Iron in PDB 3nu1: Structure of Holo Form of A Periplasmic Heme Binding Protein

The structure of Structure of Holo Form of A Periplasmic Heme Binding Protein, PDB code: 3nu1 was solved by D.Mattle, B.A.Goetz, J.S.Woo, K.P.Locher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.64 / 2.50
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.240, 89.240, 288.900, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 23.8

The binding sites of Iron atom in the Structure of Holo Form of A Periplasmic Heme Binding Protein (pdb code 3nu1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Holo Form of A Periplasmic Heme Binding Protein, PDB code: 3nu1:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Holo Form of A Periplasmic Heme Binding Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Holo Form of A Periplasmic Heme Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:61.0 occ:1.00 FE A:HEM301 0.0 61.0 1.0 NC A:HEM301 2.0 65.4 1.0 NA A:HEM301 2.0 66.5 1.0 NB A:HEM301 2.1 78.0 1.0 ND A:HEM301 2.1 71.8 1.0 NE2 A:HIS167 2.3 70.2 1.0 C1A A:HEM301 3.0 60.6 1.0 CD2 A:HIS167 3.0 70.1 1.0 C1C A:HEM301 3.1 64.1 1.0 C4C A:HEM301 3.1 67.0 1.0 C4D A:HEM301 3.1 70.7 1.0 C4B A:HEM301 3.1 67.1 1.0 C4A A:HEM301 3.1 68.1 1.0 C1B A:HEM301 3.1 69.0 1.0 C1D A:HEM301 3.1 69.4 1.0 NB A:HEM302 3.3 59.9 1.0 CHA A:HEM301 3.4 64.8 1.0 CHC A:HEM301 3.4 53.7 1.0 CHD A:HEM301 3.5 66.4 1.0 CE1 A:HIS167 3.5 67.2 1.0 CHB A:HEM301 3.5 66.3 1.0 C4B A:HEM302 3.6 56.4 1.0 C1B A:HEM302 3.7 58.8 1.0 CHC A:HEM302 4.1 55.3 1.0 FE A:HEM302 4.2 51.9 1.0 CHB A:HEM302 4.2 58.0 1.0 C3B A:HEM302 4.2 58.0 1.0 C2A A:HEM301 4.3 72.1 1.0 C2C A:HEM301 4.3 67.8 1.0 C3A A:HEM301 4.3 70.5 1.0 C3C A:HEM301 4.3 66.8 1.0 C2B A:HEM302 4.3 56.9 1.0 CG A:HIS167 4.3 67.4 1.0 C3B A:HEM301 4.3 68.6 1.0 C2B A:HEM301 4.3 63.3 1.0 C3D A:HEM301 4.3 78.3 1.0 C2D A:HEM301 4.4 77.3 1.0 NC A:HEM302 4.4 51.3 1.0 C1C A:HEM302 4.4 53.3 1.0 ND1 A:HIS167 4.5 60.8 1.0 C4A A:HEM302 4.6 58.3 1.0 NA A:HEM302 4.6 54.3 1.0 CD1 A:LEU170 5.0 77.9 1.0

Iron binding site 2 out of 4 in the Structure of Holo Form of A Periplasmic Heme Binding Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Holo Form of A Periplasmic Heme Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:51.9 occ:1.00 FE A:HEM302 0.0 51.9 1.0 NA A:HEM302 2.0 54.3 1.0 OH A:TYR70 2.1 50.8 1.0 NB A:HEM302 2.1 59.9 1.0 NC A:HEM302 2.1 51.3 1.0 ND A:HEM302 2.1 53.6 1.0 CZ A:TYR70 3.0 51.7 1.0 C1A A:HEM302 3.0 53.1 1.0 C4A A:HEM302 3.1 58.3 1.0 C4B A:HEM302 3.1 56.4 1.0 C4D A:HEM302 3.1 47.5 1.0 C1B A:HEM302 3.1 58.8 1.0 C1C A:HEM302 3.1 53.3 1.0 C1D A:HEM302 3.1 57.4 1.0 C4C A:HEM302 3.1 57.9 1.0 CHA A:HEM302 3.4 46.8 1.0 CHB A:HEM302 3.4 58.0 1.0 CHC A:HEM302 3.5 55.3 1.0 CHD A:HEM302 3.5 59.9 1.0 NB A:HEM301 3.5 78.0 1.0 CE2 A:TYR70 3.7 47.5 1.0 CE1 A:TYR70 3.7 52.0 1.0 C4B A:HEM301 3.8 67.1 1.0 C1B A:HEM301 3.9 69.0 1.0 NH1 A:ARG72 4.1 37.4 1.0 FE A:HEM301 4.2 61.0 1.0 CHC A:HEM301 4.2 53.7 1.0 C2A A:HEM302 4.3 61.3 1.0 C3A A:HEM302 4.3 60.4 1.0 C3B A:HEM302 4.3 58.0 1.0 C2B A:HEM302 4.3 56.9 1.0 C2C A:HEM302 4.3 61.2 1.0 C3D A:HEM302 4.3 50.8 1.0 C3C A:HEM302 4.3 55.4 1.0 C2D A:HEM302 4.3 51.9 1.0 C3B A:HEM301 4.4 68.6 1.0 C2B A:HEM301 4.4 63.3 1.0 CHB A:HEM301 4.4 66.3 1.0 NC A:HEM301 4.5 65.4 1.0 C1C A:HEM301 4.5 64.1 1.0 CD A:ARG72 4.6 38.4 1.0 NA A:HEM301 4.6 66.5 1.0 C4A A:HEM301 4.8 68.1 1.0 CZ A:ARG72 4.8 46.7 1.0 CD2 A:TYR70 4.9 50.5 1.0 CD1 A:TYR70 4.9 44.0 1.0

