Iron in PDB 6zlf: Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton

The structure of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton, PDB code: 6zlf 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)	48.40 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.025, 162.553, 134.376, 90.00, 93.75, 90.00
R / Rfree (%)	18.2 / 19.7

The structure of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton also contains other interesting chemical elements:

Krypton	(Kr)	48 atoms
Chlorine	(Cl)	8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton (pdb code 6zlf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton, PDB code: 6zlf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:29.2 occ:0.80 FE1 A:FEO502 0.0 29.2 0.8 O A:FEO502 2.1 28.0 0.8 OD1 A:ASP171 2.1 30.8 1.0 NE2 A:HIS234 2.2 26.6 1.0 OD2 A:ASP88 2.2 35.2 1.0 NE2 A:HIS89 2.2 31.1 1.0 O A:HOH781 2.3 36.0 0.5 O A:HOH781 3.1 36.0 0.5 CG A:ASP171 3.1 34.5 1.0 CD2 A:HIS234 3.1 26.5 1.0 CD2 A:HIS89 3.1 30.2 1.0 CE1 A:HIS89 3.2 30.3 1.0 CE1 A:HIS234 3.2 26.1 1.0 CG A:ASP88 3.2 32.7 1.0 OD2 A:ASP171 3.3 36.3 1.0 FE2 A:FEO502 3.5 30.2 0.5 OD1 A:ASP88 3.6 34.4 1.0 OH A:TYR25 3.6 63.9 1.0 OG A:SER233 4.1 31.4 1.0 CG A:HIS89 4.3 32.6 1.0 CG A:HIS234 4.3 26.4 1.0 ND1 A:HIS89 4.3 31.9 1.0 ND1 A:HIS234 4.3 27.0 1.0 CB A:ASP171 4.4 29.8 1.0 CB A:ASP88 4.5 31.1 1.0 O A:HOH749 4.5 49.2 1.0 OE2 A:GLU86 4.8 39.1 1.0 CZ A:TYR25 4.8 69.1 1.0 CD2 A:HIS84 4.8 41.1 1.0

Iron binding site 2 out of 16 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:30.2 occ:0.50 FE2 A:FEO502 0.0 30.2 0.5 OD2 A:ASP171 2.1 36.3 1.0 OE2 A:GLU86 2.1 39.1 1.0 O A:FEO502 2.1 28.0 0.8 NE2 A:HIS152 2.1 55.9 1.0 NE2 A:HIS84 2.3 42.5 1.0 O A:HOH781 2.7 36.0 0.5 CD2 A:HIS84 3.1 41.1 1.0 CD2 A:HIS152 3.1 55.3 1.0 CD A:GLU86 3.1 51.9 1.0 CG A:ASP171 3.1 34.5 1.0 CE1 A:HIS152 3.2 56.7 1.0 CE1 A:HIS84 3.5 44.0 1.0 FE1 A:FEO502 3.5 29.2 0.8 OD1 A:ASP171 3.6 30.8 1.0 O A:HOH781 3.7 36.0 0.5 CB A:GLU86 3.8 34.2 1.0 OE1 A:GLU86 3.9 45.4 1.0 CG A:GLU86 4.0 41.5 1.0 CG A:HIS152 4.2 57.5 1.0 ND1 A:HIS152 4.3 57.2 1.0 CG A:HIS84 4.3 45.9 1.0 CB A:ASP171 4.3 29.8 1.0 OD1 A:ASP88 4.5 34.4 1.0 ND1 A:HIS84 4.5 42.1 1.0 O A:HOH657 4.6 45.3 1.0 CD2 A:HIS89 4.7 30.2 1.0 OD2 A:ASP88 4.7 35.2 1.0 NE2 A:HIS89 4.8 31.1 1.0 OD1 A:ASN170 4.9 35.0 1.0 NE1 A:TRP153 4.9 54.6 1.0 CE2 A:TRP153 5.0 54.9 1.0

