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Iron in PDB 1oa1: Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A Resolution Using Synchrotron Radiation.

Protein crystallography data

The structure of Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A Resolution Using Synchrotron Radiation., PDB code: 1oa1 was solved by D.Aragao, S.Macedo, E.P.Mitchell, C.V.Romao, M.Y.Liu, C.Frazao, L.M.Saraiva, A.V.Xavier, J.Legall, W.M.A.M.Van Dongen, W.R.Hagen, M.Teixeira, M.A.Carrondo, P.F.Lindley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.50 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.053, 67.464, 134.955, 90.00, 90.00, 90.00
R / Rfree (%) 13.1 / 15.3

Iron Binding Sites:

The binding sites of Iron atom in the Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A Resolution Using Synchrotron Radiation. (pdb code 1oa1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A Resolution Using Synchrotron Radiation., PDB code: 1oa1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1oa1

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Iron binding site 1 out of 8 in the Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A 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 Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A Resolution Using Synchrotron Radiation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1554

b:6.8
occ:1.00
 FE1 A:SF41554 0.0 6.8 1.0
S2 A:SF41554 2.3 6.2 1.0
SG A:CYS3 2.3 7.6 1.0
S4 A:SF41554 2.3 6.0 1.0
S3 A:SF41554 2.3 7.2 1.0
FE4 A:SF41554 2.7 7.0 1.0
FE3 A:SF41554 2.7 7.0 1.0
FE2 A:SF41554 2.8 6.6 1.0
CB A:CYS3 3.2 6.6 1.0
NZ A:LYS23 3.9 8.0 1.0
C A:CYS3 4.0 7.1 1.0
S1 A:SF41554 4.0 7.4 1.0
CG A:GLN5 4.0 6.5 1.0
O A:CYS3 4.1 7.3 1.0
CE A:LYS23 4.1 6.7 1.0
CA A:CYS3 4.2 6.8 1.0
N A:GLN5 4.3 6.5 1.0
N A:PHE4 4.3 7.2 1.0
OE1 A:GLN5 4.7 11.5 1.0
SG A:CYS15 4.8 7.6 1.0
N A:CYS6 4.8 6.7 1.0
CA A:PHE4 4.8 6.9 1.0
CD A:GLN5 4.9 7.8 1.0
SG A:CYS6 4.9 7.3 1.0
SG A:CYS21 4.9 7.1 1.0
C A:PHE4 5.0 7.1 1.0

Iron binding site 2 out of 8 in 1oa1

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Iron binding site 2 out of 8 in the Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A 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 Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A Resolution Using Synchrotron Radiation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1554

b:6.6
occ:1.00
 FE2 A:SF41554 0.0 6.6 1.0
S3 A:SF41554 2.3 7.2 1.0
SG A:CYS21 2.3 7.1 1.0
S1 A:SF41554 2.3 7.4 1.0
S4 A:SF41554 2.3 6.0 1.0
FE3 A:SF41554 2.6 7.0 1.0
FE4 A:SF41554 2.7 7.0 1.0
FE1 A:SF41554 2.8 6.8 1.0
CB A:CYS21 3.3 6.3 1.0
S2 A:SF41554 3.9 6.2 1.0
N A:CYS21 3.9 7.4 1.0
CA A:GLY19 4.2 8.9 1.0
CA A:CYS21 4.2 7.2 1.0
CE A:LYS23 4.3 6.7 1.0
O A:HOH2171 4.4 9.1 1.0
N A:MET20 4.4 7.8 1.0
SG A:CYS6 4.5 7.3 1.0
CB A:LYS23 4.6 7.4 1.0
C A:GLY19 4.6 8.1 1.0
SG A:CYS15 4.7 7.6 1.0
CG2 A:THR71 4.7 6.8 1.0
NZ A:LYS23 4.8 8.0 1.0
SG A:CYS3 4.8 7.6 1.0
O A:HOH2034 4.9 7.3 1.0

Iron binding site 3 out of 8 in 1oa1

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Iron binding site 3 out of 8 in the Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A 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 Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A Resolution Using Synchrotron Radiation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1554

