Iron in PDB 9ia9: Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 8.05 Microjoule, Ssx

The structure of Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 8.05 Microjoule, Ssx, PDB code: 9ia9 was solved by P.Smyth, L.J.Williams, M.A.Hough, J.A.R.Worrall, R.L.Owen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.66 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.101, 122.913, 195.038, 90, 90, 90
R / Rfree (%)	17.7 / 22

The binding sites of Iron atom in the Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 8.05 Microjoule, Ssx (pdb code 9ia9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 8.05 Microjoule, Ssx, PDB code: 9ia9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 8.05 Microjoule, Ssx


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 8.05 Microjoule, Ssx within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe401 b:31.8 occ:1.00 FE F:HEM401 0.0 31.8 1.0 ND F:HEM401 1.9 31.7 1.0 NA F:HEM401 2.0 31.6 1.0 NE2 F:HIS225 2.0 31.8 1.0 N F:NO402 2.0 32.1 0.5 NC F:HEM401 2.1 31.5 1.0 NB F:HEM401 2.1 31.8 1.0 C4D F:HEM401 2.9 31.7 1.0 C1D F:HEM401 2.9 31.1 1.0 CE1 F:HIS225 3.0 31.8 1.0 C1A F:HEM401 3.0 31.5 1.0 CD2 F:HIS225 3.0 31.9 1.0 C4C F:HEM401 3.0 31.6 1.0 C4A F:HEM401 3.1 31.3 1.0 C1B F:HEM401 3.1 31.7 1.0 C4B F:HEM401 3.1 31.8 1.0 C1C F:HEM401 3.1 31.6 1.0 O F:NO402 3.2 31.1 0.5 CHA F:HEM401 3.3 31.2 1.0 CHD F:HEM401 3.4 31.2 1.0 CHB F:HEM401 3.5 31.2 1.0 CHC F:HEM401 3.5 31.1 1.0 ND1 F:HIS225 4.1 31.6 1.0 CG F:HIS225 4.1 31.9 1.0 C3D F:HEM401 4.2 32.0 1.0 C2D F:HEM401 4.2 31.7 1.0 NH1 F:ARG243 4.2 33.8 1.0 C2A F:HEM401 4.2 31.8 1.0 C3A F:HEM401 4.2 31.6 1.0 C3C F:HEM401 4.3 31.8 1.0 C2C F:HEM401 4.3 31.9 1.0 C2B F:HEM401 4.3 32.2 1.0 C3B F:HEM401 4.4 32.7 1.0 CD F:ARG243 4.6 33.6 1.0 CZ F:ARG243 4.8 34.4 1.0 NE F:ARG243 5.0 34.4 1.0

Iron binding site 2 out of 6 in the Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 8.05 Microjoule, Ssx


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 8.05 Microjoule, Ssx within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:25.8 occ:1.00 FE A:HEM401 0.0 25.8 1.0 ND A:HEM401 1.9 26.8 1.0 NA A:HEM401 2.0 25.3 1.0 N A:NO402 2.0 26.4 0.5 NE2 A:HIS225 2.0 26.4 1.0 NC A:HEM401 2.1 25.9 1.0 NB A:HEM401 2.1 26.4 1.0 C4D A:HEM401 2.9 27.2 1.0 C1D A:HEM401 2.9 27.3 1.0 C1A A:HEM401 3.0 25.7 1.0 CD2 A:HIS225 3.0 26.7 1.0 CE1 A:HIS225 3.0 26.3 1.0 C4C A:HEM401 3.1 26.4 1.0 C4A A:HEM401 3.1 25.4 1.0 C1B A:HEM401 3.1 26.6 1.0 O A:NO402 3.1 26.4 0.5 C4B A:HEM401 3.1 26.6 1.0 C1C A:HEM401 3.1 26.2 1.0 CHA A:HEM401 3.3 26.2 1.0 CHD A:HEM401 3.4 26.8 1.0 CHB A:HEM401 3.5 25.9 1.0 CHC A:HEM401 3.5 26.5 1.0 NH1 A:ARG243 4.1 26.7 1.0 ND1 A:HIS225 4.1 25.6 1.0 CG A:HIS225 4.1 26.4 1.0 C3D A:HEM401 4.2 28.3 1.0 C2D A:HEM401 4.2 27.6 1.0 C2A A:HEM401 4.2 25.5 1.0 C3A A:HEM401 4.2 25.2 1.0 C3C A:HEM401 4.3 26.5 1.0 C2B A:HEM401 4.3 27.3 1.0 C2C A:HEM401 4.3 26.3 1.0 C3B A:HEM401 4.3 27.4 1.0 CD A:ARG243 4.5 27.2 1.0 CZ A:ARG243 4.8 27.1 1.0 NE A:ARG243 5.0 27.2 1.0 ND2 A:ASN245 5.0 33.4 1.0

