Iron in PDB 1gnt: Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation.

The structure of Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation., PDB code: 1gnt was solved by S.Macedo, E.P.Mitchell, C.V.Romao, S.J.Cooper, R.Coelho, M.Y.Liu, A.V.Xavier, J.Legall, S.Bailey, D.C.Garner, W.R.Hagen, M.Teixeira, M.A.Carrondo, P.Lindley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.92 / 1.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.810, 64.530, 151.870, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 17.3

The binding sites of Iron atom in the Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation. (pdb code 1gnt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation., PDB code: 1gnt:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1554 b:8.0 occ:1.00 FE1 A:SF41554 0.0 8.0 1.0 S2 A:SF41554 2.3 7.5 1.0 SG A:CYS3 2.3 7.9 1.0 S4 A:SF41554 2.3 8.0 1.0 S3 A:SF41554 2.3 7.9 1.0 FE2 A:SF41554 2.7 8.2 1.0 FE3 A:SF41554 2.7 8.1 1.0 FE4 A:SF41554 2.8 8.3 1.0 CB A:CYS3 3.2 7.5 1.0 S1 A:SF41554 4.0 8.4 1.0 NZ A:LYS23 4.0 9.3 1.0 C A:CYS3 4.0 7.7 1.0 CG A:GLN5 4.1 8.3 1.0 O A:CYS3 4.1 8.8 1.0 CA A:CYS3 4.2 7.4 1.0 CE A:LYS23 4.2 9.5 1.0 N A:PHE4 4.3 8.0 1.0 N A:GLN5 4.3 7.4 1.0 NE2 A:GLN5 4.7 9.9 1.0 SG A:CYS15 4.8 8.8 1.0 N A:CYS6 4.8 8.0 1.0 CA A:PHE4 4.9 7.1 1.0 SG A:CYS6 4.9 8.4 1.0 SG A:CYS21 4.9 8.8 1.0 CD A:GLN5 5.0 9.0 1.0

Iron binding site 2 out of 8 in the Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1554 b:8.2 occ:1.00 FE2 A:SF41554 0.0 8.2 1.0 S1 A:SF41554 2.3 8.4 1.0 S4 A:SF41554 2.3 8.0 1.0 S3 A:SF41554 2.3 7.9 1.0 SG A:CYS15 2.4 8.8 1.0 FE3 A:SF41554 2.7 8.1 1.0 FE1 A:SF41554 2.7 8.0 1.0 FE4 A:SF41554 2.7 8.3 1.0 CB A:CYS15 3.4 8.6 1.0 S2 A:SF41554 3.9 7.5 1.0 N A:MET20 4.0 9.8 1.0 CA A:GLY19 4.1 9.9 1.0 OG1 A:THR9 4.1 8.3 1.0 O A:CYS3 4.1 8.8 1.0 CA A:THR9 4.1 9.2 1.0 CB A:THR9 4.4 9.8 1.0 C A:GLY19 4.6 9.5 1.0 CA A:CYS15 4.6 8.6 1.0 SG A:CYS6 4.6 8.4 1.0 N A:CYS15 4.6 9.0 1.0 SG A:CYS3 4.7 7.9 1.0 CB A:CYS3 4.7 7.5 1.0 C A:CYS3 4.7 7.7 1.0 N A:THR9 4.7 8.9 1.0 SG A:CYS21 4.8 8.8 1.0 CB A:MET20 4.9 10.8 1.0 N A:CYS21 4.9 9.8 1.0

Iron binding site 3 out of 8 in the Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1554 b:8.1 occ:1.00 FE3 A:SF41554 0.0 8.1 1.0 SG A:CYS6 2.3 8.4 1.0 S4 A:SF41554 2.3 8.0 1.0 S1 A:SF41554 2.3 8.4 1.0 S2 A:SF41554 2.3 7.5 1.0 FE4 A:SF41554 2.7 8.3 1.0 FE2 A:SF41554 2.7 8.2 1.0 FE1 A:SF41554 2.7 8.0 1.0 CB A:CYS6 3.3 8.5 1.0 N A:CYS6 3.8 8.0 1.0 S3 A:SF41554 3.9 7.9 1.0 CA A:CYS6 4.0 8.0 1.0 OG1 A:THR71 4.4 8.6 1.0 C A:CYS6 4.5 8.3 1.0 N A:THR9 4.5 8.9 1.0 O A:CYS6 4.5 8.5 1.0 CG2 A:THR71 4.6 8.8 1.0 O A:HOH2957 4.6 12.0 1.0 SG A:CYS21 4.7 8.8 1.0 CA A:THR9 4.7 9.2 1.0 CB A:THR9 4.8 9.8 1.0 SG A:CYS15 4.9 8.8 1.0 SG A:CYS3 4.9 7.9 1.0 C A:GLN5 4.9 7.9 1.0 C A:GLU8 4.9 9.7 1.0 N A:GLN5 4.9 7.4 1.0 CB A:CYS21 4.9 9.5 1.0 CG A:GLN5 5.0 8.3 1.0

