Iron in PDB 5gn9: Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B

The structure of Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B, PDB code: 5gn9 was solved by E.O.Balogun, D.K.Inaoka, T.Shiba, T.Tsuge, B.May, T.Sato, Y.Kido, N.Takeshi, T.Aoki, T.Honma, A.Tanaka, M.Inoue, S.Matsuoka, P.A.M.Michels, Y.Watanabe, A.L.Moore, S.Harada, K.Kita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.19 / 3.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.218, 221.812, 62.611, 90.00, 114.64, 90.00
R / Rfree (%)	19.2 / 25.2

The binding sites of Iron atom in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B (pdb code 5gn9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B, PDB code: 5gn9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B


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 Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:46.0 occ:1.00 OE1 A:GLU266 1.8 69.7 1.0 OAC A:6Y0503 2.1 38.3 1.0 OE2 A:GLU123 2.3 55.9 1.0 OE1 A:GLU162 2.3 48.2 1.0 OE1 A:GLU123 2.3 47.4 1.0 OAD A:6Y0503 2.4 43.9 1.0 CD A:GLU123 2.6 50.8 1.0 CD A:GLU266 2.9 60.0 1.0 CAL A:6Y0503 3.0 47.4 1.0 CD A:GLU162 3.0 49.6 1.0 ND1 A:HIS165 3.1 51.5 1.0 OE2 A:GLU162 3.1 46.8 1.0 CAN A:6Y0503 3.1 50.6 1.0 FE A:FE502 3.3 54.5 1.0 OE2 A:GLU266 3.6 44.4 1.0 CE1 A:HIS165 3.7 56.0 1.0 OH A:TYR220 3.8 47.9 1.0 CG A:GLU266 4.0 58.0 1.0 CB A:ALA126 4.0 57.3 1.0 CG A:GLU123 4.1 48.5 1.0 CG A:HIS165 4.2 51.2 1.0 CAE A:6Y0503 4.4 55.6 1.0 CE2 A:TYR220 4.4 52.5 1.0 CG A:GLU162 4.5 47.5 1.0 CAQ A:6Y0503 4.5 58.4 1.0 CZ A:TYR220 4.6 50.9 1.0 CB A:HIS165 4.7 52.1 1.0 OE1 A:GLU213 4.9 43.9 1.0 CB A:GLU123 4.9 44.4 1.0 NE2 A:HIS165 5.0 54.0 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B


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 Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:54.5 occ:1.00 OE2 A:GLU162 2.0 46.8 1.0 OE2 A:GLU213 2.3 56.9 1.0 OAC A:6Y0503 2.3 38.3 1.0 OE2 A:GLU266 2.3 44.4 1.0 OE1 A:GLU213 2.5 43.9 1.0 CD A:GLU213 2.7 48.9 1.0 CD A:GLU162 2.9 49.6 1.0 OE1 A:GLU266 3.0 69.7 1.0 CD A:GLU266 3.0 60.0 1.0 FE A:FE501 3.3 46.0 1.0 CAL A:6Y0503 3.4 47.4 1.0 OE1 A:GLU162 3.5 48.2 1.0 CB A:ALA126 3.8 57.3 1.0 CG A:GLU162 3.8 47.5 1.0 CAE A:6Y0503 3.9 55.6 1.0 ND1 A:HIS269 4.0 54.4 1.0 CG A:GLU213 4.2 46.0 1.0 CG A:GLU266 4.5 58.0 1.0 CAN A:6Y0503 4.6 50.6 1.0 OE2 A:GLU123 4.6 55.9 1.0 CA A:ALA126 4.7 56.5 1.0 OAD A:6Y0503 4.8 43.9 1.0 CE1 A:HIS269 4.8 53.0 1.0 CB A:ALA216 4.8 43.8 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B


