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Iron in PDB 3w54: Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B

Protein crystallography data

The structure of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B, PDB code: 3w54 was solved by 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, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.89 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 228.017, 137.920, 63.058, 90.00, 106.08, 90.00
R / Rfree (%) 18.5 / 22.7

Other elements in 3w54:

The structure of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B 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 Colletochlorin B (pdb code 3w54). 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 Colletochlorin B, PDB code: 3w54:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3w54

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


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 Colletochlorin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:25.2
occ:1.00
O A:OH503 1.9 16.3 1.0
OE1 A:GLU162 2.0 25.3 1.0
OE1 A:GLU266 2.1 25.7 1.0
OE2 A:GLU123 2.2 24.8 1.0
OE1 A:GLU123 2.3 26.3 1.0
ND1 A:HIS165 2.4 24.9 1.0
CD A:GLU123 2.5 25.2 1.0
CD A:GLU266 3.0 25.7 1.0
CD A:GLU162 3.1 26.7 1.0
CE1 A:HIS165 3.1 25.2 1.0
FE A:FE502 3.2 29.9 1.0
OE2 A:GLU266 3.3 27.2 1.0
CG A:HIS165 3.6 25.7 1.0
OE2 A:GLU162 3.6 24.3 1.0
CG A:GLU123 4.0 24.6 1.0
CB A:HIS165 4.0 27.2 1.0
CB A:ALA126 4.1 29.1 1.0
CAD A:RNB504 4.2 30.7 1.0
CG A:GLU162 4.3 25.8 1.0
NE2 A:HIS165 4.3 26.0 1.0
CB A:GLU162 4.4 25.3 1.0
CG A:GLU266 4.4 23.9 1.0
CA A:GLU162 4.4 24.6 1.0
CD2 A:HIS165 4.5 24.8 1.0
OH A:TYR220 4.7 32.3 1.0
CB A:GLU123 4.9 25.7 1.0
OE1 A:GLU213 5.0 27.7 1.0
O A:HOH643 5.0 16.0 1.0

Iron binding site 2 out of 8 in 3w54

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


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 Colletochlorin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:29.9
occ:1.00
OE2 A:GLU162 2.0 24.3 1.0
OE2 A:GLU213 2.1 28.4 1.0
OE2 A:GLU266 2.2 27.2 1.0
OE1 A:GLU213 2.2 27.7 1.0
O A:OH503 2.3 16.3 1.0
CD A:GLU213 2.5 28.0 1.0
O A:HOH643 2.5 16.0 1.0
CD A:GLU162 2.8 26.7 1.0
OE1 A:GLU162 3.0 25.3 1.0
CD A:GLU266 3.2 25.7 1.0
FE A:FE501 3.2 25.2 1.0
OE1 A:GLU266 3.5 25.7 1.0
CG A:GLU213 3.9 26.2 1.0
CL A:RNB504 4.1 35.2 1.0
O A:HOH619 4.1 13.4 1.0
ND1 A:HIS269 4.1 32.3 1.0
CG A:GLU162 4.2 25.8 1.0
CB A:ALA126 4.3 29.1 1.0
CG A:GLU266 4.4 23.9 1.0
CAD A:RNB504 4.6 30.7 1.0
CB A:ALA216 4.7 29.2 1.0
CB A:GLU266 4.7 23.5 1.0
OE2 A:GLU123 4.8 24.8 1.0
CA A:GLU266 4.8 24.5 1.0
CB A:GLU213 4.9 27.0 1.0
CE1 A:HIS269 5.0 31.7 1.0
O A:ALA126 5.0 28.9 1.0

