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Iron in PDB 1w9m: As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal

Protein crystallography data

The structure of As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal, PDB code: 1w9m was solved by D.Aragao, S.Macedo, E.P.Mitchell, D.Coelho, C.V.Romao, M.Teixeira, P.F.Lindley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.270, 66.843, 134.764, 90.00, 90.00, 90.00
R / Rfree (%) 12.8 / 17.7

Iron Binding Sites:

The binding sites of Iron atom in the As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal (pdb code 1w9m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal, PDB code: 1w9m:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1w9m

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Iron binding site 1 out of 8 in the As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1554

b:8.5
occ:1.00
 FE1 A:SF41554 0.0 8.5 1.0
S3 A:SF41554 2.3 7.9 1.0
SG A:CYS3 2.3 8.4 1.0
S4 A:SF41554 2.3 8.5 1.0
S2 A:SF41554 2.3 8.6 1.0
FE3 A:SF41554 2.7 8.7 1.0
FE2 A:SF41554 2.7 8.3 1.0
FE4 A:SF41554 2.8 8.5 1.0
CB A:CYS3 3.2 8.1 1.0
S1 A:SF41554 4.0 8.8 1.0
C A:CYS3 4.0 8.2 1.0
NZ A:LYS23 4.0 8.2 1.0
CG A:GLN5 4.0 7.5 1.0
O A:CYS3 4.1 9.1 1.0
CE A:LYS23 4.2 9.5 1.0
CA A:CYS3 4.2 8.4 1.0
N A:GLN5 4.3 8.3 1.0
N A:PHE4 4.3 7.9 1.0
OE1 A:GLN5 4.7 11.5 1.0
SG A:CYS15 4.8 8.9 1.0
N A:CYS6 4.8 7.8 1.0
CD A:GLN5 4.8 7.6 1.0
CA A:PHE4 4.9 7.8 1.0
SG A:CYS6 4.9 8.6 1.0
SG A:CYS21 4.9 8.6 1.0
C A:PHE4 4.9 8.8 1.0
O A:HOH2076 5.0 9.0 1.0

Iron binding site 2 out of 8 in 1w9m

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Iron binding site 2 out of 8 in the As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1554

b:8.3
occ:1.00
 FE2 A:SF41554 0.0 8.3 1.0
S4 A:SF41554 2.3 8.5 1.0
SG A:CYS6 2.3 8.6 1.0
S1 A:SF41554 2.3 8.8 1.0
S3 A:SF41554 2.3 7.9 1.0
FE4 A:SF41554 2.7 8.5 1.0
FE3 A:SF41554 2.7 8.7 1.0
FE1 A:SF41554 2.7 8.5 1.0
CB A:CYS6 3.3 7.4 1.0
N A:CYS6 3.8 7.8 1.0
S2 A:SF41554 3.9 8.6 1.0
CA A:CYS6 4.0 7.7 1.0
OG1 A:THR71 4.4 7.0 1.0
C A:CYS6 4.5 6.4 1.0
N A:THR9 4.5 7.7 1.0
O A:CYS6 4.5 8.4 1.0
CG2 A:THR71 4.6 8.3 1.0
CA A:THR9 4.6 7.6 1.0
SG A:CYS21 4.7 8.6 1.0
O A:HOH2738 4.7 11.0 1.0
CB A:THR9 4.8 8.6 1.0
SG A:CYS3 4.9 8.4 1.0
SG A:CYS15 4.9 8.9 1.0
CG A:GLN5 4.9 7.5 1.0
N A:GLN5 4.9 8.3 1.0
C A:GLN5 4.9 7.5 1.0
C A:GLU8 4.9 8.4 1.0
CB A:CYS21 4.9 9.6 1.0

Iron binding site 3 out of 8 in 1w9m

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Iron binding site 3 out of 8 in the As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1554

b:8.7
occ:1.00
 FE3 A:SF41554 0.0 8.7 1.0
S1 A:SF41554 2.3 8.8 1.0
S4 A:SF41554 2.3 8.5 1.0
S2 A:SF41554 2.3 8.6 1.0
SG A:CYS15 2.3 8.9 1.0
FE1 A:SF41554 2.7 8.5 1.0
FE2 A:SF41554 2.7 8.3 1.0
FE4 A:SF41554 2.7 8.5 1.0
CB A:CYS15 3.3 9.2 1.0
S3 A:SF41554 3.9 7.9 1.0
N A:MET20 4.0 9.1 1.0
O A:CYS3 4.1 9.1 1.0
OG1 A:THR9 4.1 8.7 1.0
CA A:THR9 4.1 7.6 1.0
CA A:GLY19 4.1 9.8 1.0
CB A:THR9 4.4 8.6 1.0
C A:GLY19 4.5 10.1 1.0
CA A:CYS15 4.6 8.7 1.0
SG A:CYS3 4.6 8.4 1.0
CB A:CYS3 4.7 8.1 1.0
SG A:CYS6 4.7 8.6 1.0
N A:CYS15 4.7 8.5 1.0
C A:CYS3 4.7 8.2 1.0
N A:THR9 4.7 7.7 1.0
SG A:CYS21 4.8 8.6 1.0
N A:CYS21 4.9 8.5 1.0
CB A:MET20 4.9 10.0 1.0
N A:ALA10 4.9 9.2 1.0
CA A:MET20 4.9 9.9 1.0

