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Iron in PDB 3vva: Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative

Protein crystallography data

The structure of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative, PDB code: 3vva was solved by T.Shiba, Y.Kido, K.Sakamoto, D.K.Inaoka, C.Tsuge, R.Tatsumi, E.O.Balogun, T.Nara, T.Aoki, T.Honma, A.Tanaka, M.Inoue, S.Matsuoka, H.Saimoto, 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) 39.81 / 2.59
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 152.308, 219.682, 63.481, 90.00, 114.89, 90.00
R / Rfree (%) 21.4 / 25.6

Other elements in 3vva:

The structure of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative (pdb code 3vva). 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 Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative, PDB code: 3vva:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3vva

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Iron binding site 1 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


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 Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:31.6
occ:1.00
 O A:OH503 1.8 16.7 1.0
OE1 A:GLU162 2.0 23.5 1.0
OE1 A:GLU266 2.1 25.5 1.0
OE1 A:GLU123 2.1 25.1 1.0
ND1 A:HIS165 2.2 28.4 1.0
OE2 A:GLU123 2.5 25.8 1.0
CD A:GLU123 2.6 25.9 1.0
CD A:GLU162 2.9 25.7 1.0
CD A:GLU266 3.0 24.0 1.0
CE1 A:HIS165 3.1 29.3 1.0
OE2 A:GLU162 3.2 26.0 1.0
CG A:HIS165 3.3 28.8 1.0
OE2 A:GLU266 3.3 21.6 1.0
CB A:HIS165 3.7 28.4 1.0
FE A:FE502 3.8 32.3 1.0
CG A:GLU123 4.1 26.6 1.0
CG A:GLU162 4.2 25.5 1.0
NE2 A:HIS165 4.2 29.6 1.0
CD2 A:HIS165 4.4 27.3 1.0
CG A:GLU266 4.4 23.2 1.0
CB A:GLU162 4.5 26.7 1.0
CA A:GLU162 4.6 27.8 1.0
CAX A:CHW504 4.6 34.0 1.0
CB A:ALA126 4.6 33.3 1.0
CG2 A:ILE262 4.7 32.2 1.0
OH A:TYR220 4.9 34.5 1.0

Iron binding site 2 out of 8 in 3vva

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Iron binding site 2 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


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 Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:32.3
occ:1.00
 OE2 A:GLU162 2.1 26.0 1.0
OE2 A:GLU266 2.2 21.6 1.0
OE1 A:GLU213 2.4 25.9 1.0
O A:OH503 2.4 16.7 1.0
OE2 A:GLU213 2.5 26.5 1.0
CD A:GLU213 2.7 26.1 1.0
CD A:GLU162 3.2 25.7 1.0
CD A:GLU266 3.3 24.0 1.0
OE1 A:GLU162 3.7 23.5 1.0
FE A:FE501 3.8 31.6 1.0
CB A:ALA126 3.8 33.3 1.0
OE1 A:GLU266 3.8 25.5 1.0
O A:HOH614 3.9 28.8 1.0
CG A:GLU213 4.1 27.0 1.0
CLAW A:CHW504 4.2 49.9 1.0
ND1 A:HIS269 4.4 36.3 1.0
CG A:GLU162 4.4 25.5 1.0
CG A:GLU266 4.6 23.2 1.0
CB A:ALA216 4.6 32.9 1.0
OE2 A:GLU123 4.6 25.8 1.0
CAX A:CHW504 4.6 34.0 1.0
CB A:GLU266 4.8 24.9 1.0
CA A:ALA126 4.9 33.9 1.0

Iron binding site 3 out of 8 in 3vva

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Iron binding site 3 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


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 Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:30.4
occ:1.00
 OE1 B:GLU266 1.9 30.7 1.0
OE1 B:GLU162 2.0 26.1 1.0
O B:OH503 2.1 17.6 1.0
OE2 B:GLU123 2.1 34.0 1.0
OE1 B:GLU123 2.4 37.3 1.0
ND1 B:HIS165 2.5 20.5 1.0
CD B:GLU123 2.6 35.2 1.0
CD B:GLU266 2.7 31.6 1.0
OE2 B:GLU266 2.9 29.6 1.0
FE B:FE502 3.1 32.1 1.0
CE1 B:HIS165 3.2 20.5 1.0
CD B:GLU162 3.2 27.1 1.0
CG B:HIS165 3.6 21.2 1.0
OE2 B:GLU162 3.8 26.8 1.0
CG B:GLU123 4.1 33.4 1.0
CB B:HIS165 4.1 23.1 1.0
CG B:GLU266 4.1 31.1 1.0
CG B:GLU162 4.2 25.6 1.0
CB B:GLU162 4.3 23.8 1.0
CB B:ALA126 4.3 27.1 1.0
NE2 B:HIS165 4.4 20.3 1.0
CA B:GLU162 4.4 24.8 1.0
CAX B:CHW504 4.6 34.6 1.0
CD2 B:HIS165 4.6 20.4 1.0
OH B:TYR220 4.7 26.3 1.0
CG2 B:ILE262 4.8 22.8 1.0
CB B:GLU123 4.9 32.9 1.0
O B:GLU162 4.9 26.0 1.0
CE2 B:TYR220 5.0 27.3 1.0

