Magnesium in PDB 5y8b: Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Apo Form

The structure of Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Apo Form, PDB code: 5y8b was solved by M.M.Rahman, Y.Naoe, N.Nakamura, A.Doi, Y.Shiro, H.Sugimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.039, 71.039, 78.206, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 24.6

The binding sites of Magnesium atom in the Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Apo Form (pdb code 5y8b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Apo Form, PDB code: 5y8b:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:45.7 occ:1.00 OD2 A:ASP184 2.0 37.6 1.0 O A:HOH537 2.1 37.4 1.0 OD2 A:ASP160 2.1 35.4 1.0 O A:HOH539 2.2 36.8 1.0 OD2 A:ASP104 2.4 26.7 1.0 OD1 A:ASP104 2.9 26.6 1.0 CG A:ASP104 2.9 26.6 1.0 CG A:ASP160 3.1 33.6 1.0 CG A:ASP184 3.3 37.3 1.0 OD1 A:ASP160 3.5 34.5 1.0 NZ A:LYS194 3.9 27.3 1.0 CB A:ASP184 4.0 34.4 1.0 O A:GLY335 4.0 30.8 1.0 OD1 A:ASP184 4.2 37.5 1.0 O A:HOH575 4.2 47.4 1.0 CB A:ASP104 4.3 26.0 1.0 CB A:ASP160 4.4 30.3 1.0 O A:HOH576 4.6 51.7 1.0 CD A:LYS194 4.7 28.9 1.0 CB A:ASN102 4.7 25.1 1.0 CB A:ALA162 4.9 30.2 1.0 CE A:LYS194 4.9 28.6 1.0 C A:GLY335 5.0 30.1 1.0

Magnesium binding site 2 out of 2 in the Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:43.8 occ:1.00 O A:HOH548 2.2 36.2 1.0 O A:HOH525 2.3 37.6 1.0 O A:HOH526 2.3 40.8 1.0 OD2 A:ASP270 4.0 41.4 1.0 O A:ALA286 4.5 37.7 1.0 O A:HOH533 4.5 41.0 1.0 CA A:ALA287 4.8 36.0 1.0 CB A:ALA271 4.8 26.9 1.0 O A:ALA267 4.9 27.4 1.0 N A:ALA271 4.9 29.0 1.0 CG A:ASP270 5.0 39.4 1.0

Y.Naoe, N.Nakamura, M.M.Rahman, T.Tosha, S.Nagatoishi, K.Tsumoto, Y.Shiro, H.Sugimoto. Structural Basis For Binding and Transfer of Heme in Bacterial Heme-Acquisition Systems Proteins V. 85 2217 2017.
ISSN: ESSN 1097-0134
PubMed: 28913898
DOI: 10.1002/PROT.25386