Iron binding site 3 out of 8 in 3w54

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


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 Colletochlorin B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:42.9
occ:1.00
OE1 B:GLU266 1.8 35.8 1.0
O B:OH503 2.1 24.1 1.0
OE2 B:GLU123 2.2 37.9 1.0
OE1 B:GLU123 2.2 38.8 1.0
ND1 B:HIS165 2.3 32.5 1.0
CD B:GLU123 2.5 40.1 1.0
CD B:GLU266 2.7 36.5 1.0
OE1 B:GLU162 2.9 44.1 1.0
OE2 B:GLU162 2.9 34.7 1.0
CE1 B:HIS165 3.1 33.4 1.0
CD B:GLU162 3.1 39.0 1.0
OE2 B:GLU266 3.2 34.3 1.0
CG B:HIS165 3.4 32.4 1.0
FE B:FE502 3.5 42.1 1.0
CB B:HIS165 3.8 33.4 1.0
CG B:GLU266 3.9 33.6 1.0
CG B:GLU123 4.0 39.5 1.0
NE2 B:HIS165 4.2 35.1 1.0
CG B:GLU162 4.3 38.9 1.0
CB B:ALA126 4.4 35.6 1.0
CB B:GLU162 4.4 38.7 1.0
CD2 B:HIS165 4.4 33.5 1.0
CA B:GLU162 4.4 39.3 1.0
CAD B:RNB504 4.4 56.1 1.0
OH B:TYR220 4.7 40.7 1.0
CB B:GLU123 4.8 40.0 1.0
CE2 B:TYR220 4.8 36.9 1.0
CG2 B:ILE262 4.9 30.6 1.0

Iron binding site 4 out of 8 in 3w54

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


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 Colletochlorin B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:42.1
occ:1.00
OE2 B:GLU266 2.0 34.3 1.0
OE2 B:GLU162 2.1 34.7 1.0
OE1 B:GLU213 2.2 40.2 1.0
OE2 B:GLU213 2.3 42.4 1.0
O B:OH503 2.3 24.1 1.0
CD B:GLU213 2.5 39.0 1.0
CD B:GLU266 2.9 36.5 1.0
OE1 B:GLU266 3.2 35.8 1.0
CD B:GLU162 3.2 39.0 1.0
FE B:FE501 3.5 42.9 1.0
OE1 B:GLU162 3.7 44.1 1.0
CL B:RNB504 3.8 70.8 1.0
CB B:ALA126 4.0 35.6 1.0
CG B:GLU213 4.0 38.4 1.0
CG B:GLU266 4.3 33.6 1.0
OE2 B:GLU123 4.4 37.9 1.0
CG B:GLU162 4.5 38.9 1.0
ND1 B:HIS269 4.5 35.4 1.0
CB B:ALA216 4.6 30.7 1.0
CAD B:RNB504 4.6 56.1 1.0
CB B:GLU266 4.7 33.8 1.0
CB B:GLU213 4.9 37.5 1.0
CA B:ALA126 4.9 37.3 1.0
CAT B:RNB504 5.0 63.5 1.0

Iron binding site 5 out of 8 in 3w54

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


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 Colletochlorin B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:44.7
occ:1.00
O C:OH503 1.7 19.9 1.0
OE1 C:GLU162 2.0 31.4 1.0
OE1 C:GLU123 2.2 40.5 1.0
OE2 C:GLU123 2.3 43.2 1.0
OE1 C:GLU266 2.3 40.4 1.0
ND1 C:HIS165 2.6 33.5 1.0
CD C:GLU123 2.6 43.9 1.0
CD C:GLU162 2.9 30.3 1.0
CD C:GLU266 3.1 42.2 1.0
OE2 C:GLU266 3.1 47.6 1.0
CE1 C:HIS165 3.1 33.8 1.0
OE2 C:GLU162 3.2 24.8 1.0
FE C:FE502 3.3 34.4 1.0
CG C:HIS165 3.8 32.4 1.0
CG C:GLU123 4.1 44.9 1.0
CB C:ALA126 4.2 39.6 1.0
CG C:GLU162 4.3 29.3 1.0
CAD C:RNB504 4.3 36.7 1.0
CB C:HIS165 4.4 34.1 1.0
NE2 C:HIS165 4.4 32.9 1.0
CG C:GLU266 4.5 38.9 1.0
OH C:TYR220 4.6 44.2 1.0
CB C:GLU162 4.7 29.8 1.0
CA C:GLU162 4.7 30.0 1.0
CD2 C:HIS165 4.7 33.4 1.0
CG2 C:ILE262 4.8 31.2 1.0
CE2 C:TYR220 4.9 44.1 1.0
CB C:GLU123 4.9 43.2 1.0

