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Iron in PDB 9i6g: Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 16.1 Microjoule, Ssx

Protein crystallography data

The structure of Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 16.1 Microjoule, Ssx, PDB code: 9i6g 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) 79.71 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.142, 123.022, 195.394, 90, 90, 90
R / Rfree (%) 19.3 / 21.2

Iron Binding Sites:

The binding sites of Iron atom in the Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 16.1 Microjoule, Ssx (pdb code 9i6g). 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, 16.1 Microjoule, Ssx, PDB code: 9i6g:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 9i6g

Go back to Iron Binding Sites List in 9i6g
Iron binding site 1 out of 6 in the Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 16.1 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, 16.1 Microjoule, Ssx within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe401

b:30.7
occ:1.00
 FE F:HEM401 0.0 30.7 1.0
ND F:HEM401 1.9 31.1 1.0
NA F:HEM401 2.0 30.5 1.0
NE2 F:HIS225 2.0 31.8 1.0
N F:NO402 2.0 34.0 0.8
NC F:HEM401 2.1 30.1 1.0
NB F:HEM401 2.1 30.4 1.0
C4D F:HEM401 2.9 31.2 1.0
C1D F:HEM401 2.9 30.6 1.0
CE1 F:HIS225 2.9 31.8 1.0
C1A F:HEM401 3.0 30.6 1.0
O F:NO402 3.0 36.1 0.8
CD2 F:HIS225 3.0 31.9 1.0
C4C F:HEM401 3.0 30.3 1.0
C4A F:HEM401 3.1 30.2 1.0
C1B F:HEM401 3.1 30.4 1.0
C4B F:HEM401 3.1 30.5 1.0
C1C F:HEM401 3.1 30.3 1.0
CHA F:HEM401 3.3 30.8 1.0
CHD F:HEM401 3.4 30.3 1.0
CHB F:HEM401 3.5 30.3 1.0
CHC F:HEM401 3.5 30.3 1.0
ND1 F:HIS225 4.1 32.2 1.0
CG F:HIS225 4.1 31.8 1.0
C3D F:HEM401 4.2 31.5 1.0
C2D F:HEM401 4.2 30.8 1.0
C2A F:HEM401 4.2 30.4 1.0
NH1 F:ARG243 4.2 33.2 1.0
C3A F:HEM401 4.2 30.0 1.0
C3C F:HEM401 4.3 30.9 1.0
C2C F:HEM401 4.3 30.9 1.0
C2B F:HEM401 4.3 30.7 1.0
C3B F:HEM401 4.4 30.9 1.0
CD F:ARG243 4.6 31.3 1.0
CZ F:ARG243 4.8 32.8 1.0
NE F:ARG243 5.0 32.5 1.0

Iron binding site 2 out of 6 in 9i6g

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Iron binding site 2 out of 6 in the Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 16.1 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, 16.1 Microjoule, Ssx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:26.8
occ:1.00
 FE A:HEM401 0.0 26.8 1.0
ND A:HEM401 1.9 27.8 1.0
NA A:HEM401 2.0 27.1 1.0
N A:NO402 2.0 26.4 0.5
NE2 A:HIS225 2.0 27.0 1.0
NC A:HEM401 2.1 27.3 1.0
NB A:HEM401 2.1 27.2 1.0
C4D A:HEM401 2.9 28.1 1.0
C1D A:HEM401 2.9 27.8 1.0
CE1 A:HIS225 3.0 26.9 1.0
C1A A:HEM401 3.0 27.3 1.0
O A:NO402 3.0 26.1 0.5
C4C A:HEM401 3.0 27.5 1.0
CD2 A:HIS225 3.1 27.1 1.0
C4A A:HEM401 3.1 27.0 1.0
C1B A:HEM401 3.1 27.5 1.0
C4B A:HEM401 3.1 27.3 1.0
C1C A:HEM401 3.1 27.5 1.0
CHA A:HEM401 3.3 27.5 1.0
CHD A:HEM401 3.4 27.9 1.0
CHB A:HEM401 3.5 27.2 1.0
CHC A:HEM401 3.5 27.3 1.0
ND1 A:HIS225 4.1 26.7 1.0
C3D A:HEM401 4.2 28.7 1.0
C2D A:HEM401 4.2 28.1 1.0
CG A:HIS225 4.2 27.0 1.0
C2A A:HEM401 4.2 27.1 1.0
NH1 A:ARG243 4.2 27.2 1.0
C3A A:HEM401 4.2 26.5 1.0
C3C A:HEM401 4.3 27.6 1.0
C2B A:HEM401 4.3 27.5 1.0
C2C A:HEM401 4.3 27.6 1.0
C3B A:HEM401 4.3 27.5 1.0
CD A:ARG243 4.5 27.0 1.0
CZ A:ARG243 4.8 27.5 1.0
NE A:ARG243 4.9 27.4 1.0
ND2 A:ASN245 5.0 40.4 1.0

