Iron in PDB 6zk8: Native Crystal Structure of Anaerobic F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution

The structure of Native Crystal Structure of Anaerobic F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution, PDB code: 6zk8 was solved by S.Engilberge, T.Wagner, P.Carpentier, E.Girard, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.89 / 1.83
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.871, 156.609, 76.065, 90.00, 137.62, 90.00
R / Rfree (%)	17.8 / 20.4

The binding sites of Iron atom in the Native Crystal Structure of Anaerobic F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution (pdb code 6zk8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Native Crystal Structure of Anaerobic F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution, PDB code: 6zk8:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Native Crystal Structure of Anaerobic F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Native Crystal Structure of Anaerobic F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe607 b:25.8 occ:1.00 O A:HOH817 1.9 30.0 0.4 NE2 A:HIS89 2.0 26.3 1.0 OD1 A:ASP171 2.0 27.1 1.0 NE2 A:HIS234 2.2 23.7 1.0 OD2 A:ASP88 2.3 26.8 1.0 CE1 A:HIS89 3.0 26.3 1.0 CG A:ASP171 3.0 28.1 1.0 CD2 A:HIS89 3.0 26.4 1.0 CD2 A:HIS234 3.2 24.0 1.0 OD2 A:ASP171 3.2 29.6 1.0 CE1 A:HIS234 3.3 23.4 1.0 CG A:ASP88 3.3 25.6 1.0 FE A:FE614 3.3 33.8 0.9 OD1 A:ASP88 3.5 27.1 1.0 ND1 A:HIS89 4.1 26.9 1.0 CG A:HIS89 4.1 26.7 1.0 OG A:SER233 4.3 29.3 1.0 CG A:HIS234 4.3 23.6 1.0 ND1 A:HIS234 4.3 23.5 1.0 CB A:ASP171 4.4 28.0 1.0 CB A:ASP88 4.6 24.8 1.0 CD2 A:HIS84 4.8 31.6 1.0 OE2 A:GLU86 4.8 29.4 1.0 CE1 A:HIS26 5.0 31.0 1.0 NE2 A:HIS84 5.0 31.1 1.0

Iron binding site 2 out of 4 in the Native Crystal Structure of Anaerobic F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Native Crystal Structure of Anaerobic F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe614 b:33.8 occ:0.90 O A:HOH817 1.8 30.0 0.4 OD2 A:ASP171 2.1 29.6 1.0 NE2 A:HIS152 2.2 38.8 1.0 OE2 A:GLU86 2.3 29.4 1.0 NE2 A:HIS84 2.4 31.1 1.0 CE1 A:HIS152 3.1 38.1 1.0 CD2 A:HIS84 3.1 31.6 1.0 CG A:ASP171 3.1 28.1 1.0 CD A:GLU86 3.2 31.9 1.0 CD2 A:HIS152 3.2 38.9 1.0 FE A:FE607 3.3 25.8 1.0 OD1 A:ASP171 3.5 27.1 1.0 CE1 A:HIS84 3.5 31.4 1.0 CB A:GLU86 3.7 28.9 1.0 CG A:GLU86 3.9 31.5 1.0 OE1 A:GLU86 4.1 29.8 1.0 ND1 A:HIS152 4.2 37.8 1.0 CD2 A:HIS89 4.2 26.4 1.0 NE2 A:HIS89 4.3 26.3 1.0 OD1 A:ASP88 4.3 27.1 1.0 CG A:HIS84 4.3 31.5 1.0 CG A:HIS152 4.3 37.8 1.0 CB A:ASP171 4.4 28.0 1.0 ND1 A:HIS84 4.5 32.2 1.0 O A:HOH777 4.6 30.7 1.0 CE1 A:HIS26 4.7 31.0 1.0 OD2 A:ASP88 4.8 26.8 1.0 NE2 A:HIS26 4.8 31.4 1.0 OD1 A:ASN170 4.9 32.5 1.0 CG A:ASP88 5.0 25.6 1.0

Iron binding site 3 out of 4 in the Native Crystal Structure of Anaerobic F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Native Crystal Structure of Anaerobic F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ O:Fe509 b:25.8 occ:1.00 O O:HOH711 2.0 30.0 0.4 NE2 O:HIS89 2.0 24.5 1.0 NE2 O:HIS234 2.1 21.7 1.0 OD1 O:ASP171 2.1 25.4 1.0 OD2 O:ASP88 2.4 24.7 1.0 CD2 O:HIS234 3.0 21.6 1.0 CD2 O:HIS89 3.0 24.9 1.0 CE1 O:HIS89 3.0 24.9 1.0 CG O:ASP171 3.1 25.9 1.0 CE1 O:HIS234 3.2 21.9 1.0 OD2 O:ASP171 3.3 25.6 1.0 CG O:ASP88 3.3 25.1 1.0 FE O:FE510 3.3 38.7 1.0 OD1 O:ASP88 3.6 25.5 1.0 ND1 O:HIS89 4.1 26.1 1.0 CG O:HIS89 4.1 25.7 1.0 CG O:HIS234 4.2 22.0 1.0 OG O:SER233 4.2 27.3 1.0 ND1 O:HIS234 4.2 22.7 1.0 CB O:ASP171 4.5 25.7 1.0 CB O:ASP88 4.6 24.8 1.0 OE2 O:GLU86 4.9 31.1 1.0 CD2 O:HIS84 4.9 34.0 1.0

Iron binding site 4 out of 4 in the Native Crystal Structure of Anaerobic F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Native Crystal Structure of Anaerobic F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ O:Fe510 b:38.7 occ:1.00 O O:HOH711 1.8 30.0 0.4 OE2 O:GLU86 2.2 31.1 1.0 OD2 O:ASP171 2.2 25.6 1.0 NE2 O:HIS152 2.2 37.3 1.0 NE2 O:HIS84 2.5 33.1 1.0 CE1 O:HIS152 3.1 36.5 1.0 CD2 O:HIS84 3.1 34.0 1.0 CG O:ASP171 3.1 25.9 1.0 CD O:GLU86 3.1 36.9 1.0 CD2 O:HIS152 3.3 37.6 1.0 FE O:FE509 3.3 25.8 1.0 OD1 O:ASP171 3.5 25.4 1.0 CE1 O:HIS84 3.7 33.1 1.0 CB O:GLU86 3.7 30.2 1.0 CG O:GLU86 3.9 32.5 1.0 OE1 O:GLU86 4.0 34.2 1.0 OD1 O:ASP88 4.3 25.5 1.0 CD2 O:HIS89 4.3 24.9 1.0 ND1 O:HIS152 4.3 36.4 1.0 NE2 O:HIS89 4.3 24.5 1.0 CB O:ASP171 4.3 25.7 1.0 CG O:HIS84 4.4 34.0 1.0 CG O:HIS152 4.4 36.5 1.0 O O:HOH696 4.6 30.2 1.0 ND1 O:HIS84 4.7 34.2 1.0 OD2 O:ASP88 4.7 24.7 1.0 CE1 O:HIS26 4.8 34.5 1.0 OD1 O:ASN170 4.8 31.7 1.0 NE2 O:HIS26 4.9 34.9 1.0 CG O:ASP88 4.9 25.1 1.0

S.Engilberge, T.Wagner, P.Carpentier, E.Girard, S.Shima. Krypton-Derivatization Highlights O 2 -Channeling in A Four-Electron Reducing Oxidase. Chem.Commun.(Camb.) V. 56 10863 2020.
ISSN: ESSN 1364-548X
PubMed: 32940290
DOI: 10.1039/D0CC04557H