Iron binding site 3 out of 4 in the Structure of Holo Form of A Periplasmic Heme Binding Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Holo Form of A Periplasmic Heme Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:74.5 occ:1.00 FE B:HEM301 0.0 74.5 1.0 NA B:HEM301 2.1 97.8 1.0 NC B:HEM301 2.1 90.6 1.0 NB B:HEM301 2.1 92.3 1.0 ND B:HEM301 2.1 97.8 1.0 NE2 B:HIS167 2.6 85.3 1.0 CD2 B:HIS167 2.7 77.1 1.0 C1A B:HEM301 3.0 96.8 1.0 C4A B:HEM301 3.0 91.3 1.0 C4D B:HEM301 3.1 95.0 1.0 C1B B:HEM301 3.1 88.5 1.0 C4C B:HEM301 3.1 94.7 1.0 C4B B:HEM301 3.1 86.8 1.0 C1D B:HEM301 3.1 96.4 1.0 C1C B:HEM301 3.1 94.5 1.0 CHA B:HEM301 3.4 95.5 1.0 CHB B:HEM301 3.5 84.9 1.0 CHD B:HEM301 3.5 93.0 1.0 CHC B:HEM301 3.5 86.4 1.0 NB B:HEM302 3.6 83.1 1.0 C4B B:HEM302 3.8 82.7 1.0 CE1 B:HIS167 3.9 87.1 1.0 CG B:HIS167 4.1 84.3 1.0 CHC B:HEM302 4.1 83.5 1.0 C1B B:HEM302 4.2 87.4 1.0 C2A B:HEM301 4.2 97.1 1.0 C3A B:HEM301 4.2 93.3 1.0 FE B:HEM302 4.3 71.2 1.0 C1C B:HEM302 4.3 83.2 1.0 C2B B:HEM301 4.3 88.3 1.0 C3B B:HEM301 4.3 89.2 1.0 C3C B:HEM301 4.3 0.6 1.0 C3D B:HEM301 4.3 98.3 1.0 C2C B:HEM301 4.3 0.5 1.0 C2D B:HEM301 4.3 95.6 1.0 NC B:HEM302 4.3 85.3 1.0 C3B B:HEM302 4.5 90.3 1.0 ND1 B:HIS167 4.6 85.8 1.0 C2B B:HEM302 4.7 90.4 1.0 CHB B:HEM302 4.7 88.5 1.0 CD1 B:LEU170 4.9 0.3 1.0 NA B:HEM302 5.0 70.5 1.0

Iron binding site 4 out of 4 in the Structure of Holo Form of A Periplasmic Heme Binding Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Holo Form of A Periplasmic Heme Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:71.2 occ:1.00 FE B:HEM302 0.0 71.2 1.0 NB B:HEM302 2.0 83.1 1.0 NC B:HEM302 2.1 85.3 1.0 NA B:HEM302 2.1 70.5 1.0 ND B:HEM302 2.1 82.9 1.0 OH B:TYR70 2.2 66.5 1.0 C4B B:HEM302 3.0 82.7 1.0 CZ B:TYR70 3.0 65.6 1.0 C1B B:HEM302 3.0 87.4 1.0 C1C B:HEM302 3.1 83.2 1.0 C4A B:HEM302 3.1 76.5 1.0 C4C B:HEM302 3.1 80.2 1.0 C1D B:HEM302 3.1 78.6 1.0 C1A B:HEM302 3.1 76.3 1.0 C4D B:HEM302 3.1 77.1 1.0 CHC B:HEM302 3.4 83.5 1.0 CHB B:HEM302 3.4 88.5 1.0 CHD B:HEM302 3.5 78.4 1.0 CHA B:HEM302 3.5 74.0 1.0 NB B:HEM301 3.7 92.3 1.0 CE2 B:TYR70 3.7 67.2 1.0 CE1 B:TYR70 3.8 62.6 1.0 C4B B:HEM301 3.9 86.8 1.0 NH1 B:ARG72 4.0 63.2 1.0 CHC B:HEM301 4.2 86.4 1.0 C1B B:HEM301 4.2 88.5 1.0 NC B:HEM301 4.2 90.6 1.0 C3B B:HEM302 4.2 90.3 1.0 C2B B:HEM302 4.2 90.4 1.0 C1C B:HEM301 4.3 94.5 1.0 C2C B:HEM302 4.3 79.8 1.0 FE B:HEM301 4.3 74.5 1.0 C3C B:HEM302 4.3 79.9 1.0 C3A B:HEM302 4.3 83.5 1.0 C2A B:HEM302 4.3 75.6 1.0 C2D B:HEM302 4.4 71.6 1.0 C3D B:HEM302 4.4 75.9 1.0 C3B B:HEM301 4.5 89.2 1.0 C2B B:HEM301 4.6 88.3 1.0 NA B:HEM301 4.7 97.8 1.0 CHB B:HEM301 4.8 84.9 1.0 CD B:ARG72 4.9 74.0 1.0 CD2 B:TYR70 4.9 60.7 1.0 CD1 B:TYR70 4.9 58.6 1.0 CZ B:ARG72 5.0 70.3 1.0 C4C B:HEM301 5.0 94.7 1.0

D.Mattle, A.Zeltina, J.S.Woo, B.A.Goetz, K.P.Locher. Two Stacked Heme Molecules in the Binding Pocket of the Periplasmic Heme-Binding Protein Hmut From Yersinia Pestis. J.Mol.Biol. V. 404 220 2010.
ISSN: ISSN 0022-2836
PubMed: 20888343
DOI: 10.1016/J.JMB.2010.09.005