Iron in PDB 4uqp: High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air

All present enzymatic activity of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air:
1.12.2.1;

The structure of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air, PDB code: 4uqp was solved by A.Volbeda, L.Martin, E.Barbier, O.Gutierrez-Sanz, A.L.Delacey, P.P.Liebgott, S.Dementin, M.Rousset, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.42
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.700, 100.900, 116.700, 90.00, 105.90, 90.00
R / Rfree (%)	11.983 / 15.633

The structure of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air also contains other interesting chemical elements:

Nickel	(Ni)	4 atoms
Magnesium	(Mg)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air (pdb code 4uqp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air, PDB code: 4uqp:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:8.3 occ:1.00 FE1 A:SF41265 0.0 8.3 1.0 S4 A:SF41265 2.3 8.6 1.0 SG A:CYS212 2.3 8.9 1.0 S3 A:SF41265 2.3 8.2 1.0 S2 A:SF41265 2.3 7.8 1.0 FE3 A:SF41265 2.7 8.2 1.0 FE2 A:SF41265 2.7 8.0 1.0 FE4 A:SF41265 2.8 7.8 1.0 CB A:CYS212 3.4 8.2 1.0 N A:LEU213 3.8 7.7 1.0 CA A:CYS212 3.9 8.3 1.0 S1 A:SF41265 3.9 8.1 1.0 CB A:PHE193 4.3 10.2 1.0 N A:TYR214 4.3 8.9 1.0 C A:CYS212 4.3 8.5 1.0 CD2 A:PHE193 4.4 11.8 1.0 ND1 A:HIS184 4.4 8.5 1.0 CB A:ARG189 4.6 9.0 1.0 O A:ARG189 4.7 8.6 1.0 CE1 A:HIS184 4.7 10.0 1.0 CG A:PHE193 4.8 10.7 1.0 CB A:TYR214 4.8 11.3 1.0 CA A:LEU213 4.8 7.9 1.0 SG A:CYS218 4.8 7.8 1.0 SG A:CYS187 4.9 8.2 1.0 C A:LEU213 4.9 8.1 1.0 C A:ARG189 4.9 8.4 1.0 CA A:TYR214 4.9 9.4 1.0

Iron binding site 2 out of 24 in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:8.0 occ:1.00 FE2 A:SF41265 0.0 8.0 1.0 S3 A:SF41265 2.3 8.2 1.0 S4 A:SF41265 2.3 8.6 1.0 SG A:CYS187 2.3 8.2 1.0 S1 A:SF41265 2.3 8.1 1.0 FE3 A:SF41265 2.7 8.2 1.0 FE1 A:SF41265 2.7 8.3 1.0 FE4 A:SF41265 2.7 7.8 1.0 CB A:CYS187 3.1 9.0 1.0 S2 A:SF41265 3.9 7.8 1.0 CB A:ARG189 4.0 9.0 1.0 CG1 A:VAL239 4.3 8.4 1.0 ND1 A:HIS184 4.5 8.5 1.0 CA A:CYS187 4.6 8.2 1.0 C A:ARG189 4.6 8.4 1.0 CA A:ARG189 4.6 8.2 1.0 CG2 A:VAL239 4.6 8.2 1.0 N A:ARG189 4.7 7.9 1.0 N A:LEU190 4.7 8.7 1.0 SG A:CYS218 4.8 7.8 1.0 CG A:ARG189 4.9 8.5 1.0 CH2 A:TRP237 4.9 7.5 1.0 SG A:CYS212 4.9 8.9 1.0 CB A:VAL239 5.0 7.0 1.0

Iron binding site 3 out of 24 in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:8.2 occ:1.00 FE3 A:SF41265 0.0 8.2 1.0 ND1 A:HIS184 2.1 8.5 1.0 S2 A:SF41265 2.3 7.8 1.0 S1 A:SF41265 2.3 8.1 1.0 S4 A:SF41265 2.3 8.6 1.0 FE2 A:SF41265 2.7 8.0 1.0 FE1 A:SF41265 2.7 8.3 1.0 FE4 A:SF41265 2.7 7.8 1.0 CE1 A:HIS184 2.9 10.0 1.0 CG A:HIS184 3.2 7.9 1.0 CB A:HIS184 3.6 7.9 1.0 S3 A:SF41265 3.9 8.2 1.0 CA A:HIS184 3.9 7.3 1.0 NE2 A:HIS184 4.1 11.9 1.0 CD A:PRO221 4.2 7.7 1.0 CG A:PRO221 4.2 9.1 1.0 CD2 A:HIS184 4.2 10.1 1.0 CB A:CYS187 4.5 9.0 1.0 O A:HIS184 4.6 9.0 1.0 SG A:CYS212 4.6 8.9 1.0 SG A:CYS187 4.6 8.2 1.0 CD2 A:PHE193 4.7 11.8 1.0 C A:HIS184 4.8 8.1 1.0 N A:PRO221 4.8 8.1 1.0 SG A:CYS218 4.8 7.8 1.0 CA A:GLY220 4.9 7.6 1.0 CB A:PHE193 5.0 10.2 1.0 CG A:PHE193 5.0 10.7 1.0

