Iron in PDB 8hkj: Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus

The structure of Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus, PDB code: 8hkj was solved by J.K.Stanfield, H.Onoda, H.Sugimoto, O.Shoji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	96.62, 126.06, 141.44, 86.66, 79.47, 84.97
R / Rfree (%)	23.9 / 27

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus (pdb code 8hkj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus, PDB code: 8hkj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus


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 CYP102A5 Haem Domain Isolated From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:58.0 occ:1.00 FE A:HEM501 0.0 58.0 1.0 ND A:HEM501 2.0 42.7 1.0 NC A:HEM501 2.0 45.7 1.0 NA A:HEM501 2.0 49.5 1.0 NB A:HEM501 2.1 44.4 1.0 SG A:CYS405 2.2 56.1 1.0 C1D A:HEM501 3.0 43.0 1.0 C4C A:HEM501 3.0 38.5 1.0 C4D A:HEM501 3.0 38.1 1.0 C1A A:HEM501 3.1 44.2 1.0 C1C A:HEM501 3.1 39.4 1.0 C4A A:HEM501 3.1 47.7 1.0 C4B A:HEM501 3.1 39.7 1.0 C1B A:HEM501 3.1 40.7 1.0 CB A:CYS405 3.2 51.2 1.0 CHD A:HEM501 3.4 36.8 1.0 CHA A:HEM501 3.4 39.8 1.0 CHC A:HEM501 3.5 40.5 1.0 CHB A:HEM501 3.5 44.7 1.0 CA A:CYS405 4.0 46.5 1.0 O A:ALA268 4.1 52.4 1.0 C2D A:HEM501 4.2 45.3 1.0 C3D A:HEM501 4.2 41.9 1.0 C3C A:HEM501 4.2 36.2 1.0 C2C A:HEM501 4.3 35.1 1.0 C2A A:HEM501 4.3 42.8 1.0 C3A A:HEM501 4.3 47.7 1.0 C3B A:HEM501 4.4 37.7 1.0 C2B A:HEM501 4.4 35.6 1.0 N A:GLY407 4.7 41.3 1.0 CB A:ALA268 4.7 57.1 1.0 C A:CYS405 4.7 52.1 1.0 C A:ALA268 4.9 50.7 1.0 N A:ILE406 4.9 50.8 1.0

Iron binding site 2 out of 12 in the Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus


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 CYP102A5 Haem Domain Isolated From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:47.9 occ:1.00 FE B:HEM501 0.0 47.9 1.0 ND B:HEM501 2.0 51.5 1.0 NB B:HEM501 2.0 47.5 1.0 NC B:HEM501 2.0 57.4 1.0 NA B:HEM501 2.1 53.4 1.0 SG B:CYS405 2.3 56.8 1.0 C1D B:HEM501 3.0 52.5 1.0 C4B B:HEM501 3.0 44.9 1.0 C4D B:HEM501 3.1 44.5 1.0 C4C B:HEM501 3.1 46.7 1.0 C1C B:HEM501 3.1 53.8 1.0 C1B B:HEM501 3.1 44.7 1.0 C1A B:HEM501 3.1 41.6 1.0 C4A B:HEM501 3.1 46.5 1.0 CB B:CYS405 3.4 47.6 1.0 CHD B:HEM501 3.4 51.1 1.0 CHC B:HEM501 3.4 46.8 1.0 CHA B:HEM501 3.4 41.5 1.0 CHB B:HEM501 3.5 39.8 1.0 O B:ALA268 4.0 59.8 1.0 CA B:CYS405 4.2 45.5 1.0 C2D B:HEM501 4.3 50.0 1.0 C3D B:HEM501 4.3 47.9 1.0 C2C B:HEM501 4.3 52.8 1.0 C3C B:HEM501 4.3 45.2 1.0 C3B B:HEM501 4.3 42.2 1.0 C2B B:HEM501 4.3 44.1 1.0 C2A B:HEM501 4.3 40.8 1.0 C3A B:HEM501 4.3 41.8 1.0 CB B:ALA268 4.4 53.9 1.0 C B:ALA268 4.6 56.4 1.0 N B:GLY407 4.7 44.0 1.0 C B:CYS405 4.9 47.8 1.0

