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Iron in PDB 1e9v: Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris

Protein crystallography data

The structure of Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris, PDB code: 1e9v was solved by S.J.Cooper, S.Bailey, P.J.Rizkallah, P.F.Lindley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.07 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.620, 64.598, 152.254, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 19.7

Other elements in 1e9v:

The structure of Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris also contains other interesting chemical elements:

Xenon (Xe) 14 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris (pdb code 1e9v). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris, PDB code: 1e9v:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1e9v

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Iron binding site 1 out of 8 in the Xenon Bound in Hydrophobic Channel of 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 Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:33.0
occ:1.00
FE5 A:FSO600 0.0 33.0 1.0
O10 A:FSO600 2.2 33.5 1.0
S5 A:FSO600 2.2 28.4 1.0
SG A:CYS434 2.3 20.8 1.0
S6 A:FSO600 2.5 35.9 1.0
FE6 A:FSO600 3.0 38.0 1.0
FE8 A:FSO600 3.1 35.2 1.0
CB A:CYS434 3.4 18.1 1.0
FE7 A:FSO600 3.6 27.1 1.0
O8 A:FSO600 3.7 27.1 1.0
CG A:GLU268 3.8 15.0 1.0
O A:HOH2513 4.0 27.9 1.0
O9 A:FSO600 4.0 26.8 1.0
N A:CYS434 4.1 14.2 1.0
SG A:CSS406 4.1 25.8 1.0
CD1 A:TRP292 4.1 16.9 1.0
CB A:CSS406 4.2 21.8 1.0
CA A:CYS434 4.3 16.0 1.0
CD A:GLU268 4.4 15.3 1.0
OE2 A:GLU268 4.5 15.2 1.0
CA A:CSS406 4.5 17.9 1.0
SD A:CSS406 4.6 30.7 1.0
NE1 A:TRP292 4.6 17.4 1.0
N A:ASP407 4.9 16.7 1.0

Iron binding site 2 out of 8 in 1e9v

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Iron binding site 2 out of 8 in the Xenon Bound in Hydrophobic Channel of 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 Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:38.0
occ:1.00
FE6 A:FSO600 0.0 38.0 1.0
O8 A:FSO600 1.9 27.1 1.0
S6 A:FSO600 2.2 35.9 1.0
SG A:CYS312 2.4 18.3 1.0
S5 A:FSO600 2.4 28.4 1.0
FE5 A:FSO600 3.0 33.0 1.0
FE8 A:FSO600 3.1 35.2 1.0
CB A:CYS312 3.3 16.9 1.0
CD1 A:TRP292 3.9 16.9 1.0
N A:CYS312 3.9 16.3 1.0
ND2 A:ASN311 3.9 17.7 1.0
CA A:CYS312 4.1 16.6 1.0
OE2 A:GLU494 4.1 22.1 1.0
CG A:TRP292 4.1 16.8 1.0
C A:ASN311 4.2 16.8 1.0
O A:ASN311 4.3 15.7 1.0
NE1 A:TRP292 4.4 17.4 1.0
O9 A:FSO600 4.4 26.8 1.0
CB A:TRP292 4.5 16.3 1.0
CG A:GLU494 4.6 19.5 1.0
CD2 A:TRP292 4.7 17.0 1.0
CG A:ASN311 4.7 16.7 1.0
SG A:CYS434 4.7 20.8 1.0
CE2 A:TRP292 4.8 16.9 1.0
CD A:GLU494 4.8 21.6 1.0
O10 A:FSO600 4.9 33.5 1.0
O A:HOH2513 4.9 27.9 1.0
O A:HOH2494 5.0 22.6 1.0
CD2 A:TYR493 5.0 14.1 1.0

Iron binding site 3 out of 8 in 1e9v

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Iron binding site 3 out of 8 in the Xenon Bound in Hydrophobic Channel of 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 Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:27.1
occ:1.00
FE7 A:FSO600 0.0 27.1 1.0
OE2 A:GLU268 2.2 15.2 1.0
O9 A:FSO600 2.2 26.8 1.0
NE2 A:HIS244 2.2 19.3 1.0
O10 A:FSO600 2.4 33.5 1.0
SG A:CYS459 2.5 19.2 1.0
CE1 A:HIS244 2.9 19.9 1.0
CD A:GLU268 3.0 15.3 1.0
CG A:GLU268 3.2 15.0 1.0
CD2 A:HIS244 3.4 18.3 1.0
CB A:CYS459 3.4 15.7 1.0
FE8 A:FSO600 3.5 35.2 1.0
FE5 A:FSO600 3.6 33.0 1.0
N A:CYS459 4.0 12.7 1.0
ND1 A:HIS244 4.2 19.6 1.0
CB A:GLU268 4.2 12.9 1.0
O8 A:FSO600 4.2 27.1 1.0
OE1 A:GLU268 4.2 16.6 1.0
CA A:CYS459 4.3 13.6 1.0
S6 A:FSO600 4.3 35.9 1.0
CG A:HIS244 4.4 18.7 1.0
NZ A:LYS496 4.4 23.3 1.0
SG A:CSS406 4.7 25.8 1.0
S5 A:FSO600 4.8 28.4 1.0
OE2 A:GLU494 4.8 22.1 1.0
CA A:GLY433 4.9 12.3 1.0
SD A:CSS406 4.9 30.7 1.0
CD A:LYS496 5.0 18.6 1.0