Iron binding site 3 out of 6 in 9i6g

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Iron binding site 3 out of 6 in the Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 16.1 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, 16.1 Microjoule, Ssx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:28.0
occ:1.00
 FE B:HEM401 0.0 28.0 1.0
ND B:HEM401 1.9 27.2 1.0
NA B:HEM401 2.0 26.9 1.0
NE2 B:HIS225 2.0 30.3 1.0
N B:NO402 2.0 28.6 0.7
NC B:HEM401 2.1 26.7 1.0
NB B:HEM401 2.1 26.4 1.0
C4D B:HEM401 2.9 26.7 1.0
C1D B:HEM401 2.9 27.1 1.0
CE1 B:HIS225 2.9 31.3 1.0
O B:NO402 2.9 28.7 0.7
C1A B:HEM401 3.0 26.6 1.0
CD2 B:HIS225 3.0 30.9 1.0
C4C B:HEM401 3.0 26.6 1.0
C4A B:HEM401 3.1 26.7 1.0
C1B B:HEM401 3.1 26.2 1.0
C4B B:HEM401 3.1 26.3 1.0
C1C B:HEM401 3.1 26.7 1.0
CHA B:HEM401 3.3 26.1 1.0
CHD B:HEM401 3.4 26.6 1.0
CHB B:HEM401 3.5 26.6 1.0
CHC B:HEM401 3.5 26.4 1.0
ND1 B:HIS225 4.1 31.1 1.0
CG B:HIS225 4.1 30.9 1.0
C3D B:HEM401 4.2 27.4 1.0
NH1 B:ARG243 4.2 29.5 1.0
C2D B:HEM401 4.2 27.2 1.0
C2A B:HEM401 4.2 26.7 1.0
C3A B:HEM401 4.2 26.7 1.0
C3C B:HEM401 4.3 26.6 1.0
C2C B:HEM401 4.3 26.6 1.0
C2B B:HEM401 4.3 25.6 1.0
C3B B:HEM401 4.3 26.1 1.0
CD B:ARG243 4.5 30.4 1.0
CZ B:ARG243 4.7 29.8 1.0
NE B:ARG243 4.9 30.3 1.0
ND2 B:ASN245 5.0 48.0 1.0

Iron binding site 4 out of 6 in 9i6g

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Iron binding site 4 out of 6 in the Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 16.1 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, 16.1 Microjoule, Ssx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:30.4
occ:1.00
 FE C:HEM401 0.0 30.4 1.0
ND C:HEM401 1.9 30.5 1.0
NA C:HEM401 2.0 30.0 1.0
N C:NO402 2.0 32.4 0.7
NE2 C:HIS225 2.0 31.4 1.0
NC C:HEM401 2.1 29.8 1.0
NB C:HEM401 2.1 29.8 1.0
O C:NO402 2.8 33.1 0.7
C4D C:HEM401 2.9 30.1 1.0
C1D C:HEM401 2.9 30.3 1.0
CE1 C:HIS225 2.9 30.9 1.0
C1A C:HEM401 3.0 29.5 1.0
C4C C:HEM401 3.0 29.7 1.0
CD2 C:HIS225 3.0 31.3 1.0
C4A C:HEM401 3.1 29.7 1.0
C1B C:HEM401 3.1 30.3 1.0
C4B C:HEM401 3.1 30.2 1.0
C1C C:HEM401 3.1 29.8 1.0
CHA C:HEM401 3.3 29.5 1.0
CHD C:HEM401 3.4 29.8 1.0
CHB C:HEM401 3.5 29.7 1.0
CHC C:HEM401 3.5 29.9 1.0
ND1 C:HIS225 4.1 30.9 1.0
C3D C:HEM401 4.2 30.7 1.0
CG C:HIS225 4.2 31.6 1.0
C2D C:HEM401 4.2 30.6 1.0
C2A C:HEM401 4.2 29.2 1.0
NH1 C:ARG243 4.2 30.2 1.0
C3A C:HEM401 4.2 29.3 1.0
C3C C:HEM401 4.3 29.6 1.0
C2B C:HEM401 4.3 30.6 1.0
C2C C:HEM401 4.3 30.1 1.0
C3B C:HEM401 4.3 30.7 1.0
CD C:ARG243 4.6 30.9 1.0
CZ C:ARG243 4.9 30.7 1.0

