Iron in PDB 1gnl: Hybrid Cluster Protein From Desulfovibrio Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A

The structure of Hybrid Cluster Protein From Desulfovibrio Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A, PDB code: 1gnl 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)	28.63 / 1.25
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	57.330, 61.650, 72.250, 82.77, 73.67, 87.31
R / Rfree (%)	12.9 / 14.5

Pages:

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

Binding sites:

The binding sites of Iron atom in the Hybrid Cluster Protein From Desulfovibrio Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A (pdb code 1gnl). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Hybrid Cluster Protein From Desulfovibrio Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A, PDB code: 1gnl:
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 Hybrid Cluster Protein From Desulfovibrio Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A


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 Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1544 b:4.3 occ:1.00 FE1 A:SF41544 0.0 4.3 1.0 SG A:CYS6 2.3 4.5 1.0 S4 A:SF41544 2.3 4.0 1.0 S2 A:SF41544 2.3 4.6 1.0 S3 A:SF41544 2.3 4.5 1.0 FE4 A:SF41544 2.7 4.6 1.0 FE3 A:SF41544 2.7 4.5 1.0 FE2 A:SF41544 2.8 4.2 1.0 CB A:CYS6 3.2 4.3 1.0 S1 A:SF41544 3.9 4.5 1.0 C A:CYS6 4.0 5.0 1.0 CG A:GLN8 4.0 3.9 1.0 NZ A:LYS26 4.1 5.1 1.0 O A:CYS6 4.1 5.5 1.0 CA A:CYS6 4.2 4.6 1.0 CE A:LYS26 4.2 5.8 1.0 N A:GLN8 4.3 4.3 1.0 N A:TYR7 4.4 4.8 1.0 NE2 A:GLN8 4.7 5.5 1.0 SG A:CYS18 4.7 5.2 1.0 N A:CYS9 4.8 4.6 1.0 CD A:GLN8 4.9 4.4 1.0 SG A:CYS9 4.9 4.8 1.0 CA A:TYR7 4.9 4.9 1.0 SG A:CYS24 4.9 4.6 1.0 O A:HOH2087 4.9 4.6 1.0

Iron binding site 2 out of 16 in the Hybrid Cluster Protein From Desulfovibrio Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A


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 Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1544 b:4.2 occ:1.00 FE2 A:SF41544 0.0 4.2 1.0 S3 A:SF41544 2.3 4.5 1.0 SG A:CYS24 2.3 4.6 1.0 S1 A:SF41544 2.3 4.5 1.0 S4 A:SF41544 2.4 4.0 1.0 FE3 A:SF41544 2.7 4.5 1.0 FE4 A:SF41544 2.7 4.6 1.0 FE1 A:SF41544 2.8 4.3 1.0 CB A:CYS24 3.3 5.3 1.0 S2 A:SF41544 3.9 4.6 1.0 N A:CYS24 4.0 5.4 1.0 CA A:GLY22 4.2 5.7 1.0 O A:HOH2185 4.3 5.4 1.0 CA A:CYS24 4.3 5.2 1.0 CE A:LYS26 4.4 5.8 1.0 N A:VAL23 4.5 6.1 1.0 SG A:CYS9 4.6 4.8 1.0 CB A:LYS26 4.6 5.8 1.0 C A:GLY22 4.6 5.8 1.0 SG A:CYS18 4.8 5.2 1.0 SG A:CYS6 4.8 4.5 1.0 CG2 A:THR75 4.8 3.7 1.0 O A:HOH2038 4.9 6.4 1.0 NZ A:LYS26 4.9 5.1 1.0

Iron binding site 3 out of 16 in the Hybrid Cluster Protein From Desulfovibrio Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A