Iron binding site 3 out of 6 in the Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 8.05 Microjoule, Ssx


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 8.05 Microjoule, Ssx within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:28.9 occ:1.00 FE B:HEM401 0.0 28.9 1.0 ND B:HEM401 1.9 28.2 1.0 NA B:HEM401 2.0 28.0 1.0 NE2 B:HIS225 2.0 31.0 1.0 N B:NO402 2.0 29.4 0.6 NC B:HEM401 2.1 27.6 1.0 NB B:HEM401 2.1 28.4 1.0 C4D B:HEM401 2.9 27.9 1.0 C1D B:HEM401 2.9 27.9 1.0 O B:NO402 3.0 28.6 0.6 CE1 B:HIS225 3.0 31.3 1.0 C1A B:HEM401 3.0 27.8 1.0 CD2 B:HIS225 3.0 31.4 1.0 C4C B:HEM401 3.0 27.2 1.0 C4A B:HEM401 3.1 28.1 1.0 C1B B:HEM401 3.1 28.1 1.0 C4B B:HEM401 3.1 28.2 1.0 C1C B:HEM401 3.1 27.4 1.0 CHA B:HEM401 3.3 27.7 1.0 CHD B:HEM401 3.4 27.4 1.0 CHB B:HEM401 3.5 27.9 1.0 CHC B:HEM401 3.5 27.6 1.0 ND1 B:HIS225 4.1 30.7 1.0 NH1 B:ARG243 4.1 31.4 1.0 CG B:HIS225 4.1 31.1 1.0 C3D B:HEM401 4.2 28.3 1.0 C2D B:HEM401 4.2 27.9 1.0 C2A B:HEM401 4.2 27.8 1.0 C3A B:HEM401 4.2 28.0 1.0 C3C B:HEM401 4.3 27.2 1.0 C2C B:HEM401 4.3 27.3 1.0 C2B B:HEM401 4.3 28.2 1.0 C3B B:HEM401 4.4 28.4 1.0 CD B:ARG243 4.5 31.1 1.0 CZ B:ARG243 4.7 31.5 1.0 NE B:ARG243 4.8 31.5 1.0

Iron binding site 4 out of 6 in the Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 8.05 Microjoule, Ssx


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 8.05 Microjoule, Ssx within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:33.6 occ:1.00 FE C:HEM401 0.0 33.6 1.0 ND C:HEM401 1.9 32.8 1.0 NA C:HEM401 2.0 32.2 1.0 N C:NO402 2.0 36.1 0.6 NE2 C:HIS225 2.0 33.5 1.0 NC C:HEM401 2.1 33.0 1.0 NB C:HEM401 2.1 33.1 1.0 O C:NO402 2.8 36.1 0.6 C4D C:HEM401 2.9 32.3 1.0 C1D C:HEM401 2.9 32.6 1.0 CE1 C:HIS225 2.9 33.3 1.0 C1A C:HEM401 3.0 32.0 1.0 C4C C:HEM401 3.0 33.3 1.0 C4A C:HEM401 3.1 31.8 1.0 CD2 C:HIS225 3.1 33.1 1.0 C1B C:HEM401 3.1 33.1 1.0 C4B C:HEM401 3.1 33.4 1.0 C1C C:HEM401 3.1 32.8 1.0 CHA C:HEM401 3.3 31.9 1.0 CHD C:HEM401 3.4 32.8 1.0 CHB C:HEM401 3.5 31.9 1.0 CHC C:HEM401 3.5 33.0 1.0 ND1 C:HIS225 4.1 33.2 1.0 C3D C:HEM401 4.2 32.7 1.0 C2D C:HEM401 4.2 32.4 1.0 CG C:HIS225 4.2 33.2 1.0 NH1 C:ARG243 4.2 28.5 1.0 C2A C:HEM401 4.2 31.5 1.0 C3A C:HEM401 4.2 31.5 1.0 C3C C:HEM401 4.3 32.9 1.0 C2C C:HEM401 4.3 32.5 1.0 C2B C:HEM401 4.3 33.8 1.0 C3B C:HEM401 4.4 34.0 1.0 CD C:ARG243 4.5 28.6 1.0 CZ C:ARG243 4.8 28.5 1.0 ND2 C:ASN245 4.9 39.9 1.0 NE C:ARG243 5.0 28.2 1.0 CG2 C:THR229 5.0 44.0 1.0

Iron binding site 5 out of 6 in the Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 8.05 Microjoule, Ssx


