Iron in PDB 2nap: Dissimilatory Nitrate Reductase (Nap) From Desulfovibrio Desulfuricans

The structure of Dissimilatory Nitrate Reductase (Nap) From Desulfovibrio Desulfuricans, PDB code: 2nap was solved by J.M.Dias, M.Than, A.Humm, R.Huber, G.Bourenkov, H.Bartunik, S.Bursakov, J.Calvete, J.Caldeira, C.Carneiro, J.Moura, I.Moura, M.J.Romao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.260, 106.260, 134.910, 90.00, 90.00, 120.00
R / Rfree (%)	21.8 / 26.7

The structure of Dissimilatory Nitrate Reductase (Nap) From Desulfovibrio Desulfuricans also contains other interesting chemical elements:

Molybdenum

(Mo)

1 atom

The binding sites of Iron atom in the Dissimilatory Nitrate Reductase (Nap) From Desulfovibrio Desulfuricans (pdb code 2nap). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Dissimilatory Nitrate Reductase (Nap) From Desulfovibrio Desulfuricans, PDB code: 2nap:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Dissimilatory Nitrate Reductase (Nap) From Desulfovibrio Desulfuricans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dissimilatory Nitrate Reductase (Nap) From Desulfovibrio Desulfuricans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe800 b:35.4 occ:1.00 FE1 A:SF4800 0.0 35.4 1.0 S3 A:SF4800 2.3 34.6 1.0 SG A:CYS47 2.3 32.8 1.0 S2 A:SF4800 2.3 33.4 1.0 S4 A:SF4800 2.3 35.0 1.0 FE4 A:SF4800 2.6 32.4 1.0 FE3 A:SF4800 2.6 34.5 1.0 FE2 A:SF4800 2.7 30.9 1.0 CB A:CYS47 3.4 32.9 1.0 N A:CYS47 3.8 30.6 1.0 S1 A:SF4800 3.9 30.6 1.0 CA A:CYS47 4.1 32.5 1.0 O A:HOH1074 4.5 33.3 1.0 N A:GLY50 4.6 29.7 1.0 SG A:CYS16 4.7 38.0 1.0 CD A:PRO182 4.7 23.1 1.0 CB A:PRO182 4.7 28.2 1.0 SG A:CYS20 4.7 30.1 1.0 CG2 A:VAL183 4.7 28.1 1.0 C A:CYS47 4.8 32.8 1.0 SG A:CYS13 4.8 30.2 1.0 CG A:PRO182 4.9 25.0 1.0 C A:LEU46 4.9 33.8 1.0 CA A:GLY50 4.9 36.6 1.0 O A:CYS47 5.0 35.4 1.0

Iron binding site 2 out of 4 in the Dissimilatory Nitrate Reductase (Nap) From Desulfovibrio Desulfuricans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dissimilatory Nitrate Reductase (Nap) From Desulfovibrio Desulfuricans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe800 b:30.9 occ:1.00 FE2 A:SF4800 0.0 30.9 1.0 SG A:CYS20 2.2 30.1 1.0 S4 A:SF4800 2.3 35.0 1.0 S1 A:SF4800 2.3 30.6 1.0 S3 A:SF4800 2.3 34.6 1.0 FE4 A:SF4800 2.6 32.4 1.0 FE3 A:SF4800 2.6 34.5 1.0 FE1 A:SF4800 2.7 35.4 1.0 CB A:CYS20 3.2 34.9 1.0 S2 A:SF4800 3.9 33.4 1.0 CG2 A:VAL183 4.0 28.1 1.0 N A:CYS20 4.1 33.1 1.0 CA A:CYS20 4.3 33.1 1.0 CB A:THR18 4.3 25.2 1.0 CB A:VAL183 4.3 27.6 1.0 CG2 A:THR18 4.5 23.3 1.0 SG A:CYS13 4.6 30.2 1.0 SG A:CYS16 4.7 38.0 1.0 CB A:CYS13 4.7 23.2 1.0 OG1 A:THR18 4.8 23.0 1.0 N A:CYS47 4.8 30.6 1.0 SG A:CYS47 4.9 32.8 1.0 CD2 A:LEU46 5.0 33.7 1.0