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 Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:44.6 occ:1.00 OE1 B:GLU123 1.8 57.4 1.0 OE1 B:GLU266 2.0 60.8 1.0 OAC B:6Y0503 2.0 46.6 1.0 OE1 B:GLU162 2.3 47.1 1.0 CD B:GLU123 2.6 53.7 1.0 OE2 B:GLU123 2.7 48.6 1.0 CD B:GLU266 2.8 58.2 1.0 OAD B:6Y0503 3.1 52.0 1.0 CD B:GLU162 3.1 51.3 1.0 CAL B:6Y0503 3.2 59.7 1.0 OE2 B:GLU266 3.2 53.6 1.0 OE2 B:GLU162 3.2 54.5 1.0 FE B:FE502 3.2 48.0 1.0 ND1 B:HIS165 3.3 39.5 1.0 CAN B:6Y0503 3.6 60.6 1.0 OH B:TYR220 4.0 57.9 1.0 CG B:GLU123 4.0 50.9 1.0 CG B:GLU266 4.0 54.4 1.0 CE1 B:HIS165 4.0 43.9 1.0 CB B:ALA126 4.2 49.5 1.0 CG B:HIS165 4.2 40.9 1.0 CAE B:6Y0503 4.4 70.7 1.0 CB B:HIS165 4.5 42.9 1.0 CG B:GLU162 4.6 47.0 1.0 CE2 B:TYR220 4.6 67.9 1.0 CZ B:TYR220 4.7 65.6 1.0 CB B:GLU123 4.8 48.9 1.0 CA B:GLU123 5.0 50.8 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B


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 Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:48.0 occ:1.00 OE2 B:GLU266 2.2 53.6 1.0 OE1 B:GLU213 2.3 34.1 1.0 OE2 B:GLU162 2.5 54.5 1.0 OAC B:6Y0503 2.6 46.6 1.0 OE2 B:GLU213 2.6 37.7 1.0 CD B:GLU213 2.8 38.6 1.0 CD B:GLU162 3.1 51.3 1.0 CD B:GLU266 3.2 58.2 1.0 FE B:FE501 3.2 44.6 1.0 CAL B:6Y0503 3.4 59.7 1.0 OE1 B:GLU266 3.5 60.8 1.0 OE1 B:GLU162 3.5 47.1 1.0 CAE B:6Y0503 3.6 70.7 1.0 CB B:ALA126 3.8 49.5 1.0 CG B:GLU162 4.1 47.0 1.0 CG B:GLU213 4.2 41.0 1.0 CG B:GLU266 4.5 54.4 1.0 ND1 B:HIS269 4.5 48.9 1.0 CAN B:6Y0503 4.7 60.6 1.0 CB B:ALA216 4.8 52.0 1.0 CB B:GLU266 4.9 54.1 1.0 CA B:ALA126 4.9 48.9 1.0 OE2 B:GLU123 5.0 48.6 1.0 OE1 B:GLU123 5.0 57.4 1.0 CAF B:6Y0503 5.0 73.2 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B


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 Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:61.5 occ:1.00 OE1 C:GLU266 1.9 46.5 1.0 OAC C:6Y0503 2.0 65.9 1.0 OE2 C:GLU123 2.2 59.1 1.0 OE1 C:GLU123 2.6 55.8 1.0 CD C:GLU266 2.7 52.4 1.0 OAD C:6Y0503 2.7 85.7 1.0 CD C:GLU123 2.8 61.5 1.0 FE C:FE502 3.0 56.0 1.0 OE2 C:GLU266 3.0 48.8 1.0 CAL C:6Y0503 3.1 85.0 1.0 CAN C:6Y0503 3.3 88.7 1.0 OE1 C:GLU162 3.3 71.2 1.0 OE2 C:GLU162 3.6 56.6 1.0 CD C:GLU162 3.6 64.1 1.0 ND1 C:HIS165 3.8 52.0 1.0 CG C:GLU266 4.0 53.4 1.0 CB C:ALA126 4.1 74.0 1.0 CG C:GLU123 4.3 67.0 1.0 CE1 C:HIS165 4.3 54.8 1.0 CAE C:6Y0503 4.4 94.7 1.0 OH C:TYR220 4.5 83.8 1.0 CG C:GLU162 4.6 63.0 1.0 CE2 C:TYR220 4.7 82.7 1.0 CB C:GLU162 4.7 60.1 1.0 CAQ C:6Y0503 4.7 97.5 1.0 OE1 C:GLU213 4.8 45.7 1.0 CG C:HIS165 4.9 52.2 1.0 CA C:GLU123 5.0 80.8 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B