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 Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1544 b:4.5 occ:1.00 FE3 A:SF41544 0.0 4.5 1.0 SG A:CYS9 2.3 4.8 1.0 S2 A:SF41544 2.3 4.6 1.0 S1 A:SF41544 2.3 4.5 1.0 S4 A:SF41544 2.4 4.0 1.0 FE2 A:SF41544 2.7 4.2 1.0 FE4 A:SF41544 2.7 4.6 1.0 FE1 A:SF41544 2.7 4.3 1.0 CB A:CYS9 3.3 4.6 1.0 N A:CYS9 3.8 4.6 1.0 S3 A:SF41544 3.9 4.5 1.0 CA A:CYS9 4.0 4.8 1.0 OG1 A:THR75 4.4 3.9 1.0 CG2 A:THR75 4.5 3.7 1.0 C A:CYS9 4.5 4.9 1.0 O A:CYS9 4.6 5.0 1.0 O A:HOH2038 4.6 6.4 1.0 N A:THR12 4.6 5.2 1.0 SG A:CYS24 4.7 4.6 1.0 CA A:THR12 4.8 5.4 1.0 SG A:CYS18 4.8 5.2 1.0 CG A:GLN8 4.8 3.9 1.0 SG A:CYS6 4.9 4.5 1.0 C A:GLN8 4.9 4.6 1.0 CB A:THR12 4.9 5.4 1.0 N A:GLN8 4.9 4.3 1.0 CB A:CYS24 5.0 5.3 1.0

Iron binding site 4 out of 16 in the Hybrid Cluster Protein From Desulfovibrio Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A


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 Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1544 b:4.6 occ:1.00 FE4 A:SF41544 0.0 4.6 1.0 S1 A:SF41544 2.3 4.5 1.0 SG A:CYS18 2.3 5.2 1.0 S3 A:SF41544 2.3 4.5 1.0 S2 A:SF41544 2.3 4.6 1.0 FE1 A:SF41544 2.7 4.3 1.0 FE3 A:SF41544 2.7 4.5 1.0 FE2 A:SF41544 2.7 4.2 1.0 CB A:CYS18 3.3 5.3 1.0 S4 A:SF41544 3.9 4.0 1.0 O A:CYS6 4.0 5.5 1.0 CA A:GLY22 4.1 5.7 1.0 N A:VAL23 4.1 6.1 1.0 CA A:THR12 4.2 5.4 1.0 OG1 A:THR12 4.2 5.7 1.0 CB A:THR12 4.4 5.4 1.0 CA A:CYS18 4.6 5.8 1.0 C A:GLY22 4.6 5.8 1.0 SG A:CYS6 4.6 4.5 1.0 CB A:CYS6 4.6 4.3 1.0 SG A:CYS9 4.6 4.8 1.0 N A:CYS18 4.7 5.6 1.0 C A:CYS6 4.7 5.0 1.0 SG A:CYS24 4.8 4.6 1.0 N A:THR12 4.8 5.2 1.0 CB A:VAL23 5.0 6.7 1.0

Iron binding site 5 out of 16 in the Hybrid Cluster Protein From Desulfovibrio Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A


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 Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1545 b:3.8 occ:1.00 FE5 A:FSO1545 0.0 3.8 1.0 O10 A:FSO1545 2.0 6.3 1.0 S5 A:FSO1545 2.3 4.5 1.0 S6 A:FSO1545 2.3 4.7 1.0 SG A:CYS427 2.3 4.3 1.0 FE6 A:FSO1545 2.8 4.7 1.0 FE8 A:FSO1545 3.4 6.8 1.0 CB A:CYS427 3.4 3.9 1.0 O8 A:FSO1545 3.6 5.3 1.0 FE7 A:FSO1545 3.6 3.5 1.0 CG A:GLU264 3.8 3.7 1.0 CD1 A:TRP288 3.9 4.4 1.0 O9 A:FSO1545 4.0 6.3 1.0 N A:CYS427 4.2 3.6 1.0 SG A:CYS399 4.3 6.3 1.0 CB A:CYS399 4.3 5.7 1.0 CA A:CYS427 4.4 3.4 1.0 NE1 A:TRP288 4.4 4.6 1.0 CD A:GLU264 4.5 3.3 1.0 OE2 A:GLU264 4.5 4.2 1.0 CA A:CYS399 4.7 4.7 1.0 OG A:SER263 4.7 4.2 1.0 NE2 A:HIS240 4.8 3.9 1.0 S7 A:FSO1545 4.8 8.0 1.0 CE1 A:HIS240 4.8 3.5 1.0 CG A:TRP288 4.9 4.1 1.0 SG A:CYS308 5.0 4.4 1.0 N A:ASP400 5.0 5.0 1.0 CB A:GLU264 5.0 3.4 1.0