Iron binding site 4 out of 24 in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:7.8 occ:1.00 FE4 A:SF41265 0.0 7.8 1.0 S1 A:SF41265 2.3 8.1 1.0 S2 A:SF41265 2.3 7.8 1.0 SG A:CYS218 2.3 7.8 1.0 S3 A:SF41265 2.3 8.2 1.0 FE2 A:SF41265 2.7 8.0 1.0 FE3 A:SF41265 2.7 8.2 1.0 FE1 A:SF41265 2.8 8.3 1.0 CB A:CYS218 3.2 7.6 1.0 S4 A:SF41265 3.9 8.6 1.0 CG2 A:VAL239 4.4 8.2 1.0 N A:GLY220 4.5 7.1 1.0 CA A:GLY220 4.5 7.6 1.0 CD A:PRO221 4.6 7.7 1.0 CA A:CYS218 4.6 7.7 1.0 SG A:CYS212 4.7 8.9 1.0 ND1 A:HIS184 4.7 8.5 1.0 SG A:CYS187 4.8 8.2 1.0 C A:CYS218 4.9 7.2 1.0 N A:LEU213 4.9 7.7 1.0 N A:TYR214 4.9 8.9 1.0 CB A:LEU213 5.0 8.2 1.0

Iron binding site 5 out of 24 in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:7.1 occ:1.00 FE1 A:F3S1266 0.0 7.1 1.0 S1 A:F3S1266 2.2 7.3 1.0 S2 A:F3S1266 2.3 7.5 1.0 S3 A:F3S1266 2.3 7.4 1.0 SG A:CYS248 2.3 7.3 1.0 FE4 A:F3S1266 2.7 7.3 1.0 FE3 A:F3S1266 2.7 7.3 1.0 CB A:CYS248 3.4 7.3 1.0 O Q:HOH2716 3.7 7.3 1.0 N A:CYS248 3.8 6.5 1.0 S4 A:F3S1266 3.8 7.9 1.0 CA A:CYS248 4.1 6.4 1.0 O A:HOH2417 4.1 8.0 1.0 ND2 A:ASN225 4.4 8.1 1.0 C A:CYS248 4.6 7.2 1.0 N A:SER249 4.6 7.1 1.0 SG A:CYS227 4.7 7.6 1.0 SG A:CYS245 4.7 7.5 1.0 O A:HOH2404 4.8 7.2 1.0 CE Q:LYS225 4.8 5.7 1.0 C A:GLY247 5.0 6.8 1.0

Iron binding site 6 out of 24 in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:7.3 occ:1.00 FE3 A:F3S1266 0.0 7.3 1.0 S4 A:F3S1266 2.2 7.9 1.0 S1 A:F3S1266 2.3 7.3 1.0 SG A:CYS227 2.3 7.6 1.0 S3 A:F3S1266 2.3 7.4 1.0 FE1 A:F3S1266 2.7 7.1 1.0 FE4 A:F3S1266 2.7 7.3 1.0 CB A:CYS227 3.3 7.2 1.0 ND2 A:ASN225 3.9 8.1 1.0 S2 A:F3S1266 4.0 7.5 1.0 CE2 A:PHE232 4.3 7.2 1.0 O A:HOH2417 4.4 8.0 1.0 CZ A:PHE232 4.5 7.3 1.0 CG A:ASN225 4.5 7.4 1.0 CB A:ASN225 4.6 8.1 1.0 CG2 A:VAL183 4.7 9.5 1.0 CA A:CYS227 4.7 6.7 1.0 SG A:CYS245 4.7 7.5 1.0 SG A:CYS248 4.8 7.3 1.0 CD A:PRO238 4.9 7.3 1.0

Iron binding site 7 out of 24 in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:7.3 occ:1.00 FE4 A:F3S1266 0.0 7.3 1.0 S4 A:F3S1266 2.2 7.9 1.0 S3 A:F3S1266 2.3 7.4 1.0 S2 A:F3S1266 2.3 7.5 1.0 SG A:CYS245 2.3 7.5 1.0 FE1 A:F3S1266 2.7 7.1 1.0 FE3 A:F3S1266 2.7 7.3 1.0 CB A:CYS245 3.2 7.8 1.0 CA A:CYS245 3.7 7.2 1.0 S1 A:F3S1266 3.9 7.3 1.0 N A:LEU246 4.0 6.4 1.0 N A:GLY247 4.2 6.3 1.0 C A:CYS245 4.3 6.2 1.0 N A:CYS248 4.5 6.5 1.0 CG2 A:THR223 4.7 8.5 1.0 NE2 Q:GLN230 4.7 7.0 1.0 SG A:CYS227 4.8 7.6 1.0 SG A:CYS248 4.8 7.3 1.0 CA A:GLY247 4.8 7.3 1.0 CG2 A:VAL183 4.8 9.5 1.0 N A:CYS245 5.0 7.3 1.0