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 Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:56.0 occ:1.00 OE2 C:GLU266 2.0 48.8 1.0 OE2 C:GLU162 2.0 56.6 1.0 OAC C:6Y0503 2.4 65.9 1.0 OE1 C:GLU213 2.5 45.7 1.0 OE2 C:GLU213 2.6 52.1 1.0 CD C:GLU213 2.9 50.1 1.0 FE C:FE501 3.0 61.5 1.0 CD C:GLU266 3.0 52.4 1.0 CD C:GLU162 3.1 64.1 1.0 OE1 C:GLU266 3.4 46.5 1.0 CAL C:6Y0503 3.6 85.0 1.0 OE1 C:GLU162 3.6 71.2 1.0 CB C:ALA126 3.7 74.0 1.0 CAE C:6Y0503 4.1 94.7 1.0 CG C:GLU162 4.3 63.0 1.0 CG C:GLU266 4.3 53.4 1.0 CG C:GLU213 4.4 55.2 1.0 ND1 C:HIS269 4.4 48.2 1.0 OE2 C:GLU123 4.6 59.1 1.0 CAN C:6Y0503 4.7 88.7 1.0 CB C:GLU266 4.7 47.3 1.0 CA C:GLU266 4.9 46.2 1.0 OAD C:6Y0503 4.9 85.7 1.0 CB C:ALA216 4.9 62.1 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B


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 Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:66.5 occ:1.00 OE1 D:GLU266 1.9 60.0 1.0 OAC D:6Y0503 2.0 62.7 1.0 OE1 D:GLU162 2.1 70.4 1.0 OAD D:6Y0503 2.2 95.2 1.0 OE2 D:GLU123 2.3 55.6 1.0 OE1 D:GLU123 2.5 43.4 1.0 CD D:GLU123 2.7 54.3 1.0 CAL D:6Y0503 2.8 84.3 1.0 CAN D:6Y0503 2.9 92.5 1.0 CD D:GLU266 2.9 57.6 1.0 FE D:FE502 3.1 56.1 1.0 CD D:GLU162 3.2 65.6 1.0 OE2 D:GLU266 3.3 52.1 1.0 ND1 D:HIS165 3.4 49.6 1.0 OE2 D:GLU162 3.8 54.6 1.0 CB D:ALA126 3.9 73.5 1.0 CE1 D:HIS165 3.9 51.1 1.0 OH D:TYR220 4.1 82.3 1.0 CAE D:6Y0503 4.2 98.8 1.0 CG D:GLU123 4.2 61.9 1.0 CAQ D:6Y0503 4.2 0.0 1.0 CG D:GLU266 4.3 56.6 1.0 CG D:GLU162 4.4 64.5 1.0 CE2 D:TYR220 4.5 81.2 1.0 CG D:HIS165 4.6 52.3 1.0 CB D:GLU162 4.6 61.6 1.0 CZ D:TYR220 4.8 84.2 1.0 OAK D:6Y0503 4.8 99.2 1.0 CA D:GLU123 4.8 70.8 1.0 CB D:GLU123 4.9 67.2 1.0 CA D:GLU162 4.9 62.6 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B


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 Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe502 b:56.1 occ:1.00 OAC D:6Y0503 2.0 62.7 1.0 OE2 D:GLU266 2.0 52.1 1.0 OE2 D:GLU162 2.3 54.6 1.0 OE1 D:GLU213 2.3 41.9 1.0 OE2 D:GLU213 2.4 55.4 1.0 CD D:GLU213 2.7 50.0 1.0 CD D:GLU266 2.9 57.6 1.0 CD D:GLU162 2.9 65.6 1.0 CAL D:6Y0503 3.0 84.3 1.0 OE1 D:GLU162 3.1 70.4 1.0 FE D:FE501 3.1 66.5 1.0 OE1 D:GLU266 3.1 60.0 1.0 CAE D:6Y0503 3.5 98.8 1.0 CB D:ALA126 4.0 73.5 1.0 CAN D:6Y0503 4.1 92.5 1.0 CG D:GLU213 4.2 56.0 1.0 CG D:GLU162 4.2 64.5 1.0 CG D:GLU266 4.3 56.6 1.0 ND1 D:HIS269 4.4 55.1 1.0 OAD D:6Y0503 4.4 95.2 1.0 CB D:ALA216 4.5 73.6 1.0 CB D:GLU266 4.7 52.5 1.0 CAF D:6Y0503 4.9 0.1 1.0 OE2 D:GLU123 5.0 55.6 1.0

E.O.Balogun, D.K.Inaoka, T.Shiba, T.Tsuge, B.May, T.Sato, Y.Kido, N.Takeshi, T.Aoki, T.Honma, A.Tanaka, M.Inoue, S.Matsuoka, P.A.M.Michels, Y.Watanabe, A.L.Moore, S.Harada, K.Kita. Discovery of Trypanocidal Coumarins with Dual-Inhibition For African Trypanosomes Glycerol Kinase and Alternative Oxidase To Be Published.