Iron binding site 4 out of 8 in the Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1554 b:8.3 occ:1.00 FE4 A:SF41554 0.0 8.3 1.0 S3 A:SF41554 2.3 7.9 1.0 SG A:CYS21 2.3 8.8 1.0 S2 A:SF41554 2.3 7.5 1.0 S1 A:SF41554 2.4 8.4 1.0 FE3 A:SF41554 2.7 8.1 1.0 FE2 A:SF41554 2.7 8.2 1.0 FE1 A:SF41554 2.8 8.0 1.0 CB A:CYS21 3.3 9.5 1.0 S4 A:SF41554 3.9 8.0 1.0 N A:CYS21 3.9 9.8 1.0 CA A:GLY19 4.2 9.9 1.0 CA A:CYS21 4.3 9.7 1.0 CE A:LYS23 4.4 9.5 1.0 O A:HOH2239 4.4 10.0 1.0 N A:MET20 4.5 9.8 1.0 SG A:CYS6 4.5 8.4 1.0 CB A:LYS23 4.5 9.9 1.0 C A:GLY19 4.6 9.5 1.0 SG A:CYS15 4.8 8.8 1.0 SG A:CYS3 4.8 7.9 1.0 CG2 A:THR71 4.9 8.8 1.0 O A:HOH2957 4.9 12.0 1.0 NZ A:LYS23 4.9 9.3 1.0

Iron binding site 5 out of 8 in the Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1555 b:12.9 occ:1.00 FE5 A:FSO1555 0.0 12.9 1.0 O10 A:FSO1555 1.9 11.1 0.5 O10 A:FSO1555 1.9 13.5 0.5 S6 A:FSO1555 2.3 12.9 1.0 S5 A:FSO1555 2.3 14.5 1.0 SG A:CYS434 2.3 12.9 1.0 FE6 A:FSO1555 2.8 14.6 1.0 FE8 A:FSO1555 3.1 16.1 1.0 CB A:CYS434 3.4 10.4 1.0 O8 A:FSO1555 3.5 16.1 1.0 FE7 A:FSO1555 3.6 11.1 1.0 CG A:GLU268 3.8 9.8 1.0 O A:HOH2722 3.9 31.5 1.0 CD1 A:TRP292 4.0 10.5 1.0 O9 A:FSO1555 4.0 13.8 1.0 SG A:CYS406 4.3 14.7 1.0 N A:CYS434 4.3 9.0 1.0 CB A:CYS406 4.3 12.7 1.0 CA A:CYS434 4.4 9.8 1.0 CD A:GLU268 4.5 9.3 1.0 OE2 A:GLU268 4.5 9.2 1.0 NE1 A:TRP292 4.5 9.9 1.0 S7 A:FSO1555 4.7 15.5 1.0 CA A:CYS406 4.7 11.7 1.0 CE1 A:HIS244 4.8 9.3 1.0 NE2 A:HIS244 4.8 9.7 1.0 CG A:TRP292 4.9 10.9 1.0 SG A:CYS312 5.0 11.4 1.0

Iron binding site 6 out of 8 in the Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1555 b:14.6 occ:1.00 FE6 A:FSO1555 0.0 14.6 1.0 O8 A:FSO1555 2.1 16.1 1.0 S5 A:FSO1555 2.2 14.5 1.0 S6 A:FSO1555 2.2 12.9 1.0 SG A:CYS312 2.3 11.4 1.0 FE5 A:FSO1555 2.8 12.9 1.0 FE8 A:FSO1555 3.1 16.1 1.0 CB A:CYS312 3.4 9.2 1.0 O10 A:FSO1555 3.5 11.1 0.5 N A:CYS312 3.7 8.6 1.0 CD1 A:TRP292 3.9 10.5 1.0 ND2 A:ASN311 4.1 12.4 1.0 CG A:TRP292 4.1 10.9 1.0 OE2 A:GLU494 4.1 12.4 1.0 CA A:CYS312 4.1 9.3 1.0 NE1 A:TRP292 4.2 9.9 1.0 O10 A:FSO1555 4.2 13.5 0.5 C A:ASN311 4.3 8.5 1.0 O9 A:FSO1555 4.4 13.8 1.0 O A:ASN311 4.4 9.0 1.0 CB A:TRP292 4.5 10.2 1.0 SG A:CYS434 4.6 12.9 1.0 CD2 A:TRP292 4.7 9.6 1.0 CG A:GLU494 4.7 11.5 1.0 CE2 A:TRP292 4.7 9.4 1.0 CG A:ASN311 4.7 9.1 1.0 O A:HOH2722 4.8 31.5 1.0 CE1 A:HIS244 4.9 9.3 1.0 CD A:GLU494 4.9 11.8 1.0