Iron binding site 4 out of 8 in 1w9m

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Iron binding site 4 out of 8 in the As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1554

b:8.5
occ:1.00
 FE4 A:SF41554 0.0 8.5 1.0
S2 A:SF41554 2.3 8.6 1.0
SG A:CYS21 2.3 8.6 1.0
S1 A:SF41554 2.3 8.8 1.0
S3 A:SF41554 2.3 7.9 1.0
FE2 A:SF41554 2.7 8.3 1.0
FE3 A:SF41554 2.7 8.7 1.0
FE1 A:SF41554 2.8 8.5 1.0
CB A:CYS21 3.3 9.6 1.0
N A:CYS21 3.9 8.5 1.0
S4 A:SF41554 3.9 8.5 1.0
CA A:CYS21 4.2 8.8 1.0
CA A:GLY19 4.3 9.8 1.0
CE A:LYS23 4.3 9.5 1.0
O A:HOH2184 4.4 9.8 1.0
N A:MET20 4.5 9.1 1.0
SG A:CYS6 4.5 8.6 1.0
CB A:LYS23 4.5 8.4 1.0
C A:GLY19 4.6 10.1 1.0
SG A:CYS15 4.7 8.9 1.0
CG2 A:THR71 4.8 8.3 1.0
SG A:CYS3 4.8 8.4 1.0
O A:HOH2738 4.9 11.0 1.0
NZ A:LYS23 4.9 8.2 1.0

Iron binding site 5 out of 8 in 1w9m

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Iron binding site 5 out of 8 in the As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1555

b:8.4
occ:1.00
 FE5 A:FS21555 0.0 8.4 1.0
O9 A:FS21555 2.0 10.2 1.0
S5 A:FS21555 2.3 9.4 1.0
SG A:CYS434 2.3 9.3 1.0
S6 A:FS21555 2.3 8.9 1.0
FE6 A:FS21555 2.7 10.2 1.0
FE8 A:FS21555 3.3 12.5 1.0
CB A:CYS434 3.3 8.2 1.0
O8 A:FS21555 3.6 13.9 1.0
FE7 A:FS21555 3.6 7.8 1.0
CG A:GLU268 3.8 7.3 1.0
CD1 A:TRP292 3.9 8.7 1.0
O1 A:FS21555 3.9 11.1 1.0
N A:CYS434 4.2 7.7 1.0
SG A:CSS406 4.3 10.2 1.0
CB A:CSS406 4.3 8.8 1.0
CA A:CYS434 4.4 7.6 1.0
NE1 A:TRP292 4.4 9.0 1.0
CD A:GLU268 4.5 7.3 1.0
OE2 A:GLU268 4.5 7.8 1.0
CA A:CSS406 4.7 8.5 1.0
NE2 A:HIS244 4.7 6.8 1.0
SD A:CSS406 4.8 11.3 1.0
CE1 A:HIS244 4.8 7.3 1.0
CG A:TRP292 4.9 7.8 1.0
SG A:CYS312 4.9 8.1 1.0

Iron binding site 6 out of 8 in 1w9m

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Iron binding site 6 out of 8 in the As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1555

b:10.2
occ:1.00
 FE6 A:FS21555 0.0 10.2 1.0
O8 A:FS21555 2.1 13.9 1.0
S5 A:FS21555 2.2 9.4 1.0
S6 A:FS21555 2.3 8.9 1.0
SG A:CYS312 2.3 8.1 1.0
FE5 A:FS21555 2.7 8.4 1.0
FE8 A:FS21555 3.1 12.5 1.0
CB A:CYS312 3.4 8.2 1.0
N A:CYS312 3.7 6.8 1.0
CD1 A:TRP292 3.8 8.7 1.0
ND2 A:ASN311 4.0 12.7 1.0
CA A:CYS312 4.1 6.8 1.0
OE2 A:GLU494 4.1 9.0 1.0
CG A:TRP292 4.2 7.8 1.0
NE1 A:TRP292 4.2 9.0 1.0
O9 A:FS21555 4.3 10.2 1.0
C A:ASN311 4.3 6.3 1.0
O1 A:FS21555 4.3 11.1 1.0
O A:ASN311 4.4 7.4 1.0
SG A:CYS434 4.6 9.3 1.0
CG A:ASN311 4.6 8.1 1.0
CB A:TRP292 4.6 9.0 1.0
CD2 A:TRP292 4.7 8.2 1.0
CE2 A:TRP292 4.7 8.7 1.0
CE1 A:HIS244 4.8 7.3 1.0
CG A:GLU494 4.8 9.2 1.0
CD2 A:TYR493 5.0 7.8 1.0
CD A:GLU494 5.0 9.6 1.0

