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Iron in PDB 3a38: Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.7 Angstrom Resolution

Protein crystallography data

The structure of Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.7 Angstrom Resolution, PDB code: 3a38 was solved by K.Takeda, K.Kusumoto, Y.Hirano, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 0.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.509, 58.959, 23.415, 90.00, 90.00, 90.00
R / Rfree (%) 6.6 / 7.5

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.7 Angstrom Resolution (pdb code 3a38). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.7 Angstrom Resolution, PDB code: 3a38:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3a38

Go back to Iron Binding Sites List in 3a38
Iron binding site 1 out of 4 in the Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe84

b:1.9
occ:1.00
 FE1 A:SF484 0.0 1.9 1.0
S2 A:SF484 2.2 2.0 1.0
SG A:CYS61 2.3 2.4 1.0
S3 A:SF484 2.3 2.0 1.0
S4 A:SF484 2.3 2.1 1.0
FE3 A:SF484 2.7 1.9 1.0
FE4 A:SF484 2.7 1.8 1.0
FE2 A:SF484 2.7 1.9 1.0
HB2 A:CYS61 3.0 3.3 1.0
CB A:CYS61 3.3 2.7 1.0
HB2 A:PHE48 3.5 3.1 1.0
HG12 A:ILE69 3.7 3.6 1.0
HB3 A:CYS61 3.9 3.3 1.0
S1 A:SF484 3.9 2.0 1.0
HD2 A:PHE64 3.9 3.5 1.0
HG22 A:ILE69 4.0 5.5 1.0
HE2 A:PHE64 4.0 4.3 1.0
HG A:LEU63 4.1 3.5 1.0
HB3 A:PHE48 4.1 3.1 1.0
HA A:CYS61 4.2 3.2 1.0
HD11 A:LEU63 4.3 5.4 1.0
CB A:PHE48 4.3 2.6 1.0
CA A:CYS61 4.4 2.6 1.0
HB2 A:LEU63 4.5 3.2 1.0
SG A:CYS75 4.5 2.0 1.0
H A:LEU63 4.6 2.8 1.0
CD2 A:PHE64 4.6 2.9 1.0
CG1 A:ILE69 4.7 3.0 1.0
CE2 A:PHE64 4.7 3.6 1.0
SG A:CYS43 4.7 2.1 1.0
SG A:CYS46 4.7 2.0 1.0
HA A:MET49 4.8 2.9 0.4
CG2 A:ILE69 4.8 3.6 1.0
CG A:LEU63 4.9 2.9 1.0
C A:PHE48 4.9 2.6 1.0
CD1 A:LEU63 4.9 3.6 1.0
HD2 A:PHE48 4.9 4.8 1.0
HA A:MET49 4.9 3.5 0.6
HD12 A:LEU63 5.0 5.4 1.0
O A:PHE48 5.0 3.1 1.0
H A:GLN62 5.0 3.2 0.6
HG13 A:ILE69 5.0 3.6 1.0
HB3 A:CYS43 5.0 2.7 1.0

Iron binding site 2 out of 4 in 3a38

Go back to Iron Binding Sites List in 3a38
Iron binding site 2 out of 4 in the Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe84

b:1.9
occ:1.00
 FE2 A:SF484 0.0 1.9 1.0
SG A:CYS75 2.3 2.0 1.0
S1 A:SF484 2.3 2.0 1.0
S4 A:SF484 2.3 2.1 1.0
S3 A:SF484 2.3 2.0 1.0
FE4 A:SF484 2.7 1.8 1.0
FE3 A:SF484 2.7 1.9 1.0
FE1 A:SF484 2.7 1.9 1.0
HB3 A:CYS75 3.2 2.4 1.0
H A:CYS75 3.2 2.2 1.0
CB A:CYS75 3.3 2.0 1.0
N A:CYS75 3.6 1.8 1.0
CA A:CYS75 3.9 1.9 1.0
S2 A:SF484 3.9 2.0 1.0
HE2 A:PHE64 4.1 4.3 1.0
HB2 A:CYS75 4.1 2.4 1.0
HA A:TRP78 4.2 2.4 1.0
O A:CYS75 4.2 2.0 1.0
C A:CYS75 4.2 1.9 1.0
H A:SER77 4.2 2.6 0.8
HD11 A:LEU63 4.2 5.4 1.0
H A:TRP78 4.3 2.5 1.0
H A:SER77 4.3 2.4 0.2
HD1 A:TYR19 4.3 3.3 1.0
N A:TRP78 4.3 2.1 1.0
C A:TRP74 4.4 1.9 1.0
C A:SER77 4.5 2.5 0.2
HA A:TRP74 4.6 2.2 1.0
HB2 A:TRP78 4.7 2.5 1.0
C A:SER77 4.7 1.9 0.8
SG A:CYS61 4.7 2.4 1.0
CB A:SER77 4.7 2.7 0.2
CA A:TRP78 4.7 2.0 1.0
SG A:CYS43 4.7 2.1 1.0
HA A:CYS75 4.8 2.2 1.0
N A:SER77 4.8 2.1 0.8
SG A:CYS46 4.8 2.0 1.0
CB A:SER77 4.8 3.1 0.8
N A:SER77 4.8 2.0 0.2
CA A:SER77 4.9 2.3 0.2
HD12 A:LEU63 4.9 5.4 1.0
CA A:SER77 5.0 2.3 0.8
HD13 A:LEU17 5.0 5.7 1.0

