Iron in PDB 4oo7: The 1.55A Crystal Structure of NAF1 (MINER1): the Redox-Active 2FE-2S Protein

The structure of The 1.55A Crystal Structure of NAF1 (MINER1): the Redox-Active 2FE-2S Protein, PDB code: 4oo7 was solved by S.Tamir, Y.Eisenberg-Domovich, A.R.Colman, J.T.Stofleth, C.H.Lipper, M.L.Paddock, P.A.Jenning, O.Livnah, R.Nechushtai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.38 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.009, 48.652, 73.730, 90.00, 90.00, 90.00
R / Rfree (%)	13.5 / 15

The binding sites of Iron atom in the The 1.55A Crystal Structure of NAF1 (MINER1): the Redox-Active 2FE-2S Protein (pdb code 4oo7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The 1.55A Crystal Structure of NAF1 (MINER1): the Redox-Active 2FE-2S Protein, PDB code: 4oo7:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the The 1.55A Crystal Structure of NAF1 (MINER1): the Redox-Active 2FE-2S Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The 1.55A Crystal Structure of NAF1 (MINER1): the Redox-Active 2FE-2S Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:9.6 occ:1.00 FE1 A:FES200 0.0 9.6 1.0 S1 A:FES200 2.2 11.0 1.0 S2 A:FES200 2.3 8.6 1.0 SG A:CYS101 2.3 10.3 1.0 SG A:CYS99 2.3 9.1 1.0 FE2 A:FES200 2.8 9.8 1.0 CB A:CYS101 3.3 10.4 1.0 CB A:CYS99 3.4 9.2 1.0 N A:CYS101 3.6 7.7 1.0 CA A:CYS99 3.7 7.9 1.0 N A:ARG100 3.9 8.1 1.0 CA A:CYS101 4.0 8.2 1.0 CB A:HIS114 4.1 11.2 1.0 N A:HIS114 4.2 11.7 1.0 C A:CYS99 4.3 7.8 1.0 ND1 A:HIS114 4.3 9.9 1.0 N A:TRP102 4.3 8.8 1.0 N A:SER104 4.4 10.6 1.0 C A:CYS101 4.4 8.9 1.0 CB A:SER104 4.4 12.5 1.0 CA A:HIS114 4.5 11.3 1.0 N A:ARG103 4.6 9.5 1.0 C A:ARG100 4.7 8.7 1.0 CG A:HIS114 4.7 11.0 1.0 SG A:CYS110 4.7 11.0 1.0 CA A:CYS110 4.8 11.3 1.0 CB A:CYS110 4.8 11.0 1.0 CA A:SER104 4.9 11.6 1.0 CA A:ARG100 4.9 8.4 1.0 N A:CYS99 4.9 6.8 1.0

Iron binding site 2 out of 4 in the The 1.55A Crystal Structure of NAF1 (MINER1): the Redox-Active 2FE-2S Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The 1.55A Crystal Structure of NAF1 (MINER1): the Redox-Active 2FE-2S Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:9.8 occ:1.00 FE2 A:FES200 0.0 9.8 1.0 ND1 A:HIS114 2.2 9.9 1.0 S2 A:FES200 2.2 8.6 1.0 S1 A:FES200 2.3 11.0 1.0 SG A:CYS110 2.3 11.0 1.0 FE1 A:FES200 2.8 9.6 1.0 CE1 A:HIS114 3.1 10.6 1.0 CG A:HIS114 3.2 11.0 1.0 CB A:CYS110 3.3 11.0 1.0 CB A:HIS114 3.5 11.2 1.0 CA A:CYS110 3.9 11.3 1.0 N A:HIS114 3.9 11.7 1.0 N A:GLY112 4.0 13.6 1.0 NE2 A:HIS114 4.2 12.0 1.0 CD2 A:HIS114 4.3 12.4 1.0 N A:ASP111 4.3 11.1 1.0 CA A:GLY112 4.3 12.6 1.0 CD A:PRO127 4.3 9.6 1.0 CB A:PRO127 4.4 9.4 1.0 CA A:HIS114 4.4 11.3 1.0 C A:CYS110 4.4 11.9 1.0 N A:SER113 4.4 13.6 1.0 SG A:CYS101 4.5 10.3 1.0 CG A:PRO127 4.5 9.2 1.0 C A:GLY112 4.6 12.7 1.0 CA A:CYS99 4.6 7.9 1.0 SG A:CYS99 4.7 9.1 1.0 N A:PRO127 4.8 9.0 1.0 CB A:CYS99 4.8 9.2 1.0 CA A:PRO127 5.0 7.7 1.0