Iron binding site 7 out of 8 in the Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1555 b:11.1 occ:1.00 FE7 A:FSO1555 0.0 11.1 1.0 O10 A:FSO1555 1.9 11.1 0.5 O10 A:FSO1555 2.1 13.5 0.5 OE2 A:GLU268 2.2 9.2 1.0 O9 A:FSO1555 2.2 13.8 1.0 NE2 A:HIS244 2.2 9.7 1.0 SG A:CYS459 2.4 12.5 1.0 CE1 A:HIS244 3.1 9.3 1.0 CD A:GLU268 3.1 9.3 1.0 CD2 A:HIS244 3.2 9.5 1.0 CG A:GLU268 3.3 9.8 1.0 FE8 A:FSO1555 3.4 16.1 1.0 CB A:CYS459 3.4 9.8 1.0 FE5 A:FSO1555 3.6 12.9 1.0 N A:CYS459 4.0 8.7 1.0 O8 A:FSO1555 4.0 16.1 1.0 CB A:GLU268 4.2 8.5 1.0 ND1 A:HIS244 4.2 10.7 1.0 OE1 A:GLU268 4.3 11.1 1.0 CA A:CYS459 4.3 8.8 1.0 CG A:HIS244 4.4 9.9 1.0 NZ A:LYS496 4.4 12.7 1.0 SG A:CYS406 4.5 14.7 1.0 S5 A:FSO1555 4.6 14.5 1.0 S7 A:FSO1555 4.7 15.5 1.0 S6 A:FSO1555 4.9 12.9 1.0 CA A:GLY433 4.9 8.8 1.0 OE2 A:GLU494 5.0 12.4 1.0

Iron binding site 8 out of 8 in the Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Hybrid Cluster Protein From Desulfovibrio Vulgaris. X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1555 b:16.1 occ:1.00 FE8 A:FSO1555 0.0 16.1 1.0 O9 A:FSO1555 1.9 13.8 1.0 OE2 A:GLU494 2.1 12.4 1.0 O10 A:FSO1555 2.2 11.1 0.5 O8 A:FSO1555 2.2 16.1 1.0 S6 A:FSO1555 2.4 12.9 1.0 S7 A:FSO1555 2.6 15.5 1.0 O10 A:FSO1555 3.0 13.5 0.5 CD A:GLU494 3.1 11.8 1.0 FE5 A:FSO1555 3.1 12.9 1.0 FE6 A:FSO1555 3.1 14.6 1.0 FE7 A:FSO1555 3.4 11.1 1.0 CG A:GLU494 3.5 11.5 1.0 SG A:CYS406 3.6 14.7 1.0 OE1 A:GLU494 4.1 11.2 1.0 NZ A:LYS496 4.2 12.7 1.0 ND2 A:ASN311 4.2 12.4 1.0 S5 A:FSO1555 4.2 14.5 1.0 CB A:CYS406 4.4 12.7 1.0 CE A:LYS496 4.5 10.5 1.0 CE1 A:HIS244 4.5 9.3 1.0 NE2 A:HIS244 4.5 9.7 1.0 SG A:CYS459 4.7 12.5 1.0 CB A:LYS496 4.8 9.4 1.0 SG A:CYS312 4.8 11.4 1.0 CB A:GLU494 5.0 10.2 1.0

S.Macedo, E.P.Mitchell, C.V.Romao, S.J.Cooper, R.Coelho, M.Y.Liu, A.V.Xavier, J.Legall, S.Bailey, D.C.Garner, W.R.Hagen, M.Teixeira, M.A.Carrondo, P.Lindley. Hybrid Cluster Proteins (Hcps) From Desulfovibrio Desulfuricans Atcc 27774 and Desulfovibrio Vulgaris (Hildenborough): X-Ray Structures at 1.25 A Resolution Using Synchrotron Radiation. J. Biol. Inorg. Chem. V. 7 514 2002.
ISSN: ISSN 0949-8257
PubMed: 11941509
DOI: 10.1007/S00775-001-0326-Y