Iron binding site 3 out of 4 in 3a38

Go back to Iron Binding Sites List in 3a38
Iron binding site 3 out of 4 in the Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe84

b:1.9
occ:1.00
 FE3 A:SF484 0.0 1.9 1.0
S4 A:SF484 2.2 2.1 1.0
SG A:CYS46 2.3 2.0 1.0
S1 A:SF484 2.3 2.0 1.0
S2 A:SF484 2.3 2.0 1.0
FE1 A:SF484 2.7 1.9 1.0
FE2 A:SF484 2.7 1.9 1.0
FE4 A:SF484 2.7 1.8 1.0
HB3 A:CYS46 3.1 2.5 1.0
CB A:CYS46 3.1 2.1 1.0
HB2 A:PHE48 3.2 3.1 1.0
HB2 A:CYS46 3.2 2.5 1.0
HA A:TRP78 3.3 2.4 1.0
HD2 A:PHE48 3.8 4.8 1.0
HA A:CYS43 3.8 2.4 1.0
S3 A:SF484 3.9 2.0 1.0
H A:PHE48 4.0 2.8 1.0
HD1 A:TRP78 4.1 2.5 1.0
CB A:PHE48 4.2 2.6 1.0
CA A:TRP78 4.2 2.0 1.0
H A:THR79 4.3 2.5 1.0
N A:TRP78 4.6 2.1 1.0
CD2 A:PHE48 4.6 4.0 1.0
CA A:CYS46 4.6 2.0 1.0
HB3 A:PHE48 4.6 3.1 1.0
H A:MET49 4.6 3.2 0.6
SG A:CYS61 4.6 2.4 1.0
H A:MET49 4.7 3.1 0.4
CD1 A:TRP78 4.7 2.1 1.0
C A:SER77 4.7 2.5 0.2
N A:PHE48 4.7 2.3 1.0
HB2 A:TRP78 4.7 2.5 1.0
CA A:CYS43 4.7 2.0 1.0
HB2 A:MET49 4.7 4.4 0.6
SG A:CYS75 4.8 2.0 1.0
SG A:CYS43 4.8 2.1 1.0
HB2 A:MET49 4.8 3.3 0.4
O A:SER77 4.8 3.4 0.2
HB3 A:CYS43 4.8 2.7 1.0
H A:CYS75 4.8 2.2 1.0
CA A:PHE48 4.8 2.5 1.0
O A:SER77 4.8 2.5 0.8
N A:MET49 4.9 2.7 0.6
N A:MET49 4.9 2.6 0.4
C A:SER77 4.9 1.9 0.8
CG A:PHE48 4.9 2.9 1.0
H A:TRP78 4.9 2.5 1.0
HA A:CYS46 4.9 2.4 1.0
CB A:TRP78 4.9 2.1 1.0
C A:PHE48 5.0 2.6 1.0
N A:THR79 5.0 2.1 1.0

Iron binding site 4 out of 4 in 3a38

Go back to Iron Binding Sites List in 3a38
Iron binding site 4 out of 4 in the Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe84

b:1.8
occ:1.00
 FE4 A:SF484 0.0 1.8 1.0
S3 A:SF484 2.2 2.0 1.0
SG A:CYS43 2.3 2.1 1.0
S2 A:SF484 2.3 2.0 1.0
S1 A:SF484 2.3 2.0 1.0
FE2 A:SF484 2.7 1.9 1.0
FE1 A:SF484 2.7 1.9 1.0
FE3 A:SF484 2.7 1.9 1.0
HA A:CYS43 3.1 2.4 1.0
CB A:CYS43 3.2 2.2 1.0
HB3 A:CYS43 3.3 2.7 1.0
CA A:CYS43 3.7 2.0 1.0
HG12 A:ILE69 3.7 3.6 1.0
S4 A:SF484 3.9 2.1 1.0
HA A:TRP74 3.9 2.2 1.0
H A:CYS75 4.1 2.2 1.0
HB2 A:CYS43 4.1 2.7 1.0
HE1 A:TYR19 4.1 3.4 1.0
HG22 A:ILE69 4.3 5.5 1.0
HD13 A:ILE69 4.3 5.0 1.0
HB3 A:CYS46 4.3 2.5 1.0
N A:CYS43 4.4 2.1 1.0
HD1 A:TYR19 4.4 3.3 1.0
HB A:ILE69 4.4 3.3 1.0
H A:CYS43 4.5 2.5 1.0
N A:CYS75 4.5 1.8 1.0
CG1 A:ILE69 4.5 3.0 1.0
HB2 A:CYS46 4.5 2.5 1.0
HB2 A:CYS61 4.6 3.3 1.0
CA A:TRP74 4.6 1.9 1.0
C A:TRP74 4.7 1.9 1.0
HB3 A:CYS75 4.7 2.4 1.0
HD1 A:TRP78 4.7 2.5 1.0
CB A:CYS46 4.7 2.1 1.0
SG A:CYS46 4.8 2.0 1.0
N A:TRP74 4.8 2.0 1.0
CD1 A:ILE69 4.8 3.3 1.0
SG A:CYS75 4.8 2.0 1.0
SG A:CYS61 4.9 2.4 1.0
CE1 A:TYR19 4.9 2.8 1.0
C A:CYS43 4.9 2.1 1.0
CB A:ILE69 4.9 2.7 1.0
HD12 A:ILE69 4.9 5.0 1.0
C A:GLY73 5.0 1.8 1.0
HB2 A:MET49 5.0 3.3 0.4

Reference:

K.Takeda, K.Kusumoto, Y.Hirano, K.Miki. Detailed Assessment of X-Ray Induced Structural Perturbation in A Crystalline State Protein. J.Struct.Biol. V. 169 135 2010.
ISSN: ISSN 1047-8477
PubMed: 19782139
DOI: 10.1016/J.JSB.2009.09.012
Page generated: Sun Aug 4 06:38:44 2024

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