Iron binding site 3 out of 4 in the Dissimilatory Nitrate Reductase (Nap) From Desulfovibrio Desulfuricans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dissimilatory Nitrate Reductase (Nap) From Desulfovibrio Desulfuricans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe800 b:34.5 occ:1.00 FE3 A:SF4800 0.0 34.5 1.0 S1 A:SF4800 2.3 30.6 1.0 S2 A:SF4800 2.3 33.4 1.0 SG A:CYS16 2.3 38.0 1.0 S4 A:SF4800 2.3 35.0 1.0 FE2 A:SF4800 2.6 30.9 1.0 FE4 A:SF4800 2.6 32.4 1.0 FE1 A:SF4800 2.6 35.4 1.0 CB A:CYS16 3.4 39.9 1.0 N A:CYS16 3.8 38.1 1.0 S3 A:SF4800 3.9 34.6 1.0 CA A:CYS16 3.9 36.8 1.0 OG1 A:THR18 4.0 23.0 1.0 CB A:THR18 4.0 25.2 1.0 O A:HOH1074 4.0 33.3 1.0 O A:CYS16 4.0 34.7 1.0 C A:CYS16 4.2 34.2 1.0 SG A:CYS20 4.5 30.1 1.0 SG A:CYS47 4.7 32.8 1.0 N A:THR18 4.7 27.8 1.0 SG A:CYS13 4.7 30.2 1.0 CD A:PRO182 4.8 23.1 1.0 C A:TYR15 4.8 38.4 1.0 CA A:THR18 4.9 25.9 1.0 CB A:TYR15 4.9 36.3 1.0 CG2 A:THR18 5.0 23.3 1.0 N A:GLY19 5.0 26.0 1.0

Iron binding site 4 out of 4 in the Dissimilatory Nitrate Reductase (Nap) From Desulfovibrio Desulfuricans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Dissimilatory Nitrate Reductase (Nap) From Desulfovibrio Desulfuricans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe800 b:32.4 occ:1.00 FE4 A:SF4800 0.0 32.4 1.0 S2 A:SF4800 2.3 33.4 1.0 S1 A:SF4800 2.3 30.6 1.0 S3 A:SF4800 2.3 34.6 1.0 SG A:CYS13 2.3 30.2 1.0 FE2 A:SF4800 2.6 30.9 1.0 FE1 A:SF4800 2.6 35.4 1.0 FE3 A:SF4800 2.6 34.5 1.0 CB A:CYS13 3.3 23.2 1.0 S4 A:SF4800 3.9 35.0 1.0 CB A:TYR15 4.2 36.3 1.0 CA A:GLY50 4.4 36.6 1.0 N A:CYS16 4.5 38.1 1.0 SG A:CYS20 4.5 30.1 1.0 SG A:CYS47 4.6 32.8 1.0 CB A:CYS20 4.7 34.9 1.0 N A:GLY50 4.7 29.7 1.0 N A:TYR15 4.7 36.1 1.0 CA A:CYS13 4.7 28.7 1.0 CA A:TYR15 4.8 36.1 1.0 CD1 A:TYR15 4.8 40.4 1.0 SG A:CYS16 4.8 38.0 1.0 C A:TYR15 4.9 38.4 1.0

J.M.Dias, M.E.Than, A.Humm, R.Huber, G.P.Bourenkov, H.D.Bartunik, S.Bursakov, J.Calvete, J.Caldeira, C.Carneiro, J.J.Moura, I.Moura, M.J.Romao. Crystal Structure of the First Dissimilatory Nitrate Reductase at 1.9 A Solved By Mad Methods. Structure Fold.Des. V. 7 65 1999.
ISSN: ISSN 0969-2126
PubMed: 10368307
DOI: 10.1016/S0969-2126(99)80010-0