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Iron in PDB 1e1d: Hybrid Cluster Protein From Desulfovibrio Vulgaris

Protein crystallography data

The structure of Hybrid Cluster Protein From Desulfovibrio Vulgaris, PDB code: 1e1d was solved by A.F.Arendsen, S.J.Cooper, S.Bailey, C.D.Garner, W.R.Hagen, P.F.Lindley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.500, 65.500, 155.200, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.8

Iron Binding Sites:

The binding sites of Iron atom in the Hybrid Cluster Protein From Desulfovibrio Vulgaris (pdb code 1e1d). 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, PDB code: 1e1d:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1e1d

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Iron binding site 1 out of 8 in the Hybrid Cluster Protein From Desulfovibrio Vulgaris


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:18.5
occ:1.00
 FE5 A:FSO600 0.0 18.5 1.0
O10 A:FSO600 2.1 23.9 1.0
S5 A:FSO600 2.2 18.2 1.0
S6 A:FSO600 2.2 16.9 1.0
SG A:CYS434 2.3 17.0 1.0
FE6 A:FSO600 2.7 17.5 1.0
FE8 A:FSO600 3.2 17.5 1.0
CB A:CYS434 3.5 14.5 1.0
O8 A:FSO600 3.6 14.1 1.0
FE7 A:FSO600 3.8 15.6 1.0
O A:HOH2277 3.9 42.9 1.0
CG A:GLU268 3.9 13.8 1.0
CD1 A:TRP292 4.0 17.9 1.0
SG A:CYS406 4.2 20.3 1.0
O9 A:FSO600 4.2 12.9 1.0
CB A:CYS406 4.4 11.4 1.0
N A:CYS434 4.4 13.0 1.0
NE1 A:TRP292 4.5 15.0 1.0
OE2 A:GLU268 4.5 14.6 1.0
CD A:GLU268 4.5 21.4 1.0
S7 A:FSO600 4.5 18.0 1.0
CA A:CYS434 4.6 12.3 1.0
CA A:CYS406 4.8 11.2 1.0
NE2 A:HIS244 4.9 13.9 1.0
CE1 A:HIS244 4.9 17.1 1.0
CG A:TRP292 4.9 12.9 1.0
SG A:CYS312 4.9 15.5 1.0

Iron binding site 2 out of 8 in 1e1d

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Iron binding site 2 out of 8 in the Hybrid Cluster Protein From Desulfovibrio Vulgaris


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:17.5
occ:1.00
 FE6 A:FSO600 0.0 17.5 1.0
O8 A:FSO600 2.0 14.1 1.0
S5 A:FSO600 2.2 18.2 1.0
S6 A:FSO600 2.3 16.9 1.0
SG A:CYS312 2.4 15.5 1.0
FE5 A:FSO600 2.7 18.5 1.0
FE8 A:FSO600 3.1 17.5 1.0
CB A:CYS312 3.5 12.2 1.0
O10 A:FSO600 3.8 23.9 1.0
N A:CYS312 3.8 15.3 1.0
ND2 A:ASN311 4.1 12.9 1.0
CD1 A:TRP292 4.1 17.9 1.0
OE2 A:GLU494 4.1 16.1 1.0
CA A:CYS312 4.2 10.3 1.0
C A:ASN311 4.3 13.7 1.0
O A:ASN311 4.4 11.4 1.0
CG A:TRP292 4.4 12.9 1.0
O9 A:FSO600 4.4 12.9 1.0
NE1 A:TRP292 4.5 15.0 1.0
CG A:ASN311 4.5 11.7 1.0
CE1 A:HIS244 4.7 17.1 1.0
SG A:CYS434 4.7 17.0 1.0
CB A:TRP292 4.7 14.0 1.0
CG A:GLU494 4.8 14.7 1.0
CD2 A:TRP292 4.9 15.7 1.0
CD A:GLU494 4.9 20.6 1.0
CE2 A:TRP292 5.0 15.4 1.0

Iron binding site 3 out of 8 in 1e1d

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Iron binding site 3 out of 8 in the Hybrid Cluster Protein From Desulfovibrio Vulgaris