Iron binding site 3 out of 12 in the Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:59.7 occ:1.00 FE C:HEM501 0.0 59.7 1.0 NA C:HEM501 2.0 42.2 1.0 ND C:HEM501 2.0 44.5 1.0 NC C:HEM501 2.0 41.3 1.0 NB C:HEM501 2.1 37.7 1.0 SG C:CYS405 2.3 56.6 1.0 C4C C:HEM501 3.0 36.9 1.0 C4A C:HEM501 3.1 34.7 1.0 C1D C:HEM501 3.1 39.7 1.0 C1A C:HEM501 3.1 41.5 1.0 C1B C:HEM501 3.1 30.3 1.0 C4D C:HEM501 3.1 33.7 1.0 C4B C:HEM501 3.1 29.9 1.0 C1C C:HEM501 3.1 27.9 1.0 CB C:CYS405 3.3 45.7 1.0 CHD C:HEM501 3.4 37.0 1.0 CHB C:HEM501 3.4 27.3 1.0 CHA C:HEM501 3.4 37.8 1.0 CHC C:HEM501 3.5 27.0 1.0 CA C:CYS405 4.0 46.2 1.0 O C:ALA268 4.2 43.8 1.0 C3C C:HEM501 4.3 31.0 1.0 C3A C:HEM501 4.3 40.7 1.0 C2A C:HEM501 4.3 41.1 1.0 C2D C:HEM501 4.3 39.2 1.0 C2C C:HEM501 4.3 27.2 1.0 C3D C:HEM501 4.3 37.5 1.0 C2B C:HEM501 4.3 27.0 1.0 C3B C:HEM501 4.3 27.9 1.0 CB C:ALA268 4.6 60.9 1.0 N C:GLY407 4.7 51.5 1.0 C C:CYS405 4.8 46.9 1.0 C C:ALA268 4.9 49.8 1.0 CA C:GLY407 5.0 51.2 1.0 N C:ILE406 5.0 47.6 1.0

Iron binding site 4 out of 12 in the Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:51.2 occ:1.00 FE D:HEM501 0.0 51.2 1.0 ND D:HEM501 2.0 53.4 1.0 NB D:HEM501 2.1 50.6 1.0 NC D:HEM501 2.1 55.1 1.0 NA D:HEM501 2.1 51.0 1.0 SG D:CYS405 2.3 52.9 1.0 C4D D:HEM501 3.0 59.6 1.0 C1D D:HEM501 3.0 55.3 1.0 C4C D:HEM501 3.0 57.4 1.0 C1C D:HEM501 3.1 51.3 1.0 C1B D:HEM501 3.1 53.2 1.0 C4B D:HEM501 3.1 49.1 1.0 C4A D:HEM501 3.1 52.4 1.0 C1A D:HEM501 3.1 50.4 1.0 CB D:CYS405 3.3 55.9 1.0 CHD D:HEM501 3.4 56.2 1.0 CHA D:HEM501 3.4 51.9 1.0 CHC D:HEM501 3.4 45.4 1.0 CHB D:HEM501 3.4 54.1 1.0 CA D:CYS405 4.1 56.9 1.0 C3D D:HEM501 4.2 62.0 1.0 C3C D:HEM501 4.3 54.8 1.0 C2D D:HEM501 4.3 58.9 1.0 C2C D:HEM501 4.3 52.5 1.0 O D:ALA268 4.3 68.2 1.0 C2B D:HEM501 4.3 50.4 1.0 C3B D:HEM501 4.3 52.1 1.0 C3A D:HEM501 4.3 47.3 1.0 C2A D:HEM501 4.3 47.9 1.0 N D:GLY407 4.7 56.1 1.0 C D:CYS405 4.8 58.0 1.0 CB D:ALA268 4.9 51.2 1.0 C D:ALA268 4.9 64.5 1.0 N D:ILE406 4.9 58.0 1.0