b:7.0
occ:1.00
 FE3 A:SF41554 0.0 7.0 1.0
S2 A:SF41554 2.3 6.2 1.0
SG A:CYS6 2.3 7.3 1.0
S4 A:SF41554 2.3 6.0 1.0
S1 A:SF41554 2.3 7.4 1.0
FE2 A:SF41554 2.6 6.6 1.0
FE4 A:SF41554 2.7 7.0 1.0
FE1 A:SF41554 2.7 6.8 1.0
CB A:CYS6 3.3 6.3 1.0
N A:CYS6 3.8 6.7 1.0
S3 A:SF41554 3.8 7.2 1.0
CA A:CYS6 4.0 6.4 1.0
OG1 A:THR71 4.3 6.4 1.0
CG2 A:THR71 4.5 6.8 1.0
C A:CYS6 4.5 6.5 1.0
N A:THR9 4.5 6.7 1.0
O A:CYS6 4.5 6.2 1.0
CA A:THR9 4.6 7.4 1.0
SG A:CYS21 4.7 7.1 1.0
O A:HOH2034 4.7 7.3 1.0
CB A:THR9 4.7 7.3 1.0
SG A:CYS15 4.8 7.6 1.0
SG A:CYS3 4.8 7.6 1.0
N A:GLN5 4.9 6.5 1.0
C A:GLN5 4.9 6.7 1.0
CG A:GLN5 4.9 6.5 1.0
CB A:CYS21 4.9 6.3 1.0
C A:GLU8 5.0 7.5 1.0

Iron binding site 4 out of 8 in 1oa1

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Iron binding site 4 out of 8 in the Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A 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 Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A Resolution Using Synchrotron Radiation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1554

b:7.0
occ:1.00
 FE4 A:SF41554 0.0 7.0 1.0
S1 A:SF41554 2.3 7.4 1.0
S3 A:SF41554 2.3 7.2 1.0
SG A:CYS15 2.3 7.6 1.0
S2 A:SF41554 2.3 6.2 1.0
FE3 A:SF41554 2.7 7.0 1.0
FE2 A:SF41554 2.7 6.6 1.0
FE1 A:SF41554 2.7 6.8 1.0
CB A:CYS15 3.3 7.7 1.0
S4 A:SF41554 3.9 6.0 1.0
N A:MET20 4.0 7.8 1.0
OG1 A:THR9 4.0 7.9 1.0
O A:CYS3 4.0 7.3 1.0
CA A:GLY19 4.1 8.9 1.0
CA A:THR9 4.1 7.4 1.0
CB A:THR9 4.4 7.3 1.0
C A:GLY19 4.5 8.1 1.0
CA A:CYS15 4.6 8.0 1.0
SG A:CYS3 4.6 7.6 1.0
CB A:CYS3 4.7 6.6 1.0
N A:CYS15 4.7 7.7 1.0
SG A:CYS6 4.7 7.3 1.0
C A:CYS3 4.7 7.1 1.0
SG A:CYS21 4.7 7.1 1.0
N A:THR9 4.8 6.7 1.0
CB A:MET20 4.8 8.3 1.0
N A:CYS21 4.9 7.4 1.0
N A:ALA10 4.9 8.6 1.0
CA A:MET20 4.9 8.7 1.0

Iron binding site 5 out of 8 in 1oa1

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Iron binding site 5 out of 8 in the Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A 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 Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A Resolution Using Synchrotron Radiation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1555

b:7.2
occ:1.00
 FE1 A:SF31555 0.0 7.2 1.0
S1 A:SF31555 2.3 8.1 1.0
S2 A:SF31555 2.3 8.4 1.0
SG A:CYS434 2.3 7.7 1.0
S3 A:SF31555 2.4 7.0 1.0
FE3 A:SF31555 2.7 7.8 1.0
FE4 A:SF31555 2.8 8.8 1.0
CB A:CYS434 3.5 6.9 1.0
O A:HOH2767 3.8 13.8 1.0
FE7 A:SF31555 3.9 7.3 1.0
CG A:GLU268 3.9 5.8 1.0
O A:HOH2549 4.0 8.3 1.0
CD1 A:TRP292 4.0 6.7 1.0
N A:CYS434 4.2 6.4 1.0
OE2 A:GLU494 4.2 9.8 1.0
CA A:CYS434 4.4 6.5 1.0
NE1 A:TRP292 4.5 6.6 1.0
CD A:GLU268 4.6 6.9 1.0
CB A:CYS406 4.6 6.1 1.0
SG A:CYS406 4.6 7.7 1.0
CA A:CYS406 4.6 6.5 1.0
OE2 A:GLU268 4.7 6.5 1.0
NE2 A:HIS244 5.0 5.4 1.0
N A:ASP407 5.0 7.1 1.0
CE1 A:HIS244 5.0 6.1 1.0
O A:HOH2535 5.0 10.9 1.0