Iron binding site 4 out of 8 in 1e9v

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Iron binding site 4 out of 8 in the Xenon Bound in Hydrophobic Channel of 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 Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:35.2
occ:1.00
FE8 A:FSO600 0.0 35.2 1.0
OE2 A:GLU494 2.0 22.1 1.0
O9 A:FSO600 2.1 26.8 1.0
S5 A:FSO600 2.2 28.4 1.0
O8 A:FSO600 2.4 27.1 1.0
SD A:CSS406 2.7 30.7 1.0
CD A:GLU494 2.9 21.6 1.0
FE6 A:FSO600 3.1 38.0 1.0
FE5 A:FSO600 3.1 33.0 1.0
CG A:GLU494 3.3 19.5 1.0
O10 A:FSO600 3.5 33.5 1.0
FE7 A:FSO600 3.5 27.1 1.0
SG A:CSS406 3.6 25.8 1.0
OE1 A:GLU494 4.0 22.2 1.0
S6 A:FSO600 4.0 35.9 1.0
ND2 A:ASN311 4.1 17.7 1.0
NZ A:LYS496 4.2 23.3 1.0
CB A:CSS406 4.4 21.8 1.0
CE1 A:HIS244 4.6 19.9 1.0
CE A:LYS496 4.6 20.4 1.0
CB A:GLU494 4.8 17.3 1.0
CB A:LYS496 4.8 13.8 1.0
SG A:CYS312 4.8 18.3 1.0
NE2 A:HIS244 4.8 19.3 1.0
SG A:CYS459 4.8 19.2 1.0

Iron binding site 5 out of 8 in 1e9v

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Iron binding site 5 out of 8 in the Xenon Bound in Hydrophobic Channel of 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 Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe650

b:13.9
occ:1.00
FE1 A:SF4650 0.0 13.9 1.0
S3 A:SF4650 2.3 8.7 1.0
S4 A:SF4650 2.3 10.0 1.0
S2 A:SF4650 2.3 9.5 1.0
SG A:CYS3 2.3 8.9 1.0
FE4 A:SF4650 2.7 13.4 1.0
FE3 A:SF4650 2.7 14.5 1.0
FE2 A:SF4650 2.7 14.0 1.0
CB A:CYS3 3.2 11.1 1.0
S1 A:SF4650 3.9 10.3 1.0
NZ A:LYS23 3.9 12.4 1.0
C A:CYS3 4.0 13.3 1.0
CG A:GLN5 4.1 12.7 1.0
CE A:LYS23 4.2 12.0 1.0
O A:CYS3 4.2 13.0 1.0
CA A:CYS3 4.2 12.4 1.0
N A:GLN5 4.3 11.5 1.0
N A:PHE4 4.3 12.7 1.0
NE2 A:GLN5 4.7 12.7 1.0
SG A:CYS15 4.8 11.1 1.0
N A:CYS6 4.8 12.6 1.0
CA A:PHE4 4.9 12.8 1.0
CD A:GLN5 4.9 13.4 1.0
SG A:CYS21 4.9 10.8 1.0
SG A:CYS6 4.9 11.2 1.0
O A:HOH2047 4.9 12.8 1.0