Iron binding site 5 out of 12 in the Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe501 b:63.3 occ:1.00 FE E:HEM501 0.0 63.3 1.0 ND E:HEM501 2.0 35.0 1.0 NA E:HEM501 2.0 45.7 1.0 NC E:HEM501 2.1 45.8 1.0 NB E:HEM501 2.1 42.0 1.0 SG E:CYS405 2.4 59.6 1.0 C4D E:HEM501 3.0 35.4 1.0 C1D E:HEM501 3.0 38.8 1.0 C1A E:HEM501 3.0 40.3 1.0 C4C E:HEM501 3.1 36.4 1.0 C4A E:HEM501 3.1 37.6 1.0 C1C E:HEM501 3.1 36.6 1.0 C4B E:HEM501 3.1 34.4 1.0 C1B E:HEM501 3.1 38.1 1.0 CB E:CYS405 3.2 51.3 1.0 CHA E:HEM501 3.4 38.0 1.0 CHD E:HEM501 3.4 34.3 1.0 CHC E:HEM501 3.4 34.1 1.0 CHB E:HEM501 3.5 36.8 1.0 CA E:CYS405 3.9 51.9 1.0 O E:ALA268 4.2 51.9 1.0 C2D E:HEM501 4.2 39.3 1.0 C3D E:HEM501 4.2 40.1 1.0 C2A E:HEM501 4.3 41.9 1.0 C3A E:HEM501 4.3 36.8 1.0 C2C E:HEM501 4.3 35.0 1.0 C3C E:HEM501 4.3 36.4 1.0 C3B E:HEM501 4.3 37.6 1.0 C2B E:HEM501 4.3 35.6 1.0 C E:CYS405 4.7 51.9 1.0 CB E:ALA268 4.7 57.1 1.0 N E:GLY407 4.7 59.9 1.0 N E:ILE406 4.8 51.3 1.0 C E:ALA268 4.9 52.5 1.0

Iron binding site 6 out of 12 in the Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe501 b:55.9 occ:1.00 FE F:HEM501 0.0 55.9 1.0 ND F:HEM501 2.0 54.1 1.0 NA F:HEM501 2.0 59.1 1.0 NB F:HEM501 2.0 47.6 1.0 NC F:HEM501 2.0 50.6 1.0 SG F:CYS405 2.3 66.7 1.0 C1D F:HEM501 3.0 54.8 1.0 C1C F:HEM501 3.0 49.6 1.0 C4C F:HEM501 3.1 47.8 1.0 C4D F:HEM501 3.1 49.6 1.0 C4B F:HEM501 3.1 51.7 1.0 C1A F:HEM501 3.1 60.2 1.0 C4A F:HEM501 3.1 53.5 1.0 C1B F:HEM501 3.1 48.9 1.0 CB F:CYS405 3.3 60.6 1.0 CHC F:HEM501 3.4 52.0 1.0 CHA F:HEM501 3.4 55.2 1.0 CHD F:HEM501 3.4 52.2 1.0 CHB F:HEM501 3.4 48.2 1.0 O F:ALA268 4.1 54.3 1.0 CA F:CYS405 4.1 56.7 1.0 C2C F:HEM501 4.3 46.9 1.0 C2D F:HEM501 4.3 51.7 1.0 C3C F:HEM501 4.3 48.3 1.0 C3A F:HEM501 4.3 58.6 1.0 C3D F:HEM501 4.3 50.0 1.0 C2A F:HEM501 4.3 58.2 1.0 C3B F:HEM501 4.3 47.0 1.0 C2B F:HEM501 4.3 48.0 1.0 CB F:ALA268 4.5 69.0 1.0 C F:ALA268 4.8 59.6 1.0 N F:GLY407 4.8 49.8 1.0 C F:CYS405 4.9 57.3 1.0

