Iron in PDB 3qzn: Staphylococcus Aureus Isda Neat Domain Y166A Variant in Complex with Heme

The structure of Staphylococcus Aureus Isda Neat Domain Y166A Variant in Complex with Heme, PDB code: 3qzn was solved by J.C.Grigg, C.X.Mao, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.302, 96.764, 95.770, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23.5

The binding sites of Iron atom in the Staphylococcus Aureus Isda Neat Domain Y166A Variant in Complex with Heme (pdb code 3qzn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Staphylococcus Aureus Isda Neat Domain Y166A Variant in Complex with Heme, PDB code: 3qzn:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Staphylococcus Aureus Isda Neat Domain Y166A Variant in Complex with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Staphylococcus Aureus Isda Neat Domain Y166A Variant in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:31.8 occ:0.50 FE A:HEM200 0.0 31.8 0.5 FE A:HEM200 0.0 23.5 0.5 NA A:HEM200 2.0 23.5 0.5 NE2 A:HIS83 2.0 24.5 1.0 NA A:HEM200 2.1 33.6 0.5 NB A:HEM200 2.1 31.6 0.5 ND A:HEM200 2.1 25.0 0.5 NC A:HEM200 2.1 22.1 0.5 ND A:HEM200 2.1 32.2 0.5 NC A:HEM200 2.1 30.8 0.5 NB A:HEM200 2.1 21.0 0.5 O A:HOH353 2.2 34.4 1.0 C4A A:HEM200 3.0 23.1 0.5 CD2 A:HIS83 3.0 22.9 1.0 CE1 A:HIS83 3.0 24.1 1.0 C1D A:HEM200 3.0 25.2 0.5 C4A A:HEM200 3.0 34.0 0.5 C4C A:HEM200 3.0 23.5 0.5 C1D A:HEM200 3.0 31.9 0.5 C4C A:HEM200 3.0 30.3 0.5 C1B A:HEM200 3.0 32.8 0.5 C1B A:HEM200 3.1 20.4 0.5 C1A A:HEM200 3.1 24.5 0.5 C1A A:HEM200 3.1 34.5 0.5 C4D A:HEM200 3.1 26.0 0.5 C4B A:HEM200 3.1 32.2 0.5 C4D A:HEM200 3.1 33.1 0.5 C1C A:HEM200 3.1 22.7 0.5 C1C A:HEM200 3.1 29.8 0.5 C4B A:HEM200 3.2 19.5 0.5 CHB A:HEM200 3.4 21.1 0.5 CHD A:HEM200 3.4 22.3 0.5 CHD A:HEM200 3.4 30.7 0.5 CHB A:HEM200 3.4 32.0 0.5 CHA A:HEM200 3.5 25.7 0.5 CHA A:HEM200 3.5 34.2 0.5 CHC A:HEM200 3.5 30.7 0.5 CHC A:HEM200 3.6 20.9 0.5 ND1 A:HIS83 4.1 25.2 1.0 CG A:HIS83 4.2 23.8 1.0 C3A A:HEM200 4.2 23.7 0.5 C2A A:HEM200 4.3 24.3 0.5 C3A A:HEM200 4.3 35.2 0.5 C2B A:HEM200 4.3 32.9 0.5 C3C A:HEM200 4.3 29.9 0.5 C2D A:HEM200 4.3 26.6 0.5 C3C A:HEM200 4.3 23.2 0.5 C2A A:HEM200 4.3 35.8 0.5 C2D A:HEM200 4.3 32.4 0.5 C3B A:HEM200 4.3 33.1 0.5 C2B A:HEM200 4.3 19.5 0.5 C3D A:HEM200 4.3 27.3 0.5 C3D A:HEM200 4.3 32.8 0.5 C2C A:HEM200 4.3 23.4 0.5 C2C A:HEM200 4.3 30.1 0.5 C3B A:HEM200 4.4 20.0 0.5 OH A:TYR170 4.5 36.1 1.0 CZ A:TYR170 5.0 36.2 1.0