Iron binding site 5 out of 6 in 9i6g

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Iron binding site 5 out of 6 in the Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 16.1 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, 16.1 Microjoule, Ssx within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:28.3
occ:1.00
 FE D:HEM401 0.0 28.3 1.0
ND D:HEM401 1.9 29.2 1.0
NA D:HEM401 2.0 28.6 1.0
N D:NO402 2.0 28.2 0.6
NE2 D:HIS225 2.0 27.5 1.0
NC D:HEM401 2.1 29.8 1.0
NB D:HEM401 2.1 29.1 1.0
O D:NO402 2.9 28.2 0.6
C4D D:HEM401 2.9 29.1 1.0
C1D D:HEM401 2.9 29.3 1.0
CE1 D:HIS225 2.9 27.1 1.0
C1A D:HEM401 3.0 28.2 1.0
C4C D:HEM401 3.0 30.0 1.0
CD2 D:HIS225 3.1 27.4 1.0
C4A D:HEM401 3.1 28.4 1.0
C1B D:HEM401 3.1 29.4 1.0
C4B D:HEM401 3.1 29.9 1.0
C1C D:HEM401 3.1 30.1 1.0
CHA D:HEM401 3.3 28.7 1.0
CHD D:HEM401 3.4 29.5 1.0
CHB D:HEM401 3.5 28.8 1.0
CHC D:HEM401 3.5 30.0 1.0
ND1 D:HIS225 4.1 26.9 1.0
C3D D:HEM401 4.2 29.5 1.0
CG D:HIS225 4.2 27.5 1.0
NH1 D:ARG243 4.2 34.3 1.0
C2D D:HEM401 4.2 29.4 1.0
C2A D:HEM401 4.2 27.6 1.0
C3A D:HEM401 4.2 27.6 1.0
C3C D:HEM401 4.3 30.4 1.0
C2B D:HEM401 4.3 30.1 1.0
C2C D:HEM401 4.3 30.0 1.0
C3B D:HEM401 4.3 29.8 1.0
CD D:ARG243 4.5 32.2 1.0
CZ D:ARG243 4.8 33.8 1.0
NE D:ARG243 4.9 32.8 1.0

Iron binding site 6 out of 6 in 9i6g

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Iron binding site 6 out of 6 in the Dtpb in Complex with Photocaged Nitric Oxide, 1.24 S, 16.1 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, 16.1 Microjoule, Ssx within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe401

b:30.5
occ:1.00
 FE E:HEM401 0.0 30.5 1.0
ND E:HEM401 1.9 29.9 1.0
NA E:HEM401 2.0 28.9 1.0
NE2 E:HIS225 2.0 31.1 1.0
N E:NO402 2.0 32.5 0.6
NC E:HEM401 2.1 30.5 1.0
NB E:HEM401 2.1 29.8 1.0
O E:NO402 2.6 33.4 0.6
C4D E:HEM401 2.9 29.8 1.0
C1D E:HEM401 2.9 30.5 1.0
CE1 E:HIS225 2.9 31.6 1.0
C1A E:HEM401 3.0 28.5 1.0
CD2 E:HIS225 3.0 31.7 1.0
C4C E:HEM401 3.1 30.6 1.0
C4A E:HEM401 3.1 28.5 1.0
C1B E:HEM401 3.1 29.4 1.0
C4B E:HEM401 3.1 29.8 1.0
C1C E:HEM401 3.1 30.8 1.0
CHA E:HEM401 3.3 29.0 1.0
CHD E:HEM401 3.4 30.4 1.0
CHB E:HEM401 3.5 28.8 1.0
CHC E:HEM401 3.5 30.1 1.0
ND1 E:HIS225 4.1 32.3 1.0
CG E:HIS225 4.1 32.2 1.0
C3D E:HEM401 4.1 30.5 1.0
C2D E:HEM401 4.1 30.5 1.0
C2A E:HEM401 4.2 28.1 1.0
NH1 E:ARG243 4.2 30.2 1.0
C3A E:HEM401 4.2 28.1 1.0
C3C E:HEM401 4.3 31.4 1.0
C2C E:HEM401 4.3 31.5 1.0
C2B E:HEM401 4.3 29.5 1.0
C3B E:HEM401 4.3 29.8 1.0
CD E:ARG243 4.6 31.5 1.0
CZ E:ARG243 4.8 30.9 1.0
NE E:ARG243 5.0 31.6 1.0

Reference:

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
Page generated: Sat Dec 13 17:13:44 2025

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