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Iron in PDB 3geo: Sulfite Reductase Hemoprotein Nitrite Complex

Enzymatic activity of Sulfite Reductase Hemoprotein Nitrite Complex

All present enzymatic activity of Sulfite Reductase Hemoprotein Nitrite Complex:
1.8.1.2;

Protein crystallography data

The structure of Sulfite Reductase Hemoprotein Nitrite Complex, PDB code: 3geo was solved by B.R.Crane, E.D.Getzoff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.800, 77.400, 87.800, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / n/a

Other elements in 3geo:

The structure of Sulfite Reductase Hemoprotein Nitrite Complex also contains other interesting chemical elements:

Sodium (Na) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Sulfite Reductase Hemoprotein Nitrite Complex (pdb code 3geo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Sulfite Reductase Hemoprotein Nitrite Complex, PDB code: 3geo:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 3geo

Go back to Iron Binding Sites List in 3geo
Iron binding site 1 out of 5 in the Sulfite Reductase Hemoprotein Nitrite Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Sulfite Reductase Hemoprotein Nitrite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe575

b:27.0
occ:1.00
 FE1 A:SF4575 0.0 27.0 1.0
S3 A:SF4575 2.2 26.4 1.0
SG A:CYS434 2.3 25.2 1.0
S2 A:SF4575 2.3 25.9 1.0
S4 A:SF4575 2.3 26.2 1.0
FE4 A:SF4575 2.6 28.4 1.0
FE3 A:SF4575 2.7 26.2 1.0
FE2 A:SF4575 2.8 28.9 1.0
CB A:CYS434 3.3 19.8 1.0
N A:GLY478 3.6 17.1 1.0
CA A:GLY478 3.8 17.9 1.0
S1 A:SF4575 3.9 26.6 1.0
N A:SER436 3.9 28.2 1.0
CA A:SER436 4.1 27.7 1.0
N A:CYS479 4.2 19.7 1.0
CB A:CYS483 4.2 19.9 1.0
CB A:SER436 4.4 26.0 1.0
C A:GLY478 4.4 17.3 1.0
OG1 A:THR477 4.5 18.4 1.0
SG A:CYS483 4.5 26.0 1.0
CA A:CYS434 4.6 20.0 1.0
C A:THR477 4.7 19.6 1.0
N A:VAL435 4.7 23.3 1.0
C A:CYS434 4.7 22.6 1.0
SG A:CYS479 4.9 25.2 1.0
N A:CYS483 5.0 21.9 1.0
OG A:SER436 5.0 22.7 1.0
SG A:CYS440 5.0 26.8 1.0
C A:VAL435 5.0 29.0 1.0

Iron binding site 2 out of 5 in 3geo

Go back to Iron Binding Sites List in 3geo
Iron binding site 2 out of 5 in the Sulfite Reductase Hemoprotein Nitrite Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Sulfite Reductase Hemoprotein Nitrite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe575

b:28.9
occ:1.00
 FE2 A:SF4575 0.0 28.9 1.0
S4 A:SF4575 2.3 26.2 1.0
SG A:CYS440 2.3 26.8 1.0
S1 A:SF4575 2.3 26.6 1.0
S3 A:SF4575 2.4 26.4 1.0
FE3 A:SF4575 2.7 26.2 1.0
FE4 A:SF4575 2.8 28.4 1.0
FE1 A:SF4575 2.8 27.0 1.0
CB A:CYS440 3.2 27.0 1.0
S2 A:SF4575 3.9 25.9 1.0
C3A A:SRM580 4.3 29.7 1.0
CA A:SER436 4.3 27.7 1.0
N A:SER436 4.4 28.2 1.0
N A:ALA443 4.4 29.5 1.0
CB A:LEU442 4.5 26.6 1.0
CBA A:SRM580 4.6 35.1 1.0
SG A:CYS479 4.6 25.2 1.0
C A:LEU442 4.6 30.5 1.0
CA A:CYS440 4.7 31.4 1.0
CA A:ALA443 4.7 30.3 1.0
C4A A:SRM580 4.8 28.8 1.0
CB A:ALA443 4.8 28.6 1.0
CDA A:SRM580 4.9 38.1 1.0
SG A:CYS434 4.9 25.2 1.0
N A:LEU442 5.0 33.5 1.0
SG A:CYS483 5.0 26.0 1.0
CA A:LEU442 5.0 29.5 1.0

Iron binding site 3 out of 5 in 3geo

Go back to Iron Binding Sites List in 3geo
Iron binding site 3 out of 5 in the Sulfite Reductase Hemoprotein Nitrite Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Sulfite Reductase Hemoprotein Nitrite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe575

b:26.2
occ:1.00
 FE3 A:SF4575 0.0 26.2 1.0
S2 A:SF4575 2.3 25.9 1.0
SG A:CYS479 2.3 25.2 1.0
S4 A:SF4575 2.3 26.2 1.0
S1 A:SF4575 2.3 26.6 1.0
FE2 A:SF4575 2.7 28.9 1.0
FE1 A:SF4575 2.7 27.0 1.0
FE4 A:SF4575 2.8 28.4 1.0
CB A:CYS479 3.2 21.9 1.0
N A:CYS479 3.4 19.7 1.0
CA A:CYS479 3.7 21.3 1.0
S3 A:SF4575 3.9 26.4 1.0
O A:CYS479 3.9 24.5 1.0
C A:GLY478 4.1 17.3 1.0
C A:CYS479 4.1 21.9 1.0
ND2 A:ASN481 4.1 31.3 1.0
CB A:ASN481 4.2 21.7 1.0
O A:HOH787 4.2 93.9 1.0
O A:LEU442 4.3 32.8 1.0
CA A:GLY478 4.5 17.9 1.0
CB A:LEU442 4.6 26.6 1.0
C A:LEU442 4.6 30.5 1.0
SG A:CYS440 4.6 26.8 1.0
CG A:ASN481 4.7 29.4 1.0
SG A:CYS483 4.7 26.0 1.0
N A:GLY478 4.7 17.1 1.0
N A:ASN481 4.8 20.9 1.0
O A:GLY478 4.8 16.9 1.0
CA A:ALA443 4.8 30.3 1.0
N A:ALA443 4.8 29.5 1.0
SG A:CYS434 4.9 25.2 1.0

