Zinc in PDB 5gj3: Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2)

The structure of Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2), PDB code: 5gj3 was solved by M.M.Rahman, Y.Naoe, N.Nakamura, Y.Shiro, H.Sugimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.21 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	67.326, 86.338, 118.806, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.4

The structure of Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2) also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2) (pdb code 5gj3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2), PDB code: 5gj3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:30.1 occ:1.00 O A:HOH599 1.9 25.3 1.0 OD2 A:ASP160 2.0 22.7 1.0 OD2 A:ASP184 2.0 27.9 1.0 OD2 A:ASP104 2.1 24.2 1.0 CG A:ASP104 2.8 23.5 1.0 OD1 A:ASP104 2.8 25.3 1.0 CG A:ASP160 2.9 20.0 1.0 CG A:ASP184 3.1 26.2 1.0 OD1 A:ASP160 3.1 20.8 1.0 CB A:ASP184 3.8 22.5 1.0 NZ A:LYS194 3.9 20.8 1.0 OD1 A:ASP184 4.0 25.6 1.0 CB A:ASP104 4.3 21.9 1.0 CB A:ASP160 4.3 16.3 1.0 CD A:LYS194 4.4 19.5 1.0 CB A:ASN102 4.6 15.0 1.0 CE A:LYS194 4.8 21.8 1.0 CG A:ASN102 4.9 15.1 1.0 CB A:ALA162 4.9 22.4 1.0 O A:GLY335 5.0 23.7 1.0

Zinc binding site 2 out of 4 in the Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:27.8 occ:1.00 OD2 A:ASP270 2.1 33.0 1.0 NE2 A:HIS234 2.1 18.5 1.0 OD1 A:ASP270 2.5 34.3 1.0 CG A:ASP270 2.6 33.1 1.0 CD2 A:HIS234 3.0 17.7 1.0 CE1 A:HIS234 3.2 18.4 1.0 CB A:ASP270 4.1 34.1 1.0 CG A:HIS234 4.2 18.2 1.0 ND1 A:HIS234 4.2 17.6 1.0 CG2 A:ILE265 4.3 15.6 1.0 CA A:ASP270 5.0 36.9 1.0

Zinc binding site 3 out of 4 in the Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:33.1 occ:0.50 OE1 A:GLU96 2.1 31.6 1.0 O A:HOH614 2.2 17.8 0.5 O A:HOH523 2.4 38.7 1.0 CD A:GLU96 2.9 31.1 1.0 OE2 A:GLU96 3.1 35.1 1.0 O A:HOH517 4.0 22.2 1.0 O A:HOH605 4.3 44.1 1.0 CG A:GLU96 4.3 29.5 1.0 O A:ALA201 4.6 17.9 1.0

Zinc binding site 4 out of 4 in the Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:20.2 occ:0.50 O A:HOH541 2.0 20.3 1.0 OD1 A:ASP346 2.0 19.0 1.0 O A:HOH538 2.1 21.9 0.5 CG A:ASP346 3.0 20.1 1.0 OD2 A:ASP346 3.2 20.4 1.0 OH A:TYR332 4.2 19.3 1.0 O A:GLN342 4.4 16.6 1.0 CB A:ASP346 4.4 18.2 1.0 O A:HOH622 4.5 32.7 1.0 O A:HOH601 4.7 41.4 1.0 CA A:ASP346 4.8 18.3 1.0 N A:ASP346 4.8 18.1 1.0 O A:HOH554 4.9 38.6 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