Iron in PDB 7c90: Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl)

The structure of Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl), PDB code: 7c90 was solved by S.Ghosh, I.Dhanasingh, S.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.58 / 2.13
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.760, 76.060, 66.440, 90.00, 106.85, 90.00
R / Rfree (%)	14.8 / 20

The structure of Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl) also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Sodium	(Na)	8 atoms

The binding sites of Iron atom in the Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl) (pdb code 7c90). 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 Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl), PDB code: 7c90:
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 Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl)


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 Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:21.4 occ:1.00 FE A:HEC201 0.0 21.4 1.0 NE2 A:HIS92 1.9 23.5 1.0 NC A:HEC201 2.0 21.9 1.0 NB A:HEC201 2.0 19.6 1.0 NA A:HEC201 2.0 20.5 1.0 ND A:HEC201 2.1 22.2 1.0 SD A:MET132 2.2 21.7 1.0 CE1 A:HIS92 2.9 24.1 1.0 C1B A:HEC201 3.0 19.7 1.0 C4A A:HEC201 3.0 20.9 1.0 CD2 A:HIS92 3.0 24.7 1.0 C1C A:HEC201 3.0 22.3 1.0 C4C A:HEC201 3.0 20.3 1.0 C1D A:HEC201 3.0 21.6 1.0 C4B A:HEC201 3.1 21.9 1.0 C1A A:HEC201 3.1 20.7 1.0 C4D A:HEC201 3.1 23.6 1.0 CE A:MET132 3.3 22.0 1.0 CG A:MET132 3.3 24.1 1.0 CHB A:HEC201 3.4 19.0 1.0 CHD A:HEC201 3.4 22.3 1.0 CHC A:HEC201 3.4 20.5 1.0 CHA A:HEC201 3.4 21.5 1.0 ND1 A:HIS92 4.1 21.1 1.0 CB A:MET132 4.1 25.6 1.0 CG A:HIS92 4.1 24.2 1.0 C3C A:HEC201 4.3 23.0 1.0 C2B A:HEC201 4.3 20.5 1.0 C3B A:HEC201 4.3 20.5 1.0 C2D A:HEC201 4.3 22.0 1.0 C3A A:HEC201 4.4 21.7 1.0 C2C A:HEC201 4.4 21.7 1.0 C2A A:HEC201 4.4 21.1 1.0 C3D A:HEC201 4.4 21.9 1.0 CA A:MET132 4.7 25.8 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl)


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 Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe206 b:80.4 occ:1.00 O A:HOH361 3.2 51.0 1.0 ND1 A:HIS94 3.3 39.0 1.0 OE2 A:GLU97 3.7 48.9 1.0 N A:HIS94 3.8 35.3 1.0 CB A:HIS94 4.1 37.2 1.0 CG A:HIS94 4.2 39.9 1.0 CE1 A:HIS94 4.3 43.5 1.0 CA A:GLY93 4.4 33.6 1.0 O A:HOH407 4.5 59.9 1.0 CA A:HIS94 4.6 38.8 1.0 C A:GLY93 4.6 35.7 1.0 O A:HOH346 4.8 57.7 1.0 CD A:GLU97 4.8 44.3 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl)


