Iron in PDB 7w81: Crystal Structure of the Heme-Bound Form of the Linker-NEAT3 Region of Isdh From Staphylococcus Aureus

The structure of Crystal Structure of the Heme-Bound Form of the Linker-NEAT3 Region of Isdh From Staphylococcus Aureus, PDB code: 7w81 was solved by J.M.M.Caaveiro, N.Vu, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.43 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.91, 95.31, 99.44, 90, 90, 90
R / Rfree (%)	18.5 / 22.6

The binding sites of Iron atom in the Crystal Structure of the Heme-Bound Form of the Linker-NEAT3 Region of Isdh From Staphylococcus Aureus (pdb code 7w81). 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 the Heme-Bound Form of the Linker-NEAT3 Region of Isdh From Staphylococcus Aureus, PDB code: 7w81:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of the Heme-Bound Form of the Linker-NEAT3 Region of Isdh From Staphylococcus Aureus


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 the Heme-Bound Form of the Linker-NEAT3 Region of Isdh From Staphylococcus Aureus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe700 b:21.8 occ:1.00 FE A:HEM700 0.0 21.8 1.0 NA A:HEM700 2.0 21.3 1.0 ND A:HEM700 2.1 19.5 1.0 NC A:HEM700 2.1 19.1 1.0 OH A:TYR642 2.1 19.6 1.0 NB A:HEM700 2.1 21.8 1.0 C1A A:HEM700 3.0 21.7 1.0 CZ A:TYR642 3.0 22.4 1.0 C1D A:HEM700 3.0 18.4 1.0 C1C A:HEM700 3.1 19.9 1.0 C4C A:HEM700 3.1 18.3 1.0 C4A A:HEM700 3.1 21.9 1.0 C1B A:HEM700 3.1 21.1 1.0 C4B A:HEM700 3.1 20.9 1.0 C4D A:HEM700 3.1 19.7 1.0 CHD A:HEM700 3.4 18.2 1.0 CHC A:HEM700 3.4 21.2 1.0 CHB A:HEM700 3.4 22.0 1.0 CHA A:HEM700 3.5 21.2 1.0 CG1 A:VAL564 3.6 23.6 1.0 CE2 A:TYR642 3.7 22.9 1.0 CE1 A:TYR642 3.9 23.3 1.0 OH A:TYR646 4.0 21.0 1.0 CB A:VAL564 4.2 22.5 1.0 C3A A:HEM700 4.2 23.7 1.0 C2C A:HEM700 4.2 19.3 1.0 C2A A:HEM700 4.3 24.9 1.0 C3C A:HEM700 4.3 18.3 1.0 C2B A:HEM700 4.3 22.5 1.0 C2D A:HEM700 4.3 18.7 1.0 C3B A:HEM700 4.3 22.0 1.0 CE1 A:TYR646 4.4 19.9 1.0 C3D A:HEM700 4.4 19.4 1.0 CG2 A:VAL564 4.5 22.4 1.0 CZ A:TYR646 4.5 21.0 1.0 CD2 A:TYR642 4.9 24.1 1.0

Iron binding site 2 out of 2 in the Crystal Structure of the Heme-Bound Form of the Linker-NEAT3 Region of Isdh From Staphylococcus Aureus


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 the Heme-Bound Form of the Linker-NEAT3 Region of Isdh From Staphylococcus Aureus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe700 b:22.0 occ:1.00 FE B:HEM700 0.0 22.0 1.0 NA B:HEM700 2.0 22.1 1.0 OH B:TYR642 2.0 21.4 1.0 NB B:HEM700 2.0 20.9 1.0 ND B:HEM700 2.1 18.9 1.0 NC B:HEM700 2.1 20.4 1.0 CZ B:TYR642 2.9 22.4 1.0 C4A B:HEM700 3.0 22.1 1.0 C1D B:HEM700 3.0 18.6 1.0 C4B B:HEM700 3.1 21.6 1.0 C1A B:HEM700 3.1 22.4 1.0 C1C B:HEM700 3.1 20.4 1.0 C1B B:HEM700 3.1 22.4 1.0 C4D B:HEM700 3.1 20.1 1.0 C4C B:HEM700 3.1 19.1 1.0 CHC B:HEM700 3.4 21.3 1.0 CHD B:HEM700 3.4 18.1 1.0 CHB B:HEM700 3.4 22.9 1.0 CHA B:HEM700 3.5 21.6 1.0 CG1 B:VAL564 3.6 22.9 1.0 CE2 B:TYR642 3.6 22.2 1.0 CE1 B:TYR642 3.9 22.4 1.0 OH B:TYR646 4.1 20.9 1.0 C3A B:HEM700 4.2 24.4 1.0 C2A B:HEM700 4.2 25.5 1.0 C2D B:HEM700 4.2 18.0 1.0 CB B:VAL564 4.2 23.3 1.0 C2B B:HEM700 4.3 22.9 1.0 C2C B:HEM700 4.3 20.1 1.0 C3B B:HEM700 4.3 22.6 1.0 C3D B:HEM700 4.3 19.5 1.0 C3C B:HEM700 4.3 19.5 1.0 CE1 B:TYR646 4.4 19.6 1.0 CZ B:TYR646 4.5 20.6 1.0 CG2 B:VAL564 4.5 24.4 1.0 CD2 B:TYR642 4.8 22.6 1.0

S.Valenciano-Bellido, J.M.M.Caaveiro, K.Morante, T.Sushko, M.Nakakido, S.Nagatoishi, K.Tsumoto. Structure and Role of the Linker Domain of the Iron Surface-Determinant Protein Isdh in Heme Transportation in Staphylococcus Aureus. J.Biol.Chem. V. 298 01995 2022.
ISSN: ESSN 1083-351X
PubMed: 35500652
DOI: 10.1016/J.JBC.2022.101995