Iron binding site 7 out of 12 in the Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe501 b:78.1 occ:1.00 FE G:HEM501 0.0 78.1 1.0 NB G:HEM501 2.0 68.6 1.0 NA G:HEM501 2.0 77.4 1.0 ND G:HEM501 2.1 78.6 1.0 NC G:HEM501 2.1 76.9 1.0 SG G:CYS405 2.3 74.4 1.0 C1B G:HEM501 3.0 68.2 1.0 C4A G:HEM501 3.0 71.3 1.0 C4B G:HEM501 3.0 68.3 1.0 C1D G:HEM501 3.1 84.4 1.0 C4D G:HEM501 3.1 80.7 1.0 C1C G:HEM501 3.1 68.8 1.0 C1A G:HEM501 3.1 78.8 1.0 C4C G:HEM501 3.1 76.5 1.0 CB G:CYS405 3.2 74.7 1.0 CHB G:HEM501 3.4 69.1 1.0 CHC G:HEM501 3.4 68.7 1.0 CHA G:HEM501 3.5 81.2 1.0 CHD G:HEM501 3.5 81.1 1.0 CA G:CYS405 3.9 79.4 1.0 O G:ALA268 4.1 87.6 1.0 C2B G:HEM501 4.2 69.3 1.0 C3B G:HEM501 4.2 66.9 1.0 C3A G:HEM501 4.3 71.7 1.0 C2D G:HEM501 4.3 88.9 1.0 C2A G:HEM501 4.3 75.3 1.0 C3D G:HEM501 4.3 86.4 1.0 C2C G:HEM501 4.3 66.6 1.0 C3C G:HEM501 4.3 71.2 1.0 C G:CYS405 4.8 84.3 1.0 C G:ALA268 4.8 85.5 1.0 N G:GLY407 4.8 78.6 1.0 CE1 G:PHE90 4.8 80.7 1.0 CB G:ALA268 4.9 85.9 1.0 N G:ILE406 4.9 88.1 1.0

Iron binding site 8 out of 12 in the Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe501 b:76.5 occ:1.00 FE H:HEM501 0.0 76.5 1.0 ND H:HEM501 2.0 85.6 1.0 NC H:HEM501 2.0 82.0 1.0 NA H:HEM501 2.1 79.9 1.0 NB H:HEM501 2.1 73.7 1.0 SG H:CYS405 2.2 71.3 1.0 C1D H:HEM501 3.0 89.0 1.0 C4C H:HEM501 3.0 83.0 1.0 C4D H:HEM501 3.0 86.2 1.0 C1C H:HEM501 3.1 76.4 1.0 C1A H:HEM501 3.1 76.7 1.0 C4A H:HEM501 3.1 74.7 1.0 C1B H:HEM501 3.1 72.5 1.0 C4B H:HEM501 3.1 70.5 1.0 CB H:CYS405 3.2 76.1 1.0 CHD H:HEM501 3.3 87.2 1.0 CHA H:HEM501 3.4 80.7 1.0 CHC H:HEM501 3.5 72.6 1.0 CHB H:HEM501 3.5 73.7 1.0 CA H:CYS405 4.0 83.4 1.0 C2D H:HEM501 4.2 92.1 1.0 C3C H:HEM501 4.2 80.4 1.0 C3D H:HEM501 4.2 92.6 1.0 C2C H:HEM501 4.2 76.7 1.0 C2A H:HEM501 4.3 72.0 1.0 C3A H:HEM501 4.3 70.5 1.0 C2B H:HEM501 4.3 69.3 1.0 C3B H:HEM501 4.4 65.7 1.0 O H:ALA268 4.4 81.2 1.0 N H:GLY407 4.7 85.1 1.0 C H:CYS405 4.7 87.8 1.0 CB H:ALA268 4.8 85.4 1.0 N H:ILE406 4.9 91.6 1.0