Iron binding site 6 out of 8 in 1oa1

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Iron binding site 6 out of 8 in the Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A 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 Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A Resolution Using Synchrotron Radiation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1555

b:7.8
occ:1.00
 FE3 A:SF31555 0.0 7.8 1.0
S1 A:SF31555 2.2 8.1 1.0
S3 A:SF31555 2.2 7.0 1.0
SG A:CYS312 2.3 7.0 1.0
FE1 A:SF31555 2.7 7.2 1.0
CB A:CYS312 3.3 5.8 1.0
CD1 A:TRP292 3.4 6.7 1.0
FE4 A:SF31555 3.7 8.8 1.0
ND2 A:ASN311 3.8 8.4 1.0
NE1 A:TRP292 3.8 6.6 1.0
CG A:TRP292 3.8 6.0 1.0
N A:CYS312 3.9 6.2 1.0
O A:HOH2767 4.0 13.8 1.0
CG A:GLU494 4.1 7.5 1.0
CA A:CYS312 4.2 6.0 1.0
OE2 A:GLU494 4.2 9.8 1.0
SG A:CYS434 4.4 7.7 1.0
CB A:TRP292 4.4 6.0 1.0
CE2 A:TRP292 4.4 6.8 1.0
CD2 A:TRP292 4.4 5.6 1.0
S2 A:SF31555 4.5 8.4 1.0
CD A:GLU494 4.6 10.2 1.0
C A:ASN311 4.6 6.4 1.0
CD2 A:TYR493 4.7 5.7 1.0
O A:ASN311 4.8 6.4 1.0
O A:HOH2549 4.8 8.3 1.0
CG A:ASN311 4.9 7.9 1.0

Iron binding site 7 out of 8 in 1oa1

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Iron binding site 7 out of 8 in the Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A 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 Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A Resolution Using Synchrotron Radiation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1555

b:8.8
occ:1.00
 FE4 A:SF31555 0.0 8.8 1.0
OE2 A:GLU494 2.0 9.8 1.0
S3 A:SF31555 2.3 7.0 1.0
SG A:CYS406 2.3 7.7 1.0
S2 A:SF31555 2.3 8.4 1.0
FE1 A:SF31555 2.8 7.2 1.0
CD A:GLU494 3.0 10.2 1.0
CB A:CYS406 3.3 6.1 1.0
O A:HOH2767 3.3 13.8 1.0
CG A:GLU494 3.4 7.5 1.0
FE3 A:SF31555 3.7 7.8 1.0
CA A:CYS406 3.9 6.5 1.0
FE7 A:SF31555 4.1 7.3 1.0
OE1 A:GLU494 4.2 8.9 1.0
S1 A:SF31555 4.4 8.1 1.0
SG A:CYS434 4.4 7.7 1.0
N A:GLU494 4.6 6.6 1.0
N A:CYS406 4.6 6.8 1.0
CB A:GLU494 4.8 7.2 1.0

Iron binding site 8 out of 8 in 1oa1

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Iron binding site 8 out of 8 in the Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A 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 Reduced Hybrid Cluster Protein (Hcp) From Desulfovibrio Vulgaris Hildenborough Structure at 1.55A Resolution Using Synchrotron Radiation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1555

b:7.3
occ:1.00
 FE7 A:SF31555 0.0 7.3 1.0
OE2 A:GLU268 2.1 6.5 1.0
NE2 A:HIS244 2.1 5.4 1.0
SG A:CYS459 2.3 6.7 1.0
S2 A:SF31555 2.3 8.4 1.0
O A:HOH2767 2.8 13.8 1.0
CD A:GLU268 3.0 6.9 1.0
CD2 A:HIS244 3.1 5.4 1.0
CE1 A:HIS244 3.1 6.1 1.0
CB A:CYS459 3.3 5.5 1.0
CG A:GLU268 3.3 5.8 1.0
N A:CYS459 3.9 5.2 1.0
FE1 A:SF31555 3.9 7.2 1.0
FE4 A:SF31555 4.1 8.8 1.0
CB A:GLU268 4.1 5.9 1.0
OE1 A:GLU268 4.1 6.8 1.0
CA A:CYS459 4.2 5.2 1.0
ND1 A:HIS244 4.2 5.8 1.0
CG A:HIS244 4.3 5.5 1.0
S1 A:SF31555 4.3 8.1 1.0
OE2 A:GLU494 4.4 9.8 1.0
NZ A:LYS496 4.6 8.0 1.0
CA A:GLY433 4.8 6.2 1.0
CD A:LYS496 4.9 9.6 1.0

Reference:

D.Aragao, S.Macedo, E.P.Mitchell, C.V.Romao, M.Y.Liu, C.Frazao, L.M.Saraiva, A.V.Xavier, J.Legall, W.M.A.M.Van Dongen, W.R.Hagen, M.Teixeira, M.A.Carrondo, P.F.Lindley. Reduced Hybrid Cluster Proteins (Hcp) From Desulfovibrio Desulfuricans Atcc 27774 and Desulfovibrio Vulgaris (Hildenborough): X-Ray Structures at High Resolution Using Synchrotron Radiation J.Biol.Inorg.Chem. V. 8 540 2003.
ISSN: ISSN 0949-8257
PubMed: 12764602
DOI: 10.1007/S00775-003-0443-X
Page generated: Sat Aug 3 12:12:44 2024

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