Iron binding site 2 out of 6 in the Staphylococcus Aureus Isda Neat Domain Y166A Variant in Complex with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Staphylococcus Aureus Isda Neat Domain Y166A Variant in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:23.5 occ:0.50 FE A:HEM200 0.0 23.5 0.5 FE A:HEM200 0.0 31.8 0.5 NE2 A:HIS83 2.0 24.5 1.0 NA A:HEM200 2.0 23.5 0.5 NB A:HEM200 2.1 31.6 0.5 NC A:HEM200 2.1 22.1 0.5 NA A:HEM200 2.1 33.6 0.5 NC A:HEM200 2.1 30.8 0.5 ND A:HEM200 2.1 32.2 0.5 ND A:HEM200 2.1 25.0 0.5 NB A:HEM200 2.1 21.0 0.5 O A:HOH353 2.2 34.4 1.0 C4A A:HEM200 3.0 23.1 0.5 CE1 A:HIS83 3.0 24.1 1.0 CD2 A:HIS83 3.0 22.9 1.0 C4C A:HEM200 3.0 30.3 0.5 C4C A:HEM200 3.0 23.5 0.5 C1D A:HEM200 3.0 25.2 0.5 C1B A:HEM200 3.0 32.8 0.5 C1D A:HEM200 3.0 31.9 0.5 C4A A:HEM200 3.1 34.0 0.5 C1B A:HEM200 3.1 20.4 0.5 C1A A:HEM200 3.1 24.5 0.5 C4B A:HEM200 3.1 32.2 0.5 C1A A:HEM200 3.1 34.5 0.5 C4D A:HEM200 3.1 26.0 0.5 C4D A:HEM200 3.1 33.1 0.5 C1C A:HEM200 3.1 22.7 0.5 C1C A:HEM200 3.1 29.8 0.5 C4B A:HEM200 3.2 19.5 0.5 CHB A:HEM200 3.4 21.1 0.5 CHD A:HEM200 3.4 22.3 0.5 CHD A:HEM200 3.4 30.7 0.5 CHB A:HEM200 3.4 32.0 0.5 CHA A:HEM200 3.5 25.7 0.5 CHA A:HEM200 3.5 34.2 0.5 CHC A:HEM200 3.5 30.7 0.5 CHC A:HEM200 3.5 20.9 0.5 ND1 A:HIS83 4.1 25.2 1.0 CG A:HIS83 4.1 23.8 1.0 C3A A:HEM200 4.2 23.7 0.5 C2A A:HEM200 4.3 24.3 0.5 C3C A:HEM200 4.3 29.9 0.5 C2B A:HEM200 4.3 32.9 0.5 C3A A:HEM200 4.3 35.2 0.5 C3C A:HEM200 4.3 23.2 0.5 C3B A:HEM200 4.3 33.1 0.5 C2D A:HEM200 4.3 26.6 0.5 C2D A:HEM200 4.3 32.4 0.5 C2B A:HEM200 4.3 19.5 0.5 C2A A:HEM200 4.3 35.8 0.5 C2C A:HEM200 4.3 23.4 0.5 C2C A:HEM200 4.3 30.1 0.5 C3D A:HEM200 4.3 27.3 0.5 C3D A:HEM200 4.3 32.8 0.5 C3B A:HEM200 4.4 20.0 0.5 OH A:TYR170 4.5 36.1 1.0

Iron binding site 3 out of 6 in the Staphylococcus Aureus Isda Neat Domain Y166A Variant in Complex with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Staphylococcus Aureus Isda Neat Domain Y166A Variant in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe200 b:21.2 occ:0.50 FE B:HEM200 0.0 21.2 0.5 FE B:HEM200 0.2 26.2 0.5 NE2 B:HIS168 2.0 23.0 1.0 NB B:HEM200 2.0 19.6 0.5 NB B:HEM200 2.0 27.0 0.5 NC B:HEM200 2.0 26.0 0.5 NA B:HEM200 2.0 25.7 0.5 NA B:HEM200 2.0 19.6 0.5 NC B:HEM200 2.1 21.4 