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 Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:21.5 occ:1.00 FE B:HEC201 0.0 21.5 1.0 NE2 B:HIS92 1.9 20.4 1.0 NA B:HEC201 2.0 21.7 1.0 NC B:HEC201 2.0 21.8 1.0 NB B:HEC201 2.1 21.7 1.0 ND B:HEC201 2.1 22.4 1.0 SD B:MET132 2.3 21.6 1.0 CE1 B:HIS92 2.9 21.2 1.0 CD2 B:HIS92 3.0 19.1 1.0 C4A B:HEC201 3.0 22.5 1.0 C1B B:HEC201 3.0 21.5 1.0 C4C B:HEC201 3.0 22.6 1.0 C1C B:HEC201 3.0 23.6 1.0 C1A B:HEC201 3.1 21.5 1.0 C4B B:HEC201 3.1 21.5 1.0 C1D B:HEC201 3.1 21.7 1.0 C4D B:HEC201 3.1 21.2 1.0 CHB B:HEC201 3.4 20.0 1.0 CE B:MET132 3.4 23.6 1.0 CHD B:HEC201 3.4 20.8 1.0 CHC B:HEC201 3.4 21.0 1.0 CHA B:HEC201 3.5 19.9 1.0 CG B:MET132 3.5 26.1 1.0 ND1 B:HIS92 4.0 19.6 1.0 CG B:HIS92 4.1 19.1 1.0 CB B:MET132 4.1 26.6 1.0 C3B B:HEC201 4.3 20.9 1.0 C3A B:HEC201 4.3 20.6 1.0 C3C B:HEC201 4.3 22.4 1.0 C2A B:HEC201 4.3 23.0 1.0 C2B B:HEC201 4.4 22.0 1.0 C2C B:HEC201 4.4 24.3 1.0 C3D B:HEC201 4.4 20.0 1.0 C2D B:HEC201 4.4 19.3 1.0 CA B:MET132 4.7 26.6 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl)


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 Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe206 b:90.6 occ:1.00 O B:HOH350 3.0 49.2 1.0 O B:HOH305 3.2 49.2 1.0 ND1 B:HIS94 3.2 41.3 1.0 N B:HIS94 3.9 26.5 1.0 CE B:LYS99 3.9 57.9 1.0 CE1 B:HIS94 4.0 45.5 1.0 OE2 B:GLU97 4.1 40.4 1.0 CG B:HIS94 4.2 34.7 1.0 NZ B:LYS99 4.3 61.9 1.0 CA B:GLY93 4.3 27.6 1.0 CB B:HIS94 4.4 31.4 1.0 C B:GLY93 4.6 27.3 1.0 CA B:HIS94 4.8 26.7 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl)


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 Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:22.8 occ:1.00 FE C:HEC201 0.0 22.8 1.0 NE2 C:HIS92 2.0 22.7 1.0 NB C:HEC201 2.0 21.5 1.0 NC C:HEC201 2.0 21.5 1.0 ND C:HEC201 2.1 24.1 1.0 NA C:HEC201 2.1 22.9 1.0 SD C:MET132 2.3 23.9 1.0 CE1 C:HIS92 3.0 24.7 1.0 CD2 C:HIS92 3.0 23.4 1.0 C1C C:HEC201 3.0 22.4 1.0 C4B C:HEC201 3.0 23.5 1.0 C4A C:HEC201 3.0 23.0 1.0 C4C C:HEC201 3.1 23.3 1.0 C1D C:HEC201 3.1 23.6 1.0 C1B C:HEC201 3.1 21.9 1.0 C1A C:HEC201 3.1 23.9 1.0 C4D C:HEC201 3.1 25.6 1.0 CE C:MET132 3.3 25.2 1.0 CHC C:HEC201 3.4 22.4 1.0 CHD C:HEC201 3.4 22.1 1.0 CHB C:HEC201 3.4 21.1 1.0 CHA C:HEC201 3.4 24.2 1.0 CG C:MET132 3.5 32.1 1.0 ND1 C:HIS92 4.1 23.2 1.0 CG C:HIS92 4.1 26.0 1.0 CB C:MET132 4.2 30.7 1.0 C3B C:HEC201 4.3 22.5 1.0 C3C C:HEC201 4.3 22.6 1.0 C2C C:HEC201 4.4 23.8 1.0 C2D C:HEC201 4.4 25.1 1.0 C3A C:HEC201 4.4 26.3 1.0 C2B C:HEC201 4.4 23.3 1.0 C2A C:HEC201 4.4 24.6 1.0 C3D C:HEC201 4.4 25.4 1.0 CA C:MET132 4.6 30.5 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl)