Iron binding site 3 out of 16 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe509 b:29.0 occ:0.80 FE1 F:FEO509 0.0 29.0 0.8 O F:FEO509 2.1 28.8 0.8 OD2 F:ASP88 2.1 32.3 1.0 NE2 F:HIS234 2.2 27.8 1.0 NE2 F:HIS89 2.2 30.3 1.0 OD1 F:ASP171 2.2 32.2 1.0 O F:HOH792 2.6 30.0 1.0 CG F:ASP88 3.1 33.2 1.0 CD2 F:HIS89 3.1 30.1 1.0 CG F:ASP171 3.1 33.4 1.0 CD2 F:HIS234 3.2 26.1 1.0 CE1 F:HIS89 3.2 30.0 1.0 CE1 F:HIS234 3.2 29.0 1.0 OD2 F:ASP171 3.4 33.4 1.0 O F:HOH819 3.4 30.0 1.0 OD1 F:ASP88 3.5 32.1 1.0 FE2 F:FEO509 3.6 28.7 0.6 OG F:SER233 4.1 27.9 1.0 CG F:HIS89 4.3 30.1 1.0 ND1 F:HIS89 4.3 31.2 1.0 CG F:HIS234 4.3 26.9 1.0 ND1 F:HIS234 4.3 27.7 1.0 CB F:ASP88 4.4 26.3 1.0 CB F:ASP171 4.5 27.8 1.0 O F:HOH726 4.7 30.0 1.0 OH F:TYR25 4.8 72.1 1.0 OE2 F:GLU86 4.8 40.4 1.0 CD2 F:HIS84 4.9 36.6 1.0

Iron binding site 4 out of 16 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe509 b:28.7 occ:0.60 FE2 F:FEO509 0.0 28.7 0.6 OD2 F:ASP171 2.1 33.4 1.0 OE2 F:GLU86 2.1 40.4 1.0 O F:FEO509 2.1 28.8 0.8 NE2 F:HIS152 2.1 45.6 1.0 NE2 F:HIS84 2.3 39.0 1.0 O F:HOH819 2.9 30.0 1.0 CD2 F:HIS84 3.1 36.6 1.0 CD F:GLU86 3.1 45.6 1.0 CD2 F:HIS152 3.1 45.6 1.0 CG F:ASP171 3.2 33.4 1.0 CE1 F:HIS152 3.2 45.5 1.0 CE1 F:HIS84 3.5 41.2 1.0 FE1 F:FEO509 3.6 29.0 0.8 OD1 F:ASP171 3.6 32.2 1.0 CB F:GLU86 3.8 32.8 1.0 OE1 F:GLU86 3.9 42.0 1.0 CG F:GLU86 4.0 37.1 1.0 O F:HOH792 4.1 30.0 1.0 CG F:HIS152 4.2 47.5 1.0 ND1 F:HIS152 4.3 51.4 1.0 CG F:HIS84 4.3 37.0 1.0 CB F:ASP171 4.4 27.8 1.0 OD1 F:ASP88 4.4 32.1 1.0 ND1 F:HIS84 4.5 37.7 1.0 CD2 F:HIS89 4.6 30.1 1.0 OD2 F:ASP88 4.7 32.3 1.0 O F:HOH661 4.7 36.6 1.0 NE2 F:HIS89 4.7 30.3 1.0 OD1 F:ASN170 4.9 35.3 1.0 NE1 F:TRP153 4.9 44.9 1.0 CG F:ASP88 5.0 33.2 1.0 CE2 F:TRP153 5.0 45.9 1.0

Iron binding site 5 out of 16 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe502 b:26.3 occ:0.80 FE1 G:FEO502 0.0 26.3 0.8 O G:FEO502 2.1 26.1 0.8 NE2 G:HIS234 2.2 26.2 1.0 OD1 G:ASP171 2.2 28.4 1.0 OD2 G:ASP88 2.2 31.2 1.0 NE2 G:HIS89 2.2 30.2 1.0 O G:HOH801 2.3 31.9 1.0 CG G:ASP171 3.1 31.7 1.0 CD2 G:HIS234 3.1 25.9 1.0 CD2 G:HIS89 3.1 29.1 1.0 CE1 G:HIS234 3.2 26.4 1.0 CG G:ASP88 3.2 30.0 1.0 CE1 G:HIS89 3.2 31.4 1.0 O G:HOH803 3.3 30.0 1.0 OD2 G:ASP171 3.4 34.5 1.0 FE2 G:FEO502 3.5 26.5 0.5 OD1 G:ASP88 3.5 30.5 1.0 OG G:SER233 4.1 28.1 1.0 CG G:HIS234 4.3 24.9 1.0 CG G:HIS89 4.3 28.9 1.0 ND1 G:HIS89 4.3 29.9 1.0 ND1 G:HIS234 4.3 27.1 1.0 CB G:ASP88 4.5 29.5 1.0 CB G:ASP171 4.5 27.0 1.0 OH G:TYR25 4.6 68.5 1.0 O G:HOH726 4.7 53.7 1.0 OE2 G:GLU86 4.8 34.9 1.0 CD2 G:HIS84 4.8 33.3 1.0