Iron binding site 6 out of 16 in the Hybrid Cluster Protein From Desulfovibrio Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A


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 Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1545 b:4.7 occ:1.00 FE6 A:FSO1545 0.0 4.7 1.0 O8 A:FSO1545 2.0 5.3 1.0 S5 A:FSO1545 2.2 4.5 1.0 S6 A:FSO1545 2.3 4.7 1.0 SG A:CYS308 2.3 4.4 1.0 FE5 A:FSO1545 2.8 3.8 1.0 FE8 A:FSO1545 3.0 6.8 1.0 CB A:CYS308 3.4 3.8 1.0 N A:CYS308 3.7 3.3 1.0 CD1 A:TRP288 3.7 4.4 1.0 OE2 A:GLU487 4.1 5.6 1.0 CA A:CYS308 4.1 3.4 1.0 CG A:TRP288 4.1 4.1 1.0 ND2 A:ASN307 4.2 5.2 1.0 NE1 A:TRP288 4.2 4.6 1.0 O10 A:FSO1545 4.2 6.3 1.0 O9 A:FSO1545 4.2 6.3 1.0 C A:ASN307 4.2 3.1 1.0 O A:ASN307 4.4 4.3 1.0 CB A:TRP288 4.5 4.3 1.0 CE1 A:HIS240 4.6 3.5 1.0 SG A:CYS427 4.6 4.3 1.0 CG A:ASN307 4.7 4.1 1.0 CD2 A:TRP288 4.8 4.7 1.0 CE2 A:TRP288 4.8 4.3 1.0 CG A:GLU487 4.9 4.9 1.0 FE7 A:FSO1545 4.9 3.5 1.0 CD A:GLU487 5.0 5.7 1.0 O A:HOH2481 5.0 4.8 1.0

Iron binding site 7 out of 16 in the Hybrid Cluster Protein From Desulfovibrio Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A


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 Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1545 b:3.5 occ:1.00 FE7 A:FSO1545 0.0 3.5 1.0 O10 A:FSO1545 2.1 6.3 1.0 NE2 A:HIS240 2.1 3.9 1.0 O9 A:FSO1545 2.1 6.3 1.0 OE2 A:GLU264 2.1 4.2 1.0 SG A:CYS452 2.4 4.6 1.0 CD A:GLU264 3.1 3.3 1.0 CE1 A:HIS240 3.1 3.5 1.0 CD2 A:HIS240 3.2 4.0 1.0 CG A:GLU264 3.3 3.7 1.0 CB A:CYS452 3.4 4.1 1.0 FE8 A:FSO1545 3.5 6.8 1.0 FE5 A:FSO1545 3.6 3.8 1.0 N A:CYS452 4.0 3.7 1.0 O8 A:FSO1545 4.1 5.3 1.0 CB A:GLU264 4.2 3.4 1.0 ND1 A:HIS240 4.2 3.4 1.0 OE1 A:GLU264 4.2 4.0 1.0 CG A:HIS240 4.3 3.8 1.0 NZ A:LYS489 4.3 6.1 1.0 CA A:CYS452 4.3 3.5 1.0 SG A:CYS399 4.4 6.3 1.0 S5 A:FSO1545 4.6 4.5 1.0 S7 A:FSO1545 4.8 8.0 1.0 S6 A:FSO1545 4.8 4.7 1.0 CA A:GLY426 4.9 3.3 1.0 FE6 A:FSO1545 4.9 4.7 1.0 N A:CYS427 4.9 3.6 1.0 CD A:LYS489 5.0 4.3 1.0

Iron binding site 8 out of 16 in the Hybrid Cluster Protein From Desulfovibrio Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A