Iron binding site 8 out of 24 in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:7.2 occ:1.00 FE1 A:SF41267 0.0 7.2 1.0 S2 A:SF41267 2.3 7.0 1.0 SG A:CYS147 2.3 7.1 1.0 S4 A:SF41267 2.3 7.5 1.0 S3 A:SF41267 2.3 7.0 1.0 FE2 A:SF41267 2.6 7.6 1.0 FE4 A:SF41267 2.7 7.3 1.0 FE3 A:SF41267 2.8 7.5 1.0 CB A:CYS147 3.4 7.2 1.0 CA A:CYS147 3.4 6.6 1.0 O A:HOH2415 3.8 7.9 1.0 C A:CYS147 3.9 6.0 1.0 S1 A:SF41267 3.9 7.9 1.0 CG Q:ARG70 4.2 7.1 1.0 O A:CYS147 4.2 6.3 1.0 SG A:CYS114 4.4 7.9 1.0 N A:PRO148 4.4 6.0 1.0 SG A:CYS17 4.6 7.2 1.0 CD2 Q:HIS228 4.6 6.4 1.0 O A:GLY146 4.6 6.6 1.0 CA A:PRO148 4.7 6.5 1.0 NE Q:ARG70 4.7 5.8 1.0 NE2 Q:HIS228 4.7 6.4 1.0 N A:CYS147 4.7 5.9 1.0 SG A:CYS20 4.8 7.7 1.0

Iron binding site 9 out of 24 in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:7.6 occ:1.00 FE2 A:SF41267 0.0 7.6 1.0 SG A:CYS114 2.3 7.9 1.0 S1 A:SF41267 2.3 7.9 1.0 S3 A:SF41267 2.3 7.0 1.0 S4 A:SF41267 2.3 7.5 1.0 FE1 A:SF41267 2.6 7.2 1.0 FE4 A:SF41267 2.7 7.3 1.0 FE3 A:SF41267 2.8 7.5 1.0 CB A:CYS114 3.2 7.7 1.0 S2 A:SF41267 3.9 7.0 1.0 O A:HOH2414 3.9 7.8 1.0 O A:HOH2415 3.9 7.9 1.0 N A:CYS114 4.0 6.5 1.0 O A:HOH2405 4.2 7.5 1.0 CA A:CYS114 4.2 6.5 1.0 SG A:CYS147 4.5 7.1 1.0 SG A:CYS20 4.7 7.7 1.0 SG A:CYS17 4.8 7.2 1.0 N A:CYS17 4.8 6.8 1.0 CA A:GLU16 4.9 7.1 1.0

Iron binding site 10 out of 24 in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:7.5 occ:1.00 FE3 A:SF41267 0.0 7.5 1.0 S4 A:SF41267 2.2 7.5 1.0 SG A:CYS20 2.3 7.7 1.0 S2 A:SF41267 2.3 7.0 1.0 S1 A:SF41267 2.3 7.9 1.0 FE4 A:SF41267 2.7 7.3 1.0 FE2 A:SF41267 2.8 7.6 1.0 FE1 A:SF41267 2.8 7.2 1.0 CB A:CYS20 3.5 7.1 1.0 N A:CYS20 3.7 6.0 1.0 O A:HOH2414 4.0 7.8 1.0 S3 A:SF41267 4.0 7.0 1.0 CA A:CYS20 4.1 6.7 1.0 CB A:PRO148 4.4 6.6 1.0 CA A:PRO148 4.4 6.5 1.0 CA A:GLY112 4.4 7.2 1.0 C A:GLY19 4.4 6.6 1.0 SG A:CYS17 4.7 7.2 1.0 O A:GLY146 4.7 6.6 1.0 CA A:CYS147 4.8 6.6 1.0 CA A:GLY19 4.8 6.8 1.0 SG A:CYS114 4.9 7.9 1.0 N A:GLY19 4.9 6.2 1.0 N A:PRO148 4.9 6.0 1.0 SG A:CYS147 4.9 7.1 1.0

A.Volbeda, L.Martin, E.Barbier, O.Gutierrez-Sanz, A.L.De Lacey, P.Liebgott, S.Dementin, M.Rousset, J.C.Fontecilla-Camps. Crystallographic Studies of [Nife]-Hydrogenase Mutants: Towards Consensus Structures For the Elusive Unready Oxidized States. J.Biol.Inorg.Chem. 2014.
ISSN: ESSN 1432-1327
PubMed: 25315838
DOI: 10.1007/S00775-014-1203-9