0.5 ND B:HEM200 2.1 20.5 0.5 NE2 B:HIS83 2.1 29.5 1.0 ND B:HEM200 2.1 25.9 0.5 CE1 B:HIS83 2.9 31.1 1.0 CE1 B:HIS168 2.9 22.6 1.0 C1B B:HEM200 3.0 26.2 0.5 C4A B:HEM200 3.0 25.6 0.5 C4C B:HEM200 3.0 25.9 0.5 C1B B:HEM200 3.0 18.8 0.5 C4B B:HEM200 3.0 20.3 0.5 C1A B:HEM200 3.0 19.4 0.5 C4A B:HEM200 3.1 18.6 0.5 C4B B:HEM200 3.1 27.3 0.5 C1C B:HEM200 3.1 26.8 0.5 C1C B:HEM200 3.1 21.2 0.5 CD2 B:HIS168 3.1 20.0 1.0 C4C B:HEM200 3.1 20.3 0.5 C4D B:HEM200 3.1 21.1 0.5 C1A B:HEM200 3.1 25.2 0.5 C1D B:HEM200 3.1 25.3 0.5 C1D B:HEM200 3.1 20.4 0.5 C4D B:HEM200 3.2 25.6 0.5 CD2 B:HIS83 3.3 27.0 1.0 CHB B:HEM200 3.4 25.8 0.5 CHB B:HEM200 3.4 17.1 0.5 CHD B:HEM200 3.4 25.1 0.5 CHC B:HEM200 3.4 20.1 0.5 CHA B:HEM200 3.4 19.3 0.5 CHD B:HEM200 3.5 20.4 0.5 CHC B:HEM200 3.5 26.4 0.5 CHA B:HEM200 3.5 24.5 0.5 ND1 B:HIS168 4.0 21.9 1.0 ND1 B:HIS83 4.1 31.1 1.0 CG B:HIS168 4.2 23.5 1.0 C2B B:HEM200 4.2 17.9 0.5 C3B B:HEM200 4.2 18.8 0.5 C2B B:HEM200 4.2 26.8 0.5 C3C B:HEM200 4.2 26.0 0.5 C2A B:HEM200 4.2 18.2 0.5 C3A B:HEM200 4.2 17.8 0.5 C3B B:HEM200 4.3 27.4 0.5 C3A B:HEM200 4.3 25.6 0.5 C2C B:HEM200 4.3 26.0 0.5 CG B:HIS83 4.3 26.5 1.0 C2A B:HEM200 4.3 25.0 0.5 C2C B:HEM200 4.3 20.9 0.5 C3C B:HEM200 4.3 20.4 0.5 C3D B:HEM200 4.4 21.2 0.5 C2D B:HEM200 4.4 20.6 0.5 C2D B:HEM200 4.4 24.6 0.5 C3D B:HEM200 4.4 25.4 0.5

Iron binding site 4 out of 6 in the Staphylococcus Aureus Isda Neat Domain Y166A Variant in Complex with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Staphylococcus Aureus Isda Neat Domain Y166A Variant in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe200 b:26.2 occ:0.50 FE B:HEM200 0.0 26.2 0.5 FE B:HEM200 0.2 21.2 0.5 NE2 B:HIS83 2.0 29.5 1.0 NA B:HEM200 2.0 19.6 0.5 NB B:HEM200 2.0 19.6 0.5 NC B:HEM200 2.0 26.0 0.5 NA B:HEM200 2.0 25.7 0.5 ND B:HEM200 2.1 25.9 0.5 NB B:HEM200 2.1 27.0 0.5 ND B:HEM200 2.1 20.5 0.5 NE2 B:HIS168 2.1 23.0 1.0 NC B:HEM200 2.2 21.4 0.5 CE1 B:HIS83 2.7 31.1 1.0 C4A B:HEM200 3.0 18.6 0.5 C1A B:HEM200 3.0 19.4 0.5 C1B B:HEM200 3.0 18.8 0.5 C4C B:HEM200 3.0 25.9 0.5 C4A B:HEM200 3.0 25.6 0.5 CE1 B:HIS168 3.0 22.6 1.0 C1D B:HEM200 3.0 25.3 0.5 C4B B:HEM200 3.1 20.3 0.5 C1A B:HEM200 3.1 25.2 0.5 C1B B:HEM200 3.1 26.2 0.5 C4D B:HEM200 3.1 21.1 0.5 C4D B:HEM200 3.1 25.6 0.5 C1C B:HEM200 3.1 26.8 0.5 CD2 B:HIS83 3.1 27.0 1.0 C4B B:HEM200 3.1 27.3 0.5 C4C B:HEM200 