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:15.6
occ:1.00
 FE7 A:FSO600 0.0 15.6 1.0
O10 A:FSO600 1.7 23.9 1.0
O9 A:FSO600 2.1 12.9 1.0
NE2 A:HIS244 2.2 13.9 1.0
OE2 A:GLU268 2.2 14.6 1.0
SG A:CYS459 2.4 16.8 1.0
CE1 A:HIS244 3.1 17.1 1.0
CD A:GLU268 3.2 21.4 1.0
CD2 A:HIS244 3.2 14.2 1.0
FE8 A:FSO600 3.3 17.5 1.0
CB A:CYS459 3.5 14.2 1.0
CG A:GLU268 3.5 13.8 1.0
FE5 A:FSO600 3.8 18.5 1.0
N A:CYS459 4.0 10.2 1.0
O8 A:FSO600 4.1 14.1 1.0
ND1 A:HIS244 4.2 11.7 1.0
CG A:HIS244 4.3 9.8 1.0
OE1 A:GLU268 4.3 13.9 1.0
CB A:GLU268 4.3 9.6 1.0
CA A:CYS459 4.4 11.0 1.0
NZ A:LYS496 4.4 13.1 1.0
SG A:CYS406 4.5 20.3 1.0
S7 A:FSO600 4.5 18.0 1.0
S5 A:FSO600 4.6 18.2 1.0
S6 A:FSO600 4.9 16.9 1.0
OE2 A:GLU494 5.0 16.1 1.0

Iron binding site 4 out of 8 in 1e1d

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Iron binding site 4 out of 8 in the Hybrid Cluster Protein From Desulfovibrio Vulgaris


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:17.5
occ:1.00
 FE8 A:FSO600 0.0 17.5 1.0
O9 A:FSO600 2.0 12.9 1.0
OE2 A:GLU494 2.1 16.1 1.0
O8 A:FSO600 2.2 14.1 1.0
S7 A:FSO600 2.5 18.0 1.0
S6 A:FSO600 2.6 16.9 1.0
O10 A:FSO600 2.6 23.9 1.0
FE6 A:FSO600 3.1 17.5 1.0
CD A:GLU494 3.1 20.6 1.0
FE5 A:FSO600 3.2 18.5 1.0
FE7 A:FSO600 3.3 15.6 1.0
CG A:GLU494 3.6 14.7 1.0
SG A:CYS406 3.7 20.3 1.0
NZ A:LYS496 4.1 13.1 1.0
OE1 A:GLU494 4.2 16.2 1.0
ND2 A:ASN311 4.2 12.9 1.0
S5 A:FSO600 4.2 18.2 1.0
CE A:LYS496 4.3 13.7 1.0
CE1 A:HIS244 4.4 17.1 1.0
NE2 A:HIS244 4.4 13.9 1.0
CB A:CYS406 4.6 11.4 1.0
SG A:CYS459 4.6 16.8 1.0
CB A:LYS496 4.8 11.1 1.0
SG A:CYS312 4.9 15.5 1.0
CD A:LYS496 4.9 12.4 1.0
CG A:ASN311 5.0 11.7 1.0

Iron binding site 5 out of 8 in 1e1d

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Iron binding site 5 out of 8 in the Hybrid Cluster Protein From Desulfovibrio Vulgaris


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe650

b:10.7
occ:1.00
 FE1 A:SF4650 0.0 10.7 1.0
S4 A:SF4650 2.3 11.5 1.0
SG A:CYS3 2.3 11.2 1.0
S2 A:SF4650 2.3 11.1 1.0
S3 A:SF4650 2.3 10.0 1.0
FE3 A:SF4650 2.8 10.6 1.0
FE4 A:SF4650 2.8 11.4 1.0
FE2 A:SF4650 2.8 11.5 1.0
CB A:CYS3 3.3 10.9 1.0
S1 A:SF4650 3.9 12.0 1.0
C A:CYS3 4.1 9.4 1.0
NZ A:LYS23 4.1 11.4 1.0
O A:CYS3 4.2 10.9 1.0
CG A:GLN5 4.2 9.2 1.0
CE A:LYS23 4.2 8.4 1.0
CA A:CYS3 4.3 8.8 1.0
N A:GLN5 4.3 6.3 1.0
N A:PHE4 4.5 11.6 1.0
SG A:CYS15 4.8 12.7 1.0
NE2 A:GLN5 4.8 10.6 1.0
N A:CYS6 4.9 13.1 1.0
SG A:CYS6 4.9 11.9 1.0
SG A:CYS21 4.9 13.4 1.0
CA A:PHE4 5.0 10.4 1.0

Iron binding site 6 out of 8 in 1e1d

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Iron binding site 6 out of 8 in the Hybrid Cluster Protein From Desulfovibrio Vulgaris