Iron binding site 6 out of 16 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe502 b:26.5 occ:0.50 FE2 G:FEO502 0.0 26.5 0.5 OD2 G:ASP171 2.0 34.5 1.0 O G:FEO502 2.1 26.1 0.8 OE2 G:GLU86 2.1 34.9 1.0 NE2 G:HIS152 2.2 50.5 1.0 NE2 G:HIS84 2.3 36.5 1.0 O G:HOH803 2.8 30.0 1.0 CD2 G:HIS84 3.1 33.3 1.0 CG G:ASP171 3.1 31.7 1.0 CD2 G:HIS152 3.1 49.4 1.0 CD G:GLU86 3.1 44.5 1.0 CE1 G:HIS152 3.2 51.5 1.0 CE1 G:HIS84 3.5 39.0 1.0 FE1 G:FEO502 3.5 26.3 0.8 OD1 G:ASP171 3.6 28.4 1.0 O G:HOH801 3.7 31.9 1.0 CB G:GLU86 3.8 29.6 1.0 OE1 G:GLU86 3.9 40.8 1.0 CG G:GLU86 4.0 33.9 1.0 CG G:HIS152 4.3 48.9 1.0 CB G:ASP171 4.3 27.0 1.0 ND1 G:HIS152 4.3 50.4 1.0 CG G:HIS84 4.3 36.8 1.0 OD1 G:ASP88 4.4 30.5 1.0 ND1 G:HIS84 4.5 37.9 1.0 O G:HOH687 4.6 37.0 1.0 CD2 G:HIS89 4.6 29.1 1.0 OD2 G:ASP88 4.7 31.2 1.0 NE2 G:HIS89 4.7 30.2 1.0 OD1 G:ASN170 4.9 37.4 1.0

Iron binding site 7 out of 16 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe701 b:32.1 occ:0.50 FE1 H:FEO701 0.0 32.1 0.5 OD2 H:ASP171 2.0 38.8 1.0 NE2 H:HIS152 2.1 55.4 1.0 O H:FEO701 2.1 32.5 0.8 OE2 H:GLU86 2.1 40.8 1.0 NE2 H:HIS84 2.3 43.2 1.0 CD2 H:HIS152 3.1 57.6 1.0 O H:HOH963 3.1 31.1 0.5 CG H:ASP171 3.1 37.6 1.0 CD2 H:HIS84 3.1 39.6 1.0 CE1 H:HIS152 3.1 53.7 1.0 CD H:GLU86 3.2 52.8 1.0 FE2 H:FEO701 3.5 32.5 0.8 CE1 H:HIS84 3.5 46.2 1.0 OD1 H:ASP171 3.6 34.8 1.0 CB H:GLU86 3.9 38.4 1.0 O H:HOH963 3.9 31.1 0.5 OE1 H:GLU86 3.9 54.9 1.0 CG H:GLU86 4.0 44.7 1.0 CG H:HIS152 4.2 59.0 1.0 ND1 H:HIS152 4.2 56.2 1.0 CB H:ASP171 4.3 36.3 1.0 CG H:HIS84 4.3 43.3 1.0 OD1 H:ASP88 4.5 35.9 1.0 ND1 H:HIS84 4.5 46.2 1.0 CD2 H:HIS89 4.7 32.2 1.0 OD2 H:ASP88 4.7 35.7 1.0 NE2 H:HIS89 4.8 34.1 1.0 O H:HOH915 4.8 43.4 1.0 OD1 H:ASN170 4.9 39.9 1.0 NE1 H:TRP153 5.0 56.6 1.0

