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

Protein crystallography data

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

Iron Binding Sites:

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 1gnt

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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 1gnt

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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 1gnt

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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 1gnt

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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 1gnt

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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 1gnt

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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 1gnt

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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 1gnt

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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

Reference:

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
Page generated: Sat Aug 3 06:14:36 2024

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