Iron in PDB 8dvx: Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A

The structure of Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A, PDB code: 8dvx was solved by B.F.P.Edwards, M.Huettemann, A.Vaishnav, J.Brunzelle, P.Morse, J.Wan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.38 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	34.662, 54.559, 61.782, 65.97, 87.4, 84.07
R / Rfree (%)	17.1 / 20.4

Pages:

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

Binding sites:

The binding sites of Iron atom in the Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A (pdb code 8dvx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 11 binding sites of Iron where determined in the Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A, PDB code: 8dvx:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 11 in the Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:13.4 occ:1.00 FE A:HEC201 0.0 13.4 1.0 NB A:HEC201 2.0 11.3 1.0 NE2 A:HIS18 2.0 10.3 1.0 NC A:HEC201 2.0 12.8 1.0 ND A:HEC201 2.0 12.4 1.0 NA A:HEC201 2.0 13.9 1.0 SD A:MET80 2.3 14.2 1.0 CE1 A:HIS18 2.9 13.0 1.0 C1B A:HEC201 3.0 11.8 1.0 C4A A:HEC201 3.0 11.0 1.0 C1D A:HEC201 3.0 12.8 1.0 C4B A:HEC201 3.0 13.5 1.0 C4C A:HEC201 3.1 12.9 1.0 CD2 A:HIS18 3.1 13.8 1.0 C4D A:HEC201 3.1 12.8 1.0 C1C A:HEC201 3.1 12.9 1.0 C1A A:HEC201 3.1 13.5 1.0 CE A:MET80 3.4 13.2 1.0 CHB A:HEC201 3.4 14.2 1.0 CG A:MET80 3.4 13.8 1.0 CHD A:HEC201 3.4 13.0 1.0 CHC A:HEC201 3.5 13.2 1.0 CHA A:HEC201 3.5 11.3 1.0 ND1 A:HIS18 4.1 14.5 1.0 CG A:HIS18 4.2 13.0 1.0 C2B A:HEC201 4.2 14.4 1.0 C3B A:HEC201 4.2 14.5 1.0 C3A A:HEC201 4.2 13.8 1.0 C2D A:HEC201 4.3 15.6 1.0 CB A:MET80 4.3 16.1 1.0 C2A A:HEC201 4.3 12.9 1.0 C3D A:HEC201 4.3 12.8 1.0 C2C A:HEC201 4.3 12.6 1.0 C3C A:HEC201 4.3 11.5 1.0 OH A:TYR67 4.8 26.4 1.0

Iron binding site 2 out of 11 in the Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:20.9 occ:0.85 FE2 A:FC6202 0.0 20.9 0.8 C21 A:FC6202 1.8 24.9 0.8 C26 A:FC6202 1.8 31.5 0.8 C22 A:FC6202 1.8 20.2 0.8 C23 A:FC6202 1.8 25.2 0.8 C11 A:FC6202 1.8 24.0 0.8 C24 A:FC6202 1.8 27.1 0.8 N21 A:FC6202 3.0 34.9 0.8 N25 A:FC6202 3.0 31.0 0.8 N24 A:FC6202 3.0 28.5 0.8 N11 A:FC6202 3.0 25.3 0.8 N22 A:FC6202 3.0 32.3 0.8 N23 A:FC6202 3.0 25.8 0.8 NZ A:LYS87 4.4 35.7 1.0 O A:HOH354 4.5 32.6 1.0 NZ D:LYS13 4.5 22.8 1.0 NZ A:LYS13 4.5 24.6 1.0 O A:HOH355 4.6 31.9 1.0 O D:HOH356 4.6 38.5 1.0 CE A:LYS87 4.7 28.5 1.0 NZ D:LYS87 4.8 36.1 1.0 O D:HOH317 4.8 36.8 1.0 O A:HOH321 4.8 31.6 1.0

Iron binding site 3 out of 11 in the Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:26.2 occ:0.77 FE2 A:FC6203 0.0 26.2 0.8 C22 A:FC6203 1.8 35.9 0.8 C11 A:FC6203 1.8 29.4 0.8 C21 A:FC6203 1.8 31.7 0.8 C26 A:FC6203 1.8 26.4 0.8 C24 A:FC6203 1.8 36.2 0.8 C23 A:FC6203 1.8 32.2 0.8 N25 A:FC6203 3.0 32.0 0.8 N22 A:FC6203 3.0 38.3 0.8 N11 A:FC6203 3.0 33.0 0.8 N21 A:FC6203 3.0 26.0 0.8 N24 A:FC6203 3.0 31.2 0.8 N23 A:FC6203 3.0 27.5 0.8 CD A:LYS22 4.5 32.0 1.0