Iron binding site 4 out of 5 in 3geo

Go back to Iron Binding Sites List in 3geo
Iron binding site 4 out of 5 in the Sulfite Reductase Hemoprotein Nitrite Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Sulfite Reductase Hemoprotein Nitrite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe575

b:28.4
occ:1.00
 FE4 A:SF4575 0.0 28.4 1.0
S2 A:SF4575 2.2 25.9 1.0
SG A:CYS483 2.3 26.0 1.0
S3 A:SF4575 2.3 26.4 1.0
S1 A:SF4575 2.3 26.6 1.0
FE1 A:SF4575 2.6 27.0 1.0
FE3 A:SF4575 2.8 26.2 1.0
FE2 A:SF4575 2.8 28.9 1.0
CB A:CYS483 3.0 19.9 1.0
NA A:SRM580 3.9 27.5 1.0
S4 A:SF4575 3.9 26.2 1.0
C4A A:SRM580 4.0 28.8 1.0
N A:CYS483 4.0 21.9 1.0
CA A:CYS483 4.1 19.5 1.0
FE A:SRM580 4.1 27.6 1.0
C1A A:SRM580 4.3 30.5 1.0
CHB A:SRM580 4.3 24.9 1.0
C3A A:SRM580 4.4 29.7 1.0
CB A:ASN481 4.4 21.7 1.0
SG A:CYS434 4.5 25.2 1.0
ND A:SRM580 4.5 29.9 1.0
CB A:CYS434 4.6 19.8 1.0
C1B A:SRM580 4.6 27.8 1.0
NB A:SRM580 4.6 27.2 1.0
CHA A:SRM580 4.6 26.8 1.0
C4D A:SRM580 4.7 30.1 1.0
SG A:CYS479 4.7 25.2 1.0
SG A:CYS440 4.8 26.8 1.0
ND2 A:ASN481 5.0 31.3 1.0

Iron binding site 5 out of 5 in 3geo

Go back to Iron Binding Sites List in 3geo
Iron binding site 5 out of 5 in the Sulfite Reductase Hemoprotein Nitrite Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Sulfite Reductase Hemoprotein Nitrite Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe580

b:27.6
occ:1.00
 FE A:SRM580 0.0 27.6 1.0
N A:NO2585 2.0 33.2 1.0
NB A:SRM580 2.1 27.2 1.0
ND A:SRM580 2.1 29.9 1.0
NC A:SRM580 2.1 26.1 1.0
NA A:SRM580 2.1 27.5 1.0
SG A:CYS483 2.4 26.0 1.0
O1 A:NO2585 2.7 38.1 1.0
O2 A:NO2585 2.9 36.4 1.0
C1B A:SRM580 3.0 27.8 1.0
C1D A:SRM580 3.0 31.2 1.0
C4A A:SRM580 3.0 28.8 1.0
C4B A:SRM580 3.1 26.7 1.0
C4D A:SRM580 3.1 30.1 1.0
C1C A:SRM580 3.1 25.4 1.0
C4C A:SRM580 3.1 28.5 1.0
C1A A:SRM580 3.1 30.5 1.0
CHB A:SRM580 3.4 24.9 1.0
CHD A:SRM580 3.4 31.4 1.0
CHC A:SRM580 3.4 24.7 1.0
CHA A:SRM580 3.4 26.8 1.0
CB A:CYS483 3.5 19.9 1.0
FE4 A:SF4575 4.1 28.4 1.0
C3B A:SRM580 4.3 24.6 1.0
C2D A:SRM580 4.3 33.8 1.0
C3A A:SRM580 4.3 29.7 1.0
C3D A:SRM580 4.3 33.1 1.0
C2C A:SRM580 4.3 27.9 1.0
C2B A:SRM580 4.3 27.8 1.0
CA A:CYS483 4.3 19.5 1.0
C2A A:SRM580 4.3 34.2 1.0
C3C A:SRM580 4.4 28.1 1.0
CAB A:SRM580 4.6 24.9 1.0
NZ A:LYS215 4.6 45.7 1.0
CMA A:SRM580 4.7 29.5 1.0
NZ A:LYS217 4.9 17.2 1.0
CBB A:SRM580 4.9 30.7 1.0
CDB A:SRM580 5.0 27.5 1.0

Reference:

B.R.Crane, L.M.Siegel, E.D.Getzoff. Probing the Catalytic Mechanism of Sulfite Reductase By X-Ray Crystallography: Structures of the Escherichia Coli Hemoprotein in Complex with Substrates, Inhibitors, Intermediates, and Products. Biochemistry V. 36 12120 1997.
ISSN: ISSN 0006-2960
PubMed: 9315849
DOI: 10.1021/BI971066I
Page generated: Sun Aug 4 10:41:59 2024

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