Iron binding site 6 out of 8 in 3w54

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


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 Colletochlorin B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:34.4
occ:1.00
OE2 C:GLU162 2.1 24.8 1.0
OE1 C:GLU213 2.1 34.7 1.0
OE2 C:GLU266 2.2 47.6 1.0
O C:OH503 2.2 19.9 1.0
OE2 C:GLU213 2.4 36.6 1.0
CD C:GLU213 2.6 34.9 1.0
CD C:GLU162 3.1 30.3 1.0
FE C:FE501 3.3 44.7 1.0
CD C:GLU266 3.3 42.2 1.0
OE1 C:GLU162 3.6 31.4 1.0
OE1 C:GLU266 3.8 40.4 1.0
ND1 C:HIS269 3.9 24.9 1.0
CL C:RNB504 4.0 56.3 1.0
CG C:GLU213 4.1 35.2 1.0
O C:HOH617 4.2 29.6 1.0
CB C:ALA126 4.2 39.6 1.0
CG C:GLU162 4.4 29.3 1.0
CG C:GLU266 4.4 38.9 1.0
CB C:ALA216 4.6 36.1 1.0
CB C:GLU266 4.6 37.8 1.0
CA C:GLU266 4.7 36.4 1.0
CE1 C:HIS269 4.8 25.2 1.0
CG C:HIS269 4.8 27.2 1.0
CB C:HIS269 4.9 28.6 1.0
CB C:GLU213 4.9 32.7 1.0

Iron binding site 7 out of 8 in 3w54

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


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 Colletochlorin B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:31.2
occ:1.00
OE1 D:GLU266 1.9 29.9 1.0
OE1 D:GLU162 2.0 31.3 1.0
OE2 D:GLU123 2.1 34.4 1.0
OE1 D:GLU123 2.1 35.8 1.0
O D:OH503 2.2 14.9 1.0
ND1 D:HIS165 2.4 23.3 1.0
CD D:GLU123 2.4 30.7 1.0
CD D:GLU162 2.9 31.4 1.0
CD D:GLU266 2.9 27.1 1.0
OE2 D:GLU162 3.1 35.0 1.0
CE1 D:HIS165 3.2 24.5 1.0
OE2 D:GLU266 3.2 27.4 1.0
FE D:FE502 3.5 27.8 1.0
CG D:HIS165 3.6 23.5 1.0
CG D:GLU123 3.9 28.1 1.0
CB D:HIS165 4.0 24.5 1.0
CG D:GLU162 4.2 28.0 1.0
CG D:GLU266 4.2 26.5 1.0
CB D:ALA126 4.3 24.0 1.0
NE2 D:HIS165 4.4 25.5 1.0
CA D:GLU162 4.5 25.5 1.0
CB D:GLU162 4.6 27.1 1.0
CG2 D:ILE262 4.6 24.1 1.0
CD2 D:HIS165 4.6 23.9 1.0
CAD D:RNB504 4.6 27.8 1.0
OH D:TYR220 4.7 31.6 1.0
CB D:GLU123 4.8 28.2 1.0
CE2 D:TYR220 4.9 31.3 1.0
O D:GLU162 5.0 26.5 1.0

Iron binding site 8 out of 8 in 3w54

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


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 Colletochlorin B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe502

b:27.8
occ:1.00
OE2 D:GLU162 1.9 35.0 1.0
O D:OH503 1.9 14.9 1.0
OE2 D:GLU213 2.1 25.8 1.0
OE2 D:GLU266 2.3 27.4 1.0
OE1 D:GLU213 2.3 26.8 1.0
CD D:GLU213 2.5 27.5 1.0
CD D:GLU162 3.0 31.4 1.0
CD D:GLU266 3.1 27.1 1.0
OE1 D:GLU266 3.5 29.9 1.0
FE D:FE501 3.5 31.2 1.0
OE1 D:GLU162 3.6 31.3 1.0
CL D:RNB504 4.0 47.9 1.0
CB D:ALA126 4.0 24.0 1.0
CG D:GLU213 4.0 27.6 1.0
ND1 D:HIS269 4.2 27.4 1.0
CG D:GLU162 4.2 28.0 1.0
CG D:GLU266 4.3 26.5 1.0
CB D:ALA216 4.6 26.5 1.0
CB D:GLU266 4.7 25.7 1.0
OE2 D:GLU123 4.7 34.4 1.0
CA D:GLU266 4.9 26.1 1.0
CE1 D:HIS269 5.0 24.6 1.0
CB D:GLU213 5.0 29.1 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 Dec 13 15:25:32 2020

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