Iron binding site 4 out of 11 in the Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:13.9 occ:1.00 FE B:HEC201 0.0 13.9 1.0 NB B:HEC201 2.0 10.9 1.0 ND B:HEC201 2.0 11.2 1.0 NE2 B:HIS18 2.0 12.2 1.0 NC B:HEC201 2.0 14.4 1.0 NA B:HEC201 2.1 13.9 1.0 SD B:MET80 2.3 14.3 1.0 CE1 B:HIS18 2.9 14.5 1.0 C4B B:HEC201 3.0 12.7 1.0 C4D B:HEC201 3.0 14.8 1.0 C1D B:HEC201 3.0 15.2 1.0 C1C B:HEC201 3.0 12.3 1.0 C1A B:HEC201 3.0 12.0 1.0 C4A B:HEC201 3.0 12.1 1.0 C1B B:HEC201 3.0 12.4 1.0 C4C B:HEC201 3.1 12.3 1.0 CD2 B:HIS18 3.1 15.1 1.0 CE B:MET80 3.4 16.8 1.0 CHA B:HEC201 3.4 12.2 1.0 CHC B:HEC201 3.4 14.9 1.0 CG B:MET80 3.4 13.2 1.0 CHB B:HEC201 3.5 14.3 1.0 CHD B:HEC201 3.5 14.1 1.0 ND1 B:HIS18 4.1 13.2 1.0 CG B:HIS18 4.2 13.1 1.0 C2D B:HEC201 4.2 14.6 1.0 CB B:MET80 4.2 13.2 1.0 C2B B:HEC201 4.2 14.1 1.0 C3B B:HEC201 4.2 14.3 1.0 C3D B:HEC201 4.2 13.2 1.0 C2C B:HEC201 4.2 12.3 1.0 C3A B:HEC201 4.3 11.2 1.0 C2A B:HEC201 4.3 12.0 1.0 C3C B:HEC201 4.3 12.0 1.0 OH B:TYR67 4.8 23.8 1.0

Iron binding site 5 out of 11 in the Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:20.4 occ:0.94 FE2 B:FC6202 0.0 20.4 0.9 C22 B:FC6202 1.8 23.1 0.9 C21 B:FC6202 1.8 24.8 0.9 C26 B:FC6202 1.8 23.3 0.9 C11 B:FC6202 1.8 19.4 0.9 C23 B:FC6202 1.8 24.9 0.9 C24 B:FC6202 1.8 23.7 0.9 N25 B:FC6202 3.0 17.0 0.9 N11 B:FC6202 3.0 24.0 0.9 N23 B:FC6202 3.0 19.8 0.9 N22 B:FC6202 3.0 21.9 0.9 N21 B:FC6202 3.0 20.8 0.9 N24 B:FC6202 3.0 25.4 0.9 N B:GLY89 4.4 21.4 1.0 CA B:GLY89 4.8 20.9 1.0 CB B:LYS87 4.9 17.8 1.0 N B:LYS88 5.0 19.7 1.0

Iron binding site 6 out of 11 in the Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe203 b:18.8 occ:0.82 FE2 B:FC6203 0.0 18.8 0.8 C21 B:FC6203 1.8 21.8 0.8 C22 B:FC6203 1.8 27.6 0.8 C23 B:FC6203 1.8 26.2 0.8 C26 B:FC6203 1.8 27.1 0.8 C11 B:FC6203 1.8 16.4 0.8 C24 B:FC6203 1.8 20.0 0.8 N25 B:FC6203 3.0 28.7 0.8 N22 B:FC6203 3.0 29.0 0.8 N11 B:FC6203 3.0 27.8 0.8 N21 B:FC6203 3.0 25.8 0.8 N23 B:FC6203 3.0 27.7 0.8 N24 B:FC6203 3.0 23.0 0.8 NZ C:LYS13 4.3 24.7 1.0 NZ B:LYS87 4.4 33.8 1.0 NZ C:LYS87 4.4 38.4 1.0 O B:HOH348 4.5 30.6 1.0 NZ B:LYS13 4.5 27.1 1.0 O B:HOH341 4.6 30.7 1.0 CE B:LYS87 4.8 32.3 1.0 NZ B:LYS86 4.8 47.5 1.0 O B:HOH373 4.9 36.8 1.0 CE C:LYS87 5.0 26.8 1.0

Iron binding site 7 out of 11 in the Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe204 b:25.4 occ:0.73 FE2 B:FC6204 0.0 25.4 0.7 C21 B:FC6204 1.8 24.9 0.7 C24 B:FC6204 1.8 24.9 0.7 C23 B:FC6204 1.8 29.4 0.7 C11 B:FC6204 1.8 31.5 0.7 C22 B:FC6204 1.8 29.5 0.7 C26 B:FC6204 1.8 34.0 0.7 N25 B:FC6204 3.0 29.2 0.7 N23 B:FC6204 3.0 29.2 0.7 N24 B:FC6204 3.0 28.8 0.7 N11 B:FC6204 3.0 34.6 0.7 N22 B:FC6204 3.0 28.2 0.7 N21 B:FC6204 3.0 31.3 0.7 CE B:LYS7 4.7 26.7 1.0 NZ B:LYS7 4.9 37.1 1.0