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 Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1545 b:6.8 occ:1.00 FE8 A:FSO1545 0.0 6.8 1.0 O9 A:FSO1545 1.9 6.3 1.0 OE2 A:GLU487 2.0 5.6 1.0 O8 A:FSO1545 2.2 5.3 1.0 S6 A:FSO1545 2.4 4.7 1.0 S7 A:FSO1545 2.5 8.0 1.0 FE6 A:FSO1545 3.0 4.7 1.0 CD A:GLU487 3.0 5.7 1.0 O10 A:FSO1545 3.3 6.3 1.0 FE5 A:FSO1545 3.4 3.8 1.0 CG A:GLU487 3.5 4.9 1.0 FE7 A:FSO1545 3.5 3.5 1.0 SG A:CYS399 3.6 6.3 1.0 NZ A:LYS489 4.0 6.1 1.0 OE1 A:GLU487 4.1 5.7 1.0 ND2 A:ASN307 4.1 5.2 1.0 CE A:LYS489 4.3 4.8 1.0 S5 A:FSO1545 4.4 4.5 1.0 CB A:CYS399 4.4 5.7 1.0 CE1 A:HIS240 4.5 3.5 1.0 NE2 A:HIS240 4.6 3.9 1.0 SG A:CYS308 4.6 4.4 1.0 CB A:LYS489 4.7 3.8 1.0 SG A:CYS452 4.8 4.6 1.0 CB A:GLU487 4.9 4.8 1.0 CD A:LYS489 4.9 4.3 1.0 CG A:ASN307 5.0 4.1 1.0

Iron binding site 9 out of 16 in the Hybrid Cluster Protein From Desulfovibrio Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Hybrid Cluster Protein From Desulfovibrio Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1544 b:3.6 occ:1.00 FE1 B:SF41544 0.0 3.6 1.0 S3 B:SF41544 2.3 3.6 1.0 SG B:CYS6 2.3 4.0 1.0 S2 B:SF41544 2.3 3.7 1.0 S4 B:SF41544 2.3 3.8 1.0 FE3 B:SF41544 2.7 3.6 1.0 FE4 B:SF41544 2.7 3.5 1.0 FE2 B:SF41544 2.8 3.8 1.0 CB B:CYS6 3.2 3.8 1.0 S1 B:SF41544 3.9 4.1 1.0 C B:CYS6 4.0 3.6 1.0 CG B:GLN8 4.0 3.7 1.0 NZ B:LYS26 4.0 5.0 1.0 O B:CYS6 4.1 4.1 1.0 CA B:CYS6 4.2 3.6 1.0 CE B:LYS26 4.2 4.7 1.0 N B:GLN8 4.2 3.7 1.0 N B:TYR7 4.3 3.6 1.0 NE2 B:GLN8 4.6 4.4 1.0 SG B:CYS18 4.7 4.1 1.0 CD B:GLN8 4.8 3.9 1.0 N B:CYS9 4.8 3.6 1.0 CA B:TYR7 4.9 3.4 1.0 SG B:CYS24 4.9 4.2 1.0 O B:HOH2093 4.9 4.4 1.0 SG B:CYS9 4.9 3.9 1.0 CB B:GLN8 5.0 4.0 1.0

Iron binding site 10 out of 16 in the Hybrid Cluster Protein From Desulfovibrio Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Hybrid Cluster Protein From Desulfovibrio Desulfuricans X-Ray Structure at 1.25A Resolution Using Synchrotron Radiation at A Wavelength of 0.933A within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1544 b:3.8 occ:1.00 FE2 B:SF41544 0.0 3.8 1.0 S4 B:SF41544 2.3 3.8 1.0 SG B:CYS24 2.3 4.2 1.0 S3 B:SF41544 2.3 3.6 1.0 S1 B:SF41544 2.3 4.1 1.0 FE4 B:SF41544 2.7 3.5 1.0 FE3 B:SF41544 2.7 3.6 1.0 FE1 B:SF41544 2.8 3.6 1.0 CB B:CYS24 3.3 4.5 1.0 S2 B:SF41544 3.9 3.7 1.0 N B:CYS24 3.9 4.8 1.0 CA B:CYS24 4.2 4.6 1.0 CA B:GLY22 4.3 4.9 1.0 O B:HOH2187 4.3 4.9 1.0 CE B:LYS26 4.4 4.7 1.0 N B:VAL23 4.5 5.2 1.0 SG B:CYS9 4.6 3.9 1.0 CB B:LYS26 4.6 5.2 1.0 C B:GLY22 4.7 5.0 1.0 SG B:CYS18 4.8 4.1 1.0 CG2 B:THR75 4.8 3.3 1.0 SG B:CYS6 4.8 4.0 1.0 O B:HOH2726 4.9 5.7 1.0 NZ B:LYS26 4.9 5.0 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