selective Binding of Antimicrobial Porphyrins to the Heme-Receptor Isdh-NEAT3 of Staphylococcus Aureus Protein Sci. V. 22 942 2013.
ISSN: ISSN 0961-8368
PubMed: 23649633
DOI: 10.1002/PRO.2276