Iron binding site 3 out of 4 in the The 1.55A Crystal Structure of NAF1 (MINER1): the Redox-Active 2FE-2S Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The 1.55A Crystal Structure of NAF1 (MINER1): the Redox-Active 2FE-2S Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe200 b:11.0 occ:1.00 FE1 B:FES200 0.0 11.0 1.0 S1 B:FES200 2.2 12.6 1.0 S2 B:FES200 2.3 10.4 1.0 SG B:CYS101 2.3 12.3 1.0 SG B:CYS99 2.3 9.9 1.0 FE2 B:FES200 2.7 12.3 1.0 CB B:CYS99 3.4 8.3 1.0 CB B:CYS101 3.4 10.8 1.0 N B:CYS101 3.6 10.2 1.0 CA B:CYS99 3.7 9.0 1.0 N B:ARG100 3.9 7.1 1.0 CA B:CYS101 4.0 10.8 1.0 CB B:HIS114 4.1 11.5 1.0 N B:HIS114 4.2 13.1 1.0 C B:CYS99 4.3 8.7 1.0 ND1 B:HIS114 4.3 12.9 1.0 N B:TRP102 4.3 9.4 1.0 N B:SER104 4.4 13.7 1.0 CB B:SER104 4.4 14.5 1.0 C B:CYS101 4.4 10.0 1.0 CA B:HIS114 4.6 13.3 1.0 N B:ARG103 4.6 12.0 1.0 C B:ARG100 4.7 9.1 1.0 CG B:HIS114 4.7 12.6 1.0 SG B:CYS110 4.7 13.7 1.0 CA B:CYS110 4.8 12.3 1.0 CB B:CYS110 4.9 13.8 1.0 CA B:SER104 4.9 13.9 1.0 CA B:ARG100 4.9 7.7 1.0 N B:CYS99 5.0 8.8 1.0

Iron binding site 4 out of 4 in the The 1.55A Crystal Structure of NAF1 (MINER1): the Redox-Active 2FE-2S Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The 1.55A Crystal Structure of NAF1 (MINER1): the Redox-Active 2FE-2S Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe200 b:12.3 occ:1.00 FE2 B:FES200 0.0 12.3 1.0 ND1 B:HIS114 2.2 12.9 1.0 S2 B:FES200 2.2 10.4 1.0 S1 B:FES200 2.3 12.6 1.0 SG B:CYS110 2.3 13.7 1.0 FE1 B:FES200 2.7 11.0 1.0 CE1 B:HIS114 3.1 14.8 1.0 CG B:HIS114 3.2 12.6 1.0 CB B:CYS110 3.3 13.8 1.0 CB B:HIS114 3.6 11.5 1.0 CA B:CYS110 3.9 12.3 1.0 N B:HIS114 3.9 13.1 1.0 N B:GLY112 4.0 17.0 1.0 NE2 B:HIS114 4.2 15.8 1.0 CD2 B:HIS114 4.3 15.6 1.0 CD B:PRO127 4.3 9.8 1.0 CB B:PRO127 4.3 10.4 1.0 CA B:GLY112 4.3 17.0 1.0 N B:ASP111 4.3 12.9 1.0 CA B:HIS114 4.4 13.3 1.0 SG B:CYS101 4.4 12.3 1.0 N B:SER113 4.5 14.6 1.0 C B:CYS110 4.5 12.9 1.0 CG B:PRO127 4.5 10.1 1.0 C B:GLY112 4.6 13.7 1.0 SG B:CYS99 4.6 9.9 1.0 CA B:CYS99 4.6 9.0 1.0 N B:PRO127 4.7 8.8 1.0 CB B:CYS99 4.8 8.3 1.0 CA B:PRO127 4.9 9.8 1.0

S.Tamir, Y.Eisenberg-Domovich, A.R.Conlan, J.T.Stofleth, C.H.Lipper, M.L.Paddock, R.Mittler, P.A.Jennings, O.Livnah, R.Nechushtai. A Point Mutation in the [2FE-2S] Cluster Binding Region of the Naf-1 Protein (H114C) Dramatically Hinders the Cluster Donor Properties. Acta Crystallogr.,Sect.D V. 70 1572 2014.
ISSN: ISSN 0907-4449
PubMed: 24914968
DOI: 10.1107/S1399004714005458