Iron binding site 8 out of 16 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe701 b:32.5 occ:0.80 FE2 H:FEO701 0.0 32.5 0.8 O H:FEO701 2.1 32.5 0.8 OD1 H:ASP171 2.2 34.8 1.0 OD2 H:ASP88 2.2 35.7 1.0 NE2 H:HIS234 2.2 29.3 1.0 NE2 H:HIS89 2.2 34.1 1.0 O H:HOH963 2.4 31.1 0.5 O H:HOH963 2.9 31.1 0.5 CG H:ASP171 3.1 37.6 1.0 CD2 H:HIS89 3.2 32.2 1.0 CD2 H:HIS234 3.2 29.1 1.0 CG H:ASP88 3.2 36.4 1.0 CE1 H:HIS89 3.2 35.6 1.0 CE1 H:HIS234 3.2 29.4 1.0 OD2 H:ASP171 3.3 38.8 1.0 FE1 H:FEO701 3.5 32.1 0.5 OD1 H:ASP88 3.6 35.9 1.0 OG H:SER233 4.1 35.9 1.0 CG H:HIS89 4.3 34.6 1.0 CG H:HIS234 4.3 29.9 1.0 ND1 H:HIS89 4.3 35.2 1.0 ND1 H:HIS234 4.4 30.4 1.0 CB H:ASP171 4.4 36.3 1.0 CB H:ASP88 4.5 36.8 1.0 O H:HOH803 4.6 30.0 0.6 OE2 H:GLU86 4.7 40.8 1.0 CD2 H:HIS84 4.8 39.6 1.0 CD H:GLU86 5.0 52.8 1.0

Iron binding site 9 out of 16 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe503 b:25.0 occ:0.80 FE1 I:FEO503 0.0 25.0 0.8 O I:FEO503 2.1 23.6 0.8 NE2 I:HIS89 2.2 27.0 1.0 OD1 I:ASP171 2.2 27.2 1.0 NE2 I:HIS234 2.2 24.9 1.0 OD2 I:ASP88 2.2 28.8 1.0 O I:HOH601 2.5 30.0 1.0 CG I:ASP171 3.1 31.4 1.0 CD2 I:HIS89 3.1 27.9 1.0 CD2 I:HIS234 3.2 23.6 1.0 CE1 I:HIS89 3.2 25.6 1.0 CG I:ASP88 3.2 29.8 1.0 CE1 I:HIS234 3.2 24.8 1.0 OD2 I:ASP171 3.3 31.0 1.0 O I:HOH832 3.4 30.0 1.0 OH I:TYR25 3.5 67.6 1.0 FE2 I:FEO503 3.5 24.0 0.5 OD1 I:ASP88 3.5 29.6 1.0 OG I:SER233 4.1 27.4 1.0 CG I:HIS89 4.2 27.9 1.0 ND1 I:HIS89 4.3 25.7 1.0 CG I:HIS234 4.3 23.5 1.0 ND1 I:HIS234 4.3 24.6 1.0 CB I:ASP171 4.5 24.5 1.0 CB I:ASP88 4.5 23.4 1.0 OE2 I:GLU86 4.7 35.4 1.0 O I:HOH759 4.7 30.0 1.0 CZ I:TYR25 4.8 65.2 1.0 CD2 I:HIS84 4.8 34.8 1.0

Iron binding site 10 out of 16 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe503 b:24.0 occ:0.50 FE2 I:FEO503 0.0 24.0 0.5 OD2 I:ASP171 2.0 31.0 1.0 OE2 I:GLU86 2.1 35.4 1.0 O I:FEO503 2.1 23.6 0.8 NE2 I:HIS152 2.1 50.2 1.0 NE2 I:HIS84 2.3 36.5 1.0 O I:HOH832 2.8 30.0 1.0 CD2 I:HIS84 3.0 34.8 1.0 CD2 I:HIS152 3.1 51.2 1.0 CG I:ASP171 3.1 31.4 1.0 CD I:GLU86 3.1 44.4 1.0 CE1 I:HIS152 3.2 49.8 1.0 CE1 I:HIS84 3.4 38.1 1.0 FE1 I:FEO503 3.5 25.0 0.8 OD1 I:ASP171 3.6 27.2 1.0 CB I:GLU86 3.8 28.7 1.0 O I:HOH601 3.8 30.0 1.0 OE1 I:GLU86 4.0 37.4 1.0 CG I:GLU86 4.0 34.8 1.0 CG I:HIS152 4.2 48.9 1.0 ND1 I:HIS152 4.3 51.9 1.0 CG I:HIS84 4.3 34.6 1.0 CB I:ASP171 4.3 24.5 1.0 OD1 I:ASP88 4.4 29.6 1.0 ND1 I:HIS84 4.5 36.0 1.0 O I:HOH671 4.6 33.4 1.0 CD2 I:HIS89 4.6 27.9 1.0 NE2 I:HIS89 4.7 27.0 1.0 OD2 I:ASP88 4.7 28.8 1.0 OD1 I:ASN170 4.9 31.1 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