Iron binding site 6 out of 8 in 1e9v

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Iron binding site 6 out of 8 in the Xenon Bound in Hydrophobic Channel of 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 Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe650

b:14.0
occ:1.00
FE2 A:SF4650 0.0 14.0 1.0
S3 A:SF4650 2.2 8.7 1.0
S1 A:SF4650 2.3 10.3 1.0
S4 A:SF4650 2.3 10.0 1.0
SG A:CYS21 2.4 10.8 1.0
FE3 A:SF4650 2.6 14.5 1.0
FE4 A:SF4650 2.7 13.4 1.0
FE1 A:SF4650 2.7 13.9 1.0
CB A:CYS21 3.3 12.5 1.0
S2 A:SF4650 3.9 9.5 1.0
N A:CYS21 4.0 14.3 1.0
CA A:GLY19 4.2 13.9 1.0
CA A:CYS21 4.3 13.6 1.0
CE A:LYS23 4.3 12.0 1.0
N A:MET20 4.4 14.4 1.0
O A:HOH2155 4.4 12.9 1.0
SG A:CYS6 4.5 11.2 1.0
CB A:LYS23 4.6 12.6 1.0
C A:GLY19 4.6 14.9 1.0
SG A:CYS15 4.7 11.1 1.0
SG A:CYS3 4.8 8.9 1.0
CG2 A:THR71 4.9 10.8 1.0
NZ A:LYS23 4.9 12.4 1.0
O A:HOH2697 4.9 18.2 1.0

Iron binding site 7 out of 8 in 1e9v

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Iron binding site 7 out of 8 in the Xenon Bound in Hydrophobic Channel of 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 Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe650

b:14.5
occ:1.00
FE3 A:SF4650 0.0 14.5 1.0
S2 A:SF4650 2.3 9.5 1.0
SG A:CYS6 2.3 11.2 1.0
S1 A:SF4650 2.3 10.3 1.0
S4 A:SF4650 2.3 10.0 1.0
FE2 A:SF4650 2.6 14.0 1.0
FE4 A:SF4650 2.7 13.4 1.0
FE1 A:SF4650 2.7 13.9 1.0
CB A:CYS6 3.2 13.3 1.0
N A:CYS6 3.8 12.6 1.0
S3 A:SF4650 3.8 8.7 1.0
CA A:CYS6 4.0 12.6 1.0
OG1 A:THR71 4.4 11.1 1.0
C A:CYS6 4.5 12.2 1.0
N A:THR9 4.5 12.3 1.0
O A:CYS6 4.5 12.1 1.0
CG2 A:THR71 4.6 10.8 1.0
CA A:THR9 4.6 12.6 1.0
SG A:CYS21 4.7 10.8 1.0
O A:HOH2697 4.7 18.2 1.0
CB A:THR9 4.8 12.2 1.0
SG A:CYS15 4.8 11.1 1.0
C A:GLN5 4.8 13.5 1.0
SG A:CYS3 4.9 8.9 1.0
CG A:GLN5 4.9 12.7 1.0
CB A:CYS21 4.9 12.5 1.0
N A:GLN5 4.9 11.5 1.0
C A:GLU8 4.9 12.9 1.0

Iron binding site 8 out of 8 in 1e9v

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Iron binding site 8 out of 8 in the Xenon Bound in Hydrophobic Channel of 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 Xenon Bound in Hydrophobic Channel of Hybrid Cluster Protein From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe650

b:13.4
occ:1.00
FE4 A:SF4650 0.0 13.4 1.0
S1 A:SF4650 2.3 10.3 1.0
S3 A:SF4650 2.3 8.7 1.0
SG A:CYS15 2.3 11.1 1.0
S2 A:SF4650 2.3 9.5 1.0
FE2 A:SF4650 2.7 14.0 1.0
FE1 A:SF4650 2.7 13.9 1.0
FE3 A:SF4650 2.7 14.5 1.0
CB A:CYS15 3.3 13.0 1.0
S4 A:SF4650 3.9 10.0 1.0
N A:MET20 3.9 14.4 1.0
OG1 A:THR9 4.0 11.2 1.0
CA A:GLY19 4.1 13.9 1.0
CA A:THR9 4.1 12.6 1.0
O A:CYS3 4.1 13.0 1.0
CB A:THR9 4.4 12.2 1.0
C A:GLY19 4.5 14.9 1.0
CA A:CYS15 4.6 13.3 1.0
SG A:CYS3 4.6 8.9 1.0
CB A:CYS3 4.6 11.1 1.0
SG A:CYS6 4.7 11.2 1.0
N A:CYS15 4.7 13.3 1.0
C A:CYS3 4.7 13.3 1.0
SG A:CYS21 4.7 10.8 1.0
N A:THR9 4.8 12.3 1.0
CB A:MET20 4.9 16.6 1.0
N A:CYS21 4.9 14.3 1.0
N A:ALA10 4.9 14.5 1.0
CA A:MET20 5.0 15.6 1.0

Reference:

S.J.Cooper, C.D.Garner, W.R.Hagen, P.F.Lindley, S.Bailey. Ferricyanide Soaked Hybrid Cluster Protein at 1.2A and Xenon Mapping of the Hydrophobic Cavity at 1.8A To Be Published.
Page generated: Sun Dec 13 14:12:13 2020

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