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 8.05 Microjoule, Ssx within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:28.9 occ:1.00 FE D:HEM401 0.0 28.9 1.0 ND D:HEM401 1.9 28.3 1.0 NA D:HEM401 2.0 29.3 1.0 N D:NO402 2.0 29.7 0.5 NE2 D:HIS225 2.0 28.3 1.0 NC D:HEM401 2.1 28.9 1.0 NB D:HEM401 2.1 29.2 1.0 O D:NO402 2.7 30.0 0.5 C4D D:HEM401 2.9 28.5 1.0 C1D D:HEM401 2.9 28.2 1.0 C1A D:HEM401 3.0 29.6 1.0 CE1 D:HIS225 3.0 27.7 1.0 CD2 D:HIS225 3.0 28.1 1.0 C4C D:HEM401 3.0 29.0 1.0 C4A D:HEM401 3.1 29.0 1.0 C1B D:HEM401 3.1 29.5 1.0 C4B D:HEM401 3.1 29.9 1.0 C1C D:HEM401 3.1 29.4 1.0 CHA D:HEM401 3.3 29.1 1.0 CHD D:HEM401 3.4 28.3 1.0 CHB D:HEM401 3.5 29.1 1.0 CHC D:HEM401 3.5 29.7 1.0 ND1 D:HIS225 4.1 27.2 1.0 CG D:HIS225 4.1 28.2 1.0 NH1 D:ARG243 4.2 28.2 1.0 C2D D:HEM401 4.2 28.2 1.0 C3D D:HEM401 4.2 28.2 1.0 C2A D:HEM401 4.2 29.5 1.0 C3A D:HEM401 4.2 29.1 1.0 C3C D:HEM401 4.3 28.8 1.0 C2C D:HEM401 4.3 29.0 1.0 C2B D:HEM401 4.3 29.9 1.0 C3B D:HEM401 4.4 30.0 1.0 CD D:ARG243 4.6 28.2 1.0 CZ D:ARG243 4.8 28.9 1.0 ND2 D:ASN245 5.0 32.7 1.0 NE D:ARG243 5.0 28.6 1.0

Iron binding site 6 out of 6 in the Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 8.05 Microjoule, Ssx


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 8.05 Microjoule, Ssx within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe401 b:30.9 occ:1.00 FE E:HEM401 0.0 30.9 1.0 ND E:HEM401 1.9 30.3 1.0 NA E:HEM401 2.0 29.6 1.0 NE2 E:HIS225 2.0 31.3 1.0 N E:NO402 2.0 32.1 0.4 NC E:HEM401 2.1 29.4 1.0 NB E:HEM401 2.1 30.1 1.0 O E:NO402 2.7 32.3 0.4 C4D E:HEM401 2.9 29.6 1.0 C1D E:HEM401 2.9 30.2 1.0 CE1 E:HIS225 3.0 31.6 1.0 C1A E:HEM401 3.0 29.0 1.0 CD2 E:HIS225 3.0 31.1 1.0 C4C E:HEM401 3.0 29.6 1.0 C4A E:HEM401 3.0 29.3 1.0 C1B E:HEM401 3.1 30.0 1.0 C4B E:HEM401 3.1 30.5 1.0 C1C E:HEM401 3.1 29.8 1.0 CHA E:HEM401 3.3 28.8 1.0 CHD E:HEM401 3.4 30.1 1.0 CHB E:HEM401 3.5 29.4 1.0 CHC E:HEM401 3.5 30.0 1.0 ND1 E:HIS225 4.1 31.5 1.0 CG E:HIS225 4.1 31.6 1.0 NH1 E:ARG243 4.2 30.3 1.0 C2D E:HEM401 4.2 30.2 1.0 C3D E:HEM401 4.2 30.0 1.0 C2A E:HEM401 4.2 28.4 1.0 C3A E:HEM401 4.2 28.4 1.0 C3C E:HEM401 4.3 29.3 1.0 C2B E:HEM401 4.3 29.9 1.0 C2C E:HEM401 4.3 29.5 1.0 C3B E:HEM401 4.3 30.8 1.0 CD E:ARG243 4.5 30.8 1.0 CZ E:ARG243 4.7 30.5 1.0 NE E:ARG243 4.9 30.9 1.0 ND2 E:ASN245 5.0 38.5 1.0

P.Smyth, S.Jaho, L.J.Williams, G.Karras, A.Fitzpatrick, A.J.Thompson, S.Battah, D.Axford, S.Horrell, M.Lucic, K.Ishihara, M.Kataoka, H.Matsuura, K.Shimba, K.Tono, T.Tosha, H.Sugimoto, S.Owada, M.A.Hough, J.A.R.Worrall, R.L.Owen. Time-Resolved Serial Synchrotron and Serial Femtosecond Crystallography of Heme Proteins Using Photocaged Nitric Oxide. Iucrj 2025.
ISSN: ESSN 2052-2525
PubMed: 40843530
DOI: 10.1107/S2052252525006645