Iron binding site 9 out of 12 in the Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe501 b:106.1 occ:1.00 FE I:HEM501 0.0 106.1 1.0 NA I:HEM501 2.0 108.2 1.0 ND I:HEM501 2.0 112.0 1.0 NC I:HEM501 2.0 105.6 1.0 NB I:HEM501 2.1 104.2 1.0 SG I:CYS405 2.3 109.5 1.0 C1D I:HEM501 3.0 112.7 1.0 C4A I:HEM501 3.0 105.9 1.0 C4C I:HEM501 3.0 106.6 1.0 C1A I:HEM501 3.0 110.6 1.0 C4D I:HEM501 3.1 115.1 1.0 C1B I:HEM501 3.1 102.9 1.0 C1C I:HEM501 3.1 103.2 1.0 CB I:CYS405 3.1 109.9 1.0 C4B I:HEM501 3.2 101.0 1.0 CHD I:HEM501 3.4 110.2 1.0 CHB I:HEM501 3.4 104.2 1.0 CHA I:HEM501 3.4 114.2 1.0 CHC I:HEM501 3.5 101.8 1.0 CA I:CYS405 3.9 111.5 1.0 C2D I:HEM501 4.2 116.1 1.0 C3A I:HEM501 4.2 107.6 1.0 C2A I:HEM501 4.2 108.4 1.0 C3D I:HEM501 4.3 117.5 1.0 C3C I:HEM501 4.3 104.2 1.0 O I:ALA268 4.3 109.1 1.0 C2C I:HEM501 4.3 102.0 1.0 C2B I:HEM501 4.3 98.8 1.0 C3B I:HEM501 4.4 97.3 1.0 CB I:ALA268 4.8 114.5 1.0 CE1 I:PHE90 4.8 112.8 1.0 C I:CYS405 4.8 112.5 1.0 C I:ALA268 5.0 111.3 1.0

Iron binding site 10 out of 12 in the Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of the CYP102A5 Haem Domain Isolated From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ J:Fe501 b:100.6 occ:1.00 FE J:HEM501 0.0 100.6 1.0 NC J:HEM501 2.0 93.0 1.0 ND J:HEM501 2.0 95.3 1.0 NB J:HEM501 2.1 91.2 1.0 NA J:HEM501 2.1 97.7 1.0 SG J:CYS405 2.3 116.2 1.0 C1C J:HEM501 3.0 91.6 1.0 C4C J:HEM501 3.0 93.4 1.0 C4D J:HEM501 3.0 97.0 1.0 C4B J:HEM501 3.0 90.8 1.0 C1D J:HEM501 3.0 96.9 1.0 C1A J:HEM501 3.1 96.5 1.0 C1B J:HEM501 3.1 91.5 1.0 C4A J:HEM501 3.2 91.2 1.0 CB J:CYS405 3.3 108.4 1.0 CHC J:HEM501 3.4 91.3 1.0 CHD J:HEM501 3.4 96.7 1.0 CHA J:HEM501 3.4 96.3 1.0 CHB J:HEM501 3.5 89.8 1.0 O J:ALA268 4.0 101.7 1.0 CA J:CYS405 4.1 103.2 1.0 C2C J:HEM501 4.2 91.0 1.0 C3C J:HEM501 4.2 90.2 1.0 C3D J:HEM501 4.2 98.9 1.0 C2D J:HEM501 4.2 97.9 1.0 C3B J:HEM501 4.3 92.5 1.0 C2A J:HEM501 4.3 94.6 1.0 C2B J:HEM501 4.3 95.0 1.0 C3A J:HEM501 4.4 91.2 1.0 CE2 J:PHE90 4.6 116.6 1.0 OG1 J:THR272 4.7 94.1 1.0 CB J:ALA268 4.7 102.8 1.0 C J:ALA268 4.8 104.3 1.0 C J:CYS405 5.0 102.4 1.0

J.K.Stanfield, H.Onoda, S.Ariyasu, C.Kasai, E.M.Burfoot, H.Sugimoto, O.Shoji. Investigating the Applicability of the CYP102A1-Decoy-Molecule System to Other Members of the CYP102A Subfamily. J.Inorg.Biochem. 2023.
ISSN: ISSN 0162-0134