Iron binding site 7 out of 8 in 1w9m

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Iron binding site 7 out of 8 in the As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1555

b:7.8
occ:1.00
 FE7 A:FS21555 0.0 7.8 1.0
O9 A:FS21555 2.0 10.2 1.0
O1 A:FS21555 2.1 11.1 1.0
NE2 A:HIS244 2.1 6.8 1.0
OE2 A:GLU268 2.1 7.8 1.0
SG A:CYS459 2.4 8.1 1.0
CD A:GLU268 3.1 7.3 1.0
CE1 A:HIS244 3.1 7.3 1.0
CD2 A:HIS244 3.2 6.6 1.0
CG A:GLU268 3.3 7.3 1.0
CB A:CYS459 3.3 7.6 1.0
FE8 A:FS21555 3.5 12.5 1.0
FE5 A:FS21555 3.6 8.4 1.0
N A:CYS459 4.0 6.3 1.0
O8 A:FS21555 4.1 13.9 1.0
CB A:GLU268 4.2 6.5 1.0
ND1 A:HIS244 4.2 7.7 1.0
OE1 A:GLU268 4.3 7.7 1.0
CA A:CYS459 4.3 6.7 1.0
CG A:HIS244 4.3 6.8 1.0
NZ A:LYS496 4.3 9.5 1.0
SG A:CSS406 4.4 10.2 1.0
S5 A:FS21555 4.5 9.4 1.0
SD A:CSS406 4.8 11.3 1.0
CA A:GLY433 4.8 7.8 1.0
S6 A:FS21555 4.9 8.9 1.0
N A:CYS434 4.9 7.7 1.0

Iron binding site 8 out of 8 in 1w9m

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Iron binding site 8 out of 8 in the As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of As-Isolated Hybrid Cluster Protein From Desulfovibrio Vulgaris X-Ray Structure at 1.35A Resolution Using Iron Anomalous Signal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1555

b:12.5
occ:1.00
 FE8 A:FS21555 0.0 12.5 1.0
O1 A:FS21555 1.9 11.1 1.0
OE2 A:GLU494 2.1 9.0 1.0
O8 A:FS21555 2.3 13.9 1.0
S6 A:FS21555 2.4 8.9 1.0
SD A:CSS406 2.5 11.3 1.0
CD A:GLU494 3.1 9.6 1.0
FE6 A:FS21555 3.1 10.2 1.0
O9 A:FS21555 3.2 10.2 1.0
FE5 A:FS21555 3.3 8.4 1.0
CG A:GLU494 3.5 9.2 1.0
FE7 A:FS21555 3.5 7.8 1.0
SG A:CSS406 3.6 10.2 1.0
ND2 A:ASN311 4.0 12.7 1.0
NZ A:LYS496 4.0 9.5 1.0
OE1 A:GLU494 4.1 9.6 1.0
CB A:CSS406 4.3 8.8 1.0
CE A:LYS496 4.3 7.9 1.0
S5 A:FS21555 4.3 9.4 1.0
CE1 A:HIS244 4.6 7.3 1.0
NE2 A:HIS244 4.6 6.8 1.0
CB A:LYS496 4.6 6.8 1.0
SG A:CYS459 4.7 8.1 1.0
SG A:CYS312 4.8 8.1 1.0
CB A:GLU494 4.9 8.4 1.0
CD A:LYS496 4.9 7.8 1.0
CG A:ASN311 5.0 8.1 1.0

Reference:

D.Aragao, E.P.Mitchell, C.F.Frazao, M.A.Carrondo, P.F.Lindley. Structural and Functional Relationships in the Hybrid Cluster Protein Family:Structure of the Anaerobically Purified Hybrid Cluster Protein From Desulfovibrio Vulgaris at 1.35 A Resolution Acta Crystallogr.,Sect.D V. 64 665 2008.
ISSN: ISSN 0907-4449
PubMed: 18560155
DOI: 10.1107/S0907444908009165
Page generated: Sat Aug 3 16:27:42 2024

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