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 Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe204 b:82.4 occ:1.00 O C:HOH373 3.2 51.7 1.0 OE2 C:GLU97 3.4 44.0 1.0 ND1 C:HIS94 3.4 42.2 1.0 N C:HIS94 3.7 36.2 1.0 CB C:HIS94 4.0 39.3 1.0 CG C:HIS94 4.2 39.3 1.0 O C:HOH368 4.2 62.0 1.0 CE1 C:HIS94 4.5 41.6 1.0 CA C:HIS94 4.5 36.5 1.0 O C:HOH341 4.5 49.4 1.0 CA C:GLY93 4.5 33.0 1.0 CD C:GLU97 4.5 38.0 1.0 C C:GLY93 4.6 35.1 1.0 CD2 C:HIS95 4.9 44.9 1.0 OE1 C:GLU97 4.9 36.0 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl)


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 Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:22.9 occ:1.00 FE D:HEC201 0.0 22.9 1.0 NE2 D:HIS92 1.9 22.4 1.0 NB D:HEC201 2.0 21.4 1.0 NC D:HEC201 2.1 20.7 1.0 NA D:HEC201 2.1 23.8 1.0 ND D:HEC201 2.1 22.1 1.0 SD D:MET132 2.4 23.0 1.0 CD2 D:HIS92 2.9 21.7 1.0 CE1 D:HIS92 2.9 24.8 1.0 C4A D:HEC201 3.0 21.0 1.0 C1B D:HEC201 3.0 21.3 1.0 C1A D:HEC201 3.0 22.9 1.0 C4B D:HEC201 3.1 24.0 1.0 C1C D:HEC201 3.1 20.6 1.0 C4D D:HEC201 3.1 22.5 1.0 C4C D:HEC201 3.1 22.1 1.0 C1D D:HEC201 3.1 21.6 1.0 CE D:MET132 3.4 24.6 1.0 CHB D:HEC201 3.4 20.2 1.0 CHD D:HEC201 3.4 20.8 1.0 CHA D:HEC201 3.4 21.7 1.0 CHC D:HEC201 3.4 20.9 1.0 CG D:MET132 3.5 24.5 1.0 ND1 D:HIS92 4.0 23.2 1.0 CG D:HIS92 4.1 22.4 1.0 CB D:MET132 4.2 25.2 1.0 C3B D:HEC201 4.3 21.4 1.0 C3D D:HEC201 4.3 22.0 1.0 C3A D:HEC201 4.4 22.9 1.0 C2B D:HEC201 4.4 21.7 1.0 C2D D:HEC201 4.4 22.7 1.0 C3C D:HEC201 4.4 21.7 1.0 C2A D:HEC201 4.4 23.5 1.0 C2C D:HEC201 4.4 21.0 1.0 CA D:MET132 4.7 26.4 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl)


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 Cytochrome Cl From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt (Ma-Cytcl) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe203 b:92.9 occ:1.00 OE2 D:GLU97 3.4 39.6 1.0 CD2 D:HIS94 3.5 48.8 1.0 N D:HIS94 3.7 30.6 1.0 CB D:HIS94 3.9 38.8 1.0 CG D:HIS94 4.0 44.5 1.0 CA D:HIS94 4.4 34.2 1.0 CA D:GLY93 4.4 27.3 1.0 CD D:GLU97 4.5 38.7 1.0 C D:GLY93 4.6 28.6 1.0 NE2 D:HIS94 4.7 50.2 1.0 OE1 D:GLU97 4.8 37.0 1.0

S.Ghosh, I.Dhanasingh, J.Ryu, S.W.Kim, S.H.Lee. Crystal Structure of Cytochromeclfrom the Aquatic Methylotrophic Bacteriummethylophaga Aminisulfidivoransmpt. J Microbiol Biotechnol. V. 30 1261 2020.
ISSN: ESSN 1738-8872
PubMed: 32627749
DOI: 10.4014/JMB.2006.06029