Iron binding site 4 out of 8 in 3vva

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Iron binding site 4 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


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 Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:32.1
occ:1.00
 OE2 B:GLU266 1.9 29.6 1.0
OE2 B:GLU213 2.2 27.6 1.0
OE2 B:GLU162 2.3 26.8 1.0
O B:OH503 2.3 17.6 1.0
OE1 B:GLU213 2.3 27.4 1.0
OE1 B:GLU162 2.5 26.1 1.0
CD B:GLU213 2.6 27.6 1.0
CD B:GLU162 2.7 27.1 1.0
CD B:GLU266 3.0 31.6 1.0
FE B:FE501 3.1 30.4 1.0
OE1 B:GLU266 3.5 30.7 1.0
CB B:ALA126 4.0 27.1 1.0
CG B:GLU213 4.1 28.4 1.0
CLAW B:CHW504 4.2 40.9 1.0
ND1 B:HIS269 4.2 25.4 1.0
CG B:GLU266 4.2 31.1 1.0
CG B:GLU162 4.3 25.6 1.0
CB B:GLU266 4.5 31.3 1.0
OE2 B:GLU123 4.7 34.0 1.0
CA B:GLU266 4.7 33.2 1.0
OE1 B:GLU123 4.7 37.3 1.0
CB B:ALA216 4.8 32.0 1.0
CAX B:CHW504 4.9 34.6 1.0
CB B:GLU213 5.0 29.7 1.0
CE1 B:HIS269 5.0 24.7 1.0

Iron binding site 5 out of 8 in 3vva

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Iron binding site 5 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


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 Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:46.0
occ:1.00
 O C:OH503 1.8 12.8 1.0
OE1 C:GLU162 2.0 35.6 1.0
OE1 C:GLU266 2.2 39.5 1.0
OE1 C:GLU123 2.3 36.8 1.0
ND1 C:HIS165 2.3 27.7 1.0
OE2 C:GLU123 2.4 36.9 1.0
CD C:GLU123 2.7 37.4 1.0
CD C:GLU162 3.0 36.2 1.0
CD C:GLU266 3.2 40.5 1.0
CE1 C:HIS165 3.2 27.7 1.0
CG C:HIS165 3.3 28.1 1.0
OE2 C:GLU162 3.4 34.0 1.0
OE2 C:GLU266 3.5 40.1 1.0
FE C:FE502 3.5 39.6 1.0
CB C:HIS165 3.7 30.7 1.0
CG C:GLU123 4.2 37.3 1.0
CG C:GLU162 4.2 34.8 1.0
CB C:GLU162 4.3 34.0 1.0
NE2 C:HIS165 4.3 27.9 1.0
CB C:ALA126 4.4 34.3 1.0
CD2 C:HIS165 4.4 27.4 1.0
CA C:GLU162 4.5 35.0 1.0
CG C:GLU266 4.5 38.0 1.0
CAX C:CHW504 4.6 54.6 1.0
OH C:TYR220 4.6 44.1 1.0
CG2 C:ILE262 4.8 28.6 1.0
O C:GLU162 4.9 39.2 1.0
CE2 C:TYR220 4.9 41.9 1.0
CB C:GLU123 5.0 38.0 1.0

Iron binding site 6 out of 8 in 3vva

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Iron binding site 6 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