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe650

b:11.5
occ:1.00
 FE2 A:SF4650 0.0 11.5 1.0
SG A:CYS21 2.3 13.4 1.0
S3 A:SF4650 2.3 10.0 1.0
S1 A:SF4650 2.4 12.0 1.0
S4 A:SF4650 2.4 11.5 1.0
FE3 A:SF4650 2.7 10.6 1.0
FE1 A:SF4650 2.8 10.7 1.0
FE4 A:SF4650 2.8 11.4 1.0
CB A:CYS21 3.3 12.0 1.0
N A:CYS21 3.9 11.9 1.0
S2 A:SF4650 3.9 11.1 1.0
CA A:CYS21 4.2 11.9 1.0
CA A:GLY19 4.3 10.9 1.0
CE A:LYS23 4.4 8.4 1.0
O A:HOH2075 4.5 14.3 1.0
SG A:CYS6 4.5 11.9 1.0
N A:MET20 4.6 10.2 1.0
CB A:LYS23 4.6 9.5 1.0
C A:GLY19 4.7 9.5 1.0
SG A:CYS15 4.8 12.7 1.0
SG A:CYS3 4.8 11.2 1.0
CG2 A:THR71 4.9 12.3 1.0
NZ A:LYS23 4.9 11.4 1.0

Iron binding site 7 out of 8 in 1e1d

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Iron binding site 7 out of 8 in the Hybrid Cluster Protein From Desulfovibrio Vulgaris


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe650

b:10.6
occ:1.00
 FE3 A:SF4650 0.0 10.6 1.0
SG A:CYS6 2.2 11.9 1.0
S2 A:SF4650 2.3 11.1 1.0
S1 A:SF4650 2.3 12.0 1.0
S4 A:SF4650 2.4 11.5 1.0
FE2 A:SF4650 2.7 11.5 1.0
FE1 A:SF4650 2.8 10.7 1.0
FE4 A:SF4650 2.8 11.4 1.0
CB A:CYS6 3.3 14.0 1.0
N A:CYS6 3.8 13.1 1.0
S3 A:SF4650 3.9 10.0 1.0
CA A:CYS6 4.0 10.9 1.0
C A:CYS6 4.4 12.8 1.0
O A:CYS6 4.5 12.2 1.0
OG1 A:THR71 4.5 10.3 1.0
CG2 A:THR71 4.6 12.3 1.0
N A:THR9 4.6 11.5 1.0
SG A:CYS21 4.7 13.4 1.0
CA A:THR9 4.7 11.7 1.0
O A:HOH2010 4.7 20.1 1.0
N A:GLN5 4.8 6.3 1.0
C A:GLN5 4.9 12.6 1.0
SG A:CYS15 4.9 12.7 1.0
CB A:THR9 4.9 12.3 1.0
SG A:CYS3 4.9 11.2 1.0
CB A:CYS21 4.9 12.0 1.0
C A:GLU8 4.9 14.2 1.0

Iron binding site 8 out of 8 in 1e1d

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Iron binding site 8 out of 8 in the Hybrid Cluster Protein From Desulfovibrio Vulgaris


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe650

b:11.4
occ:1.00
 FE4 A:SF4650 0.0 11.4 1.0
SG A:CYS15 2.3 12.7 1.0
S1 A:SF4650 2.3 12.0 1.0
S2 A:SF4650 2.3 11.1 1.0
S3 A:SF4650 2.4 10.0 1.0
FE1 A:SF4650 2.8 10.7 1.0
FE3 A:SF4650 2.8 10.6 1.0
FE2 A:SF4650 2.8 11.5 1.0
CB A:CYS15 3.3 13.8 1.0
S4 A:SF4650 4.0 11.5 1.0
N A:MET20 4.1 10.2 1.0
CA A:THR9 4.1 11.7 1.0
O A:CYS3 4.1 10.9 1.0
OG1 A:THR9 4.1 13.6 1.0
CA A:GLY19 4.2 10.9 1.0
CB A:THR9 4.4 12.3 1.0
CA A:CYS15 4.6 12.5 1.0
C A:GLY19 4.6 9.5 1.0
N A:CYS15 4.7 13.4 1.0
SG A:CYS6 4.7 11.9 1.0
SG A:CYS3 4.7 11.2 1.0
CB A:CYS3 4.8 10.9 1.0
C A:CYS3 4.8 9.4 1.0
SG A:CYS21 4.8 13.4 1.0
N A:THR9 4.8 11.5 1.0
N A:CYS21 4.9 11.9 1.0
CB A:MET20 4.9 15.6 1.0
N A:ALA10 5.0 10.6 1.0

Reference:

S.J.Cooper, C.D.Garner, W.R.Hagen, P.F.Lindley, S.Bailey. Hybrid-Cluster Protein (Hcp) From Desulfovibrio Vulgaris (Hildenborough) at 1.6 A Resolution. Biochemistry V. 39 15044 2000.
ISSN: ISSN 0006-2960
PubMed: 11106482
DOI: 10.1021/BI001483M
Page generated: Sat Aug 3 04:10:10 2024

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