3.1 20.3 0.5 C1D B:HEM200 3.1 20.4 0.5 C1C B:HEM200 3.2 21.2 0.5 CD2 B:HIS168 3.2 20.0 1.0 CHB B:HEM200 3.4 17.1 0.5 CHD B:HEM200 3.4 25.1 0.5 CHA B:HEM200 3.4 19.3 0.5 CHB B:HEM200 3.4 25.8 0.5 CHA B:HEM200 3.5 24.5 0.5 CHC B:HEM200 3.5 20.1 0.5 CHD B:HEM200 3.5 20.4 0.5 CHC B:HEM200 3.5 26.4 0.5 ND1 B:HIS83 3.9 31.1 1.0 CG B:HIS83 4.1 26.5 1.0 C3A B:HEM200 4.2 17.8 0.5 C2A B:HEM200 4.2 18.2 0.5 ND1 B:HIS168 4.2 21.9 1.0 C2B B:HEM200 4.2 17.9 0.5 C3C B:HEM200 4.2 26.0 0.5 C3B B:HEM200 4.2 18.8 0.5 C3A B:HEM200 4.3 25.6 0.5 C2A B:HEM200 4.3 25.0 0.5 C2D B:HEM200 4.3 24.6 0.5 C2C B:HEM200 4.3 26.0 0.5 C2B B:HEM200 4.3 26.8 0.5 C3D B:HEM200 4.3 25.4 0.5 CG B:HIS168 4.3 23.5 1.0 C3B B:HEM200 4.3 27.4 0.5 C3D B:HEM200 4.4 21.2 0.5 C2C B:HEM200 4.4 20.9 0.5 C3C B:HEM200 4.4 20.4 0.5 C2D B:HEM200 4.4 20.6 0.5

Iron binding site 5 out of 6 in the Staphylococcus Aureus Isda Neat Domain Y166A Variant in Complex with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Staphylococcus Aureus Isda Neat Domain Y166A Variant in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:21.3 occ:0.50 FE C:HEM200 0.0 21.3 0.5 FE C:HEM200 0.2 27.4 0.5 NC C:HEM200 2.0 27.9 0.5 ND C:HEM200 2.0 27.4 0.5 NC C:HEM200 2.0 20.2 0.5 NE2 C:HIS83 2.0 25.8 1.0 NA C:HEM200 2.1 21.0 0.5 NB C:HEM200 2.1 20.7 0.5 NE2 C:HIS168 2.1 26.8 1.0 NA C:HEM200 2.1 27.5 0.5 ND C:HEM200 2.1 21.7 0.5 NB C:HEM200 2.1 27.7 0.5 C4C C:HEM200 2.9 27.4 0.5 CE1 C:HIS168 2.9 25.2 1.0 C1D C:HEM200 3.0 27.2 0.5 CD2 C:HIS83 3.0 24.0 1.0 C1C C:HEM200 3.0 28.1 0.5 C4D C:HEM200 3.0 27.4 0.5 C4C C:HEM200 3.0 21.2 0.5 CE1 C:HIS83 3.1 25.8 1.0 C4A C:HEM200 3.1 20.6 0.5 C1C C:HEM200 3.1 20.7 0.5 C1B C:HEM200 3.1 19.4 0.5 C1D C:HEM200 3.1 22.5 0.5 C1A C:HEM200 3.1 21.0 0.5 C4B C:HEM200 3.1 20.3 0.5 C1A C:HEM200 3.1 26.6 0.5 C4B C:HEM200 3.1 28.6 0.5 C4D C:HEM200 3.1 21.9 0.5 C4A C:HEM200 3.2 27.4 0.5 C1B C:HEM200 3.2 28.3 0.5 CD2 C:HIS168 3.2 23.6 1.0 CHD C:HEM200 3.3 26.4 0.5 CHD C:HEM200 3.4 20.8 0.5 CHB C:HEM200 3.4 19.2 0.5 CHA C:HEM200 3.4 27.2 0.5 CHC C:HEM200 3.5 19.4 0.5 CHC C:HEM200 3.5 27.9 0.5 CHA C:HEM200 3.5 21.1 0.5 CHB C:HEM200 3.5 27.3 0.5 ND1 C:HIS168 4.1 23.3 1.0 ND1 C:HIS83 4.1 26.0 1.0 CG C:HIS83 4.1 24.6 1.0 C3C C:HEM200 4.1 28.2 0.5 C2C C:HEM200 4.2 28.7 0.5 C2D C:HEM200 4.2 26.9 0.5 C3D C:HEM200 4.2 27.9 0.5 C3C C:HEM200 4.3 20.0 0.5 C2C C:HEM200 4.3 19.6 0.5 C3A C:HEM200 4.3 20.3 0.5 CG C:HIS168 4.3 25.9 1.0 C2A C:HEM200 4.3 21.5 0.5 C2B C:HEM200 4.3 19.7 0.5 C3B C:HEM200 4.3 20.1 0.5 C2D C:HEM200 4.3 22.8 0.5 C2A C:HEM200 4.3 25.6 0.5 C3D C:HEM200 4.4 22.2 0.5 C3A C:HEM200 4.4 26.7 0.5 C3B C:HEM200 4.4 28.5 0.5 C2B C:HEM200 4.4 28.1 0.5