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 Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:39.6
occ:1.00
 OE2 C:GLU162 2.0 34.0 1.0
OE1 C:GLU213 2.1 32.9 1.0
OE2 C:GLU266 2.2 40.1 1.0
OE2 C:GLU213 2.3 31.3 1.0
O C:OH503 2.4 12.8 1.0
CD C:GLU213 2.5 32.7 1.0
CD C:GLU162 3.0 36.2 1.0
CD C:GLU266 3.1 40.5 1.0
OE1 C:GLU162 3.4 35.6 1.0
FE C:FE501 3.5 46.0 1.0
OE1 C:GLU266 3.5 39.5 1.0
CLAW C:CHW504 3.9 64.5 1.0
CB C:ALA126 3.9 34.3 1.0
CG C:GLU213 4.0 32.4 1.0
ND1 C:HIS269 4.0 35.5 1.0
CG C:GLU162 4.2 34.8 1.0
CG C:GLU266 4.3 38.0 1.0
CAX C:CHW504 4.7 54.6 1.0
OE2 C:GLU123 4.7 36.9 1.0
CB C:ALA216 4.8 38.4 1.0
CB C:GLU266 4.8 36.3 1.0
CE1 C:HIS269 4.8 32.7 1.0
CA C:GLU266 4.9 35.1 1.0
CB C:GLU213 4.9 33.1 1.0

Iron binding site 7 out of 8 in 3vva

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Iron binding site 7 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


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 Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:43.2
occ:1.00
 OE1 D:GLU266 1.9 28.9 1.0
O D:OH503 2.1 13.6 1.0
OE1 D:GLU123 2.2 30.5 1.0
OE2 D:GLU123 2.3 29.9 1.0
ND1 D:HIS165 2.3 37.3 1.0
OE1 D:GLU162 2.4 24.6 1.0
CD D:GLU123 2.5 32.0 1.0
CD D:GLU266 2.9 28.6 1.0
CE1 D:HIS165 3.1 37.7 1.0
OE2 D:GLU266 3.3 25.8 1.0
CG D:HIS165 3.3 37.4 1.0
CD D:GLU162 3.5 26.7 1.0
FE D:FE502 3.7 35.8 1.0
CB D:HIS165 3.7 35.5 1.0
CG D:GLU123 4.0 32.7 1.0
CG D:GLU266 4.2 28.1 1.0
NE2 D:HIS165 4.3 38.5 1.0
CA D:GLU162 4.3 30.7 1.0
OE2 D:GLU162 4.3 26.2 1.0
CD2 D:HIS165 4.4 37.6 1.0
CG D:GLU162 4.4 27.6 1.0
CB D:GLU162 4.4 29.7 1.0
OH D:TYR220 4.6 35.0 1.0
CG2 D:ILE262 4.7 30.6 1.0
O D:GLU162 4.8 34.9 1.0
CB D:ALA126 4.9 39.5 1.0
CB D:GLU123 4.9 33.9 1.0
CAX D:CHW504 4.9 52.6 1.0
CE2 D:TYR220 4.9 36.8 1.0

Iron binding site 8 out of 8 in 3vva

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Iron binding site 8 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


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 Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe502

b:35.8
occ:1.00
 OE2 D:GLU266 2.1 25.8 1.0
OE2 D:GLU213 2.2 32.5 1.0
OE2 D:GLU162 2.4 26.2 1.0
O D:OH503 2.4 13.6 1.0
OE1 D:GLU213 2.6 32.2 1.0
OE1 D:GLU162 2.8 24.6 1.0
CD D:GLU213 2.8 32.5 1.0
CD D:GLU162 2.9 26.7 1.0
CD D:GLU266 3.2 28.6 1.0
OE1 D:GLU266 3.7 28.9 1.0
FE D:FE501 3.7 43.2 1.0
CLAW D:CHW504 4.0 61.1 1.0
CG D:GLU213 4.3 33.0 1.0
CB D:ALA126 4.3 39.5 1.0
CG D:GLU162 4.4 27.6 1.0
CG D:GLU266 4.5 28.1 1.0
ND1 D:HIS269 4.5 28.6 1.0
CB D:GLU266 4.7 30.1 1.0
CB D:ALA216 4.7 34.0 1.0
OE2 D:GLU123 4.8 29.9 1.0
CA D:GLU266 4.9 30.1 1.0

Reference:

T.Shiba, Y.Kido, K.Sakamoto, D.K.Inaoka, C.Tsuge, R.Tatsumi, G.Takahashi, E.O.Balogun, T.Nara, T.Aoki, T.Honma, A.Tanaka, M.Inoue, S.Matsuoka, H.Saimoto, A.L.Moore, S.Harada, K.Kita. Structure of the Trypanosome Cyanide-Insensitive Alternative Oxidase Proc.Natl.Acad.Sci.Usa V. 110 4580 2013.
ISSN: ISSN 0027-8424
PubMed: 23487766
DOI: 10.1073/PNAS.1218386110
Page generated: Sun Aug 4 22:26:58 2024

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