Iron binding site 8 out of 11 in the Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe205 b:25.9 occ:0.65 FE2 B:FC6205 0.0 25.9 0.7 C11 B:FC6205 1.8 31.3 0.7 C23 B:FC6205 1.8 34.6 0.7 C26 B:FC6205 1.8 29.0 0.7 C21 B:FC6205 1.8 30.5 0.7 C22 B:FC6205 1.8 28.8 0.7 C24 B:FC6205 1.8 28.2 0.7 N11 B:FC6205 3.0 30.5 0.7 N23 B:FC6205 3.0 33.9 0.7 N24 B:FC6205 3.0 31.8 0.7 N21 B:FC6205 3.0 30.8 0.7 N22 B:FC6205 3.0 37.7 0.7 N25 B:FC6205 3.0 26.7 0.7 NZ B:LYS100 4.3 33.6 1.0 CE B:LYS100 4.9 38.9 1.0 O B:HOH330 5.0 42.2 1.0

Iron binding site 9 out of 11 in the Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:14.0 occ:1.00 FE C:HEC201 0.0 14.0 1.0 NB C:HEC201 2.0 11.7 1.0 ND C:HEC201 2.0 11.4 1.0 NE2 C:HIS18 2.0 12.4 1.0 NC C:HEC201 2.1 13.0 1.0 NA C:HEC201 2.1 14.5 1.0 SD C:MET80 2.3 14.3 1.0 C4B C:HEC201 3.0 10.0 1.0 C4D C:HEC201 3.0 11.1 1.0 C1B C:HEC201 3.0 13.6 1.0 C1A C:HEC201 3.0 13.2 1.0 CE1 C:HIS18 3.0 14.2 1.0 C1D C:HEC201 3.0 15.0 1.0 CD2 C:HIS18 3.0 10.9 1.0 C4C C:HEC201 3.0 12.8 1.0 C4A C:HEC201 3.1 14.3 1.0 C1C C:HEC201 3.1 12.3 1.0 CE C:MET80 3.4 14.8 1.0 CHA C:HEC201 3.4 14.9 1.0 CG C:MET80 3.4 13.2 1.0 CHC C:HEC201 3.4 13.5 1.0 CHB C:HEC201 3.4 15.5 1.0 CHD C:HEC201 3.5 15.1 1.0 ND1 C:HIS18 4.1 17.3 1.0 CG C:HIS18 4.2 12.1 1.0 C2B C:HEC201 4.2 17.2 1.0 C3B C:HEC201 4.2 14.5 1.0 C2D C:HEC201 4.2 16.6 1.0 CB C:MET80 4.2 16.5 1.0 C3D C:HEC201 4.3 14.7 1.0 C2A C:HEC201 4.3 12.0 1.0 C3C C:HEC201 4.3 10.8 1.0 C3A C:HEC201 4.3 15.4 1.0 C2C C:HEC201 4.3 16.4 1.0 OH C:TYR67 4.7 20.0 1.0

Iron binding site 10 out of 11 in the Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of Acetylated Pig Somatic Cytochrome C (ALY39) at 1.5A within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:18.4 occ:0.97 FE2 C:FC6202 0.0 18.4 1.0 C23 C:FC6202 1.8 15.1 1.0 C21 C:FC6202 1.8 15.5 1.0 C24 C:FC6202 1.8 24.6 1.0 C26 C:FC6202 1.9 18.8 1.0 C22 C:FC6202 1.9 19.9 1.0 C11 C:FC6202 1.9 19.9 1.0 N23 C:FC6202 3.0 22.9 1.0 N24 C:FC6202 3.0 25.3 1.0 N25 C:FC6202 3.0 20.4 1.0 N21 C:FC6202 3.0 23.0 1.0 N11 C:FC6202 3.0 26.7 1.0 N22 C:FC6202 3.1 19.3 1.0 N C:GLY89 4.4 19.6 1.0 CA C:GLY89 4.8 18.4 1.0 CB C:LYS87 4.9 15.8 1.0 N C:LYS88 4.9 19.3 1.0

P.R.Morse, H.Kalpage, J.Wan, A.Vaishnav, D.D.Chowdhury, J.S.Brunzelle, B.F.P.Edwards, M.Huettemann. Lysine 39 Acetylation of Cytochrome C in Ischemic Skeletal Muscle Stimulates Respiration While Attenuating Cell Death Nat Commun 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-39820-8