Iron binding site 6 out of 6 in the Staphylococcus Aureus Isda Neat Domain Y166A Variant in Complex with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Staphylococcus Aureus Isda Neat Domain Y166A Variant in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:27.4 occ:0.50 FE C:HEM200 0.0 27.4 0.5 FE C:HEM200 0.2 21.3 0.5 NC C:HEM200 1.9 20.2 0.5 NE2 C:HIS168 2.0 26.8 1.0 NC C:HEM200 2.0 27.9 0.5 NB C:HEM200 2.0 27.7 0.5 NA C:HEM200 2.1 27.5 0.5 ND C:HEM200 2.1 21.7 0.5 ND C:HEM200 2.1 27.4 0.5 NB C:HEM200 2.1 20.7 0.5 NE2 C:HIS83 2.1 25.8 1.0 NA C:HEM200 2.2 21.0 0.5 CE1 C:HIS168 2.8 25.2 1.0 C4C C:HEM200 2.9 21.2 0.5 C1D C:HEM200 3.0 22.5 0.5 C1C C:HEM200 3.0 20.7 0.5 C4C C:HEM200 3.0 27.4 0.5 C1C C:HEM200 3.0 28.1 0.5 C1B C:HEM200 3.1 28.3 0.5 C4B C:HEM200 3.1 28.6 0.5 C4A C:HEM200 3.1 27.4 0.5 C1D C:HEM200 3.1 27.2 0.5 C1A C:HEM200 3.1 26.6 0.5 C4D C:HEM200 3.1 27.4 0.5 CD2 C:HIS83 3.1 24.0 1.0 C4B C:HEM200 3.1 20.3 0.5 C4D C:HEM200 3.1 21.9 0.5 CE1 C:HIS83 3.1 25.8 1.0 CD2 C:HIS168 3.2 23.6 1.0 C1A C:HEM200 3.2 21.0 0.5 C1B C:HEM200 3.2 19.4 0.5 C4A C:HEM200 3.2 20.6 0.5 CHD C:HEM200 3.3 20.8 0.5 CHD C:HEM200 3.4 26.4 0.5 CHC C:HEM200 3.4 27.9 0.5 CHB C:HEM200 3.4 27.3 0.5 CHC C:HEM200 3.4 19.4 0.5 CHA C:HEM200 3.5 27.2 0.5 CHA C:HEM200 3.5 21.1 0.5 CHB C:HEM200 3.5 19.2 0.5 ND1 C:HIS168 4.0 23.3 1.0 C3C C:HEM200 4.2 20.0 0.5 CG C:HIS168 4.2 25.9 1.0 C2C C:HEM200 4.2 19.6 0.5 C3C C:HEM200 4.2 28.2 0.5 ND1 C:HIS83 4.2 26.0 1.0 C2C C:HEM200 4.2 28.7 0.5 C2D C:HEM200 4.3 22.8 0.5 CG C:HIS83 4.3 24.6 1.0 C3B C:HEM200 4.3 28.5 0.5 C2B C:HEM200 4.3 28.1 0.5 C3A C:HEM200 4.3 26.7 0.5 C2A C:HEM200 4.3 25.6 0.5 C3D C:HEM200 4.3 22.2 0.5 C2D C:HEM200 4.3 26.9 0.5 C3D C:HEM200 4.3 27.9 0.5 C3B C:HEM200 4.4 20.1 0.5 C2B C:HEM200 4.4 19.7 0.5 C2A C:HEM200 4.4 21.5 0.5 C3A C:HEM200 4.4 20.3 0.5

J.C.Grigg, C.X.Mao, M.E.Murphy. Iron-Coordinating Tyrosine Is A Key Determinant of Neat Domain Heme Transfer. J.Mol.Biol. V. 413 684 2011.
ISSN: ISSN 0022-2836
PubMed: 21893067
DOI: 10.1016/J.JMB.2011.08.047