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Iron in PDB 1xd9: Crystal Structure of the Nitrogenase Fe Protein ASP39ASN with Mgadp Bound

Enzymatic activity of Crystal Structure of the Nitrogenase Fe Protein ASP39ASN with Mgadp Bound

All present enzymatic activity of Crystal Structure of the Nitrogenase Fe Protein ASP39ASN with Mgadp Bound:
1.18.6.1;

Protein crystallography data

The structure of Crystal Structure of the Nitrogenase Fe Protein ASP39ASN with Mgadp Bound, PDB code: 1xd9 was solved by S.B.Jang, M.S.Jeong, L.C.Seefeldt, J.W.Peters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.052, 92.214, 61.375, 90.00, 101.23, 90.00
R / Rfree (%) 22.9 / 29.9

Other elements in 1xd9:

The structure of Crystal Structure of the Nitrogenase Fe Protein ASP39ASN with Mgadp Bound also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Nitrogenase Fe Protein ASP39ASN with Mgadp Bound (pdb code 1xd9). 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 the Nitrogenase Fe Protein ASP39ASN with Mgadp Bound, PDB code: 1xd9:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1xd9

Go back to Iron Binding Sites List in 1xd9
Iron binding site 1 out of 4 in the Crystal Structure of the Nitrogenase Fe Protein ASP39ASN with Mgadp Bound


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 the Nitrogenase Fe Protein ASP39ASN with Mgadp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe290

b:39.6
occ:1.00
 FE1 A:SF4290 0.0 39.6 1.0
SG B:CYS97 2.2 49.9 1.0
S2 A:SF4290 2.2 35.0 1.0
S4 A:SF4290 2.2 42.2 1.0
S3 A:SF4290 2.4 34.5 1.0
FE3 A:SF4290 2.5 37.8 1.0
FE4 A:SF4290 2.6 37.9 1.0
FE2 A:SF4290 2.7 38.1 1.0
CB B:CYS97 3.3 49.6 1.0
CA B:CYS97 3.5 55.2 1.0
N B:ALA98 3.6 52.7 1.0
S1 A:SF4290 3.9 38.9 1.0
C B:CYS97 4.0 53.0 1.0
CA B:GLY134 4.1 48.5 1.0
SG B:CYS132 4.3 45.8 1.0
SG A:CYS132 4.4 39.3 1.0
N B:GLY134 4.5 53.1 1.0
N B:GLY99 4.6 49.8 1.0
CA B:ALA98 4.7 54.3 1.0
CB B:ALA98 4.7 62.0 1.0
SG A:CYS97 4.7 39.9 1.0
CB A:CYS132 4.8 48.2 1.0
N B:CYS97 4.9 57.4 1.0

Iron binding site 2 out of 4 in 1xd9

Go back to Iron Binding Sites List in 1xd9
Iron binding site 2 out of 4 in the Crystal Structure of the Nitrogenase Fe Protein ASP39ASN with Mgadp Bound


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 the Nitrogenase Fe Protein ASP39ASN with Mgadp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe290

b:38.1
occ:1.00
 FE2 A:SF4290 0.0 38.1 1.0
SG A:CYS97 2.1 39.9 1.0
S3 A:SF4290 2.2 34.5 1.0
S4 A:SF4290 2.3 42.2 1.0
S1 A:SF4290 2.3 38.9 1.0
FE4 A:SF4290 2.6 37.9 1.0
FE1 A:SF4290 2.7 39.6 1.0
FE3 A:SF4290 2.8 37.8 1.0
CB A:CYS97 3.2 50.4 1.0
CA A:CYS97 3.6 51.8 1.0
N A:ALA98 3.8 52.1 1.0
S2 A:SF4290 4.0 35.0 1.0
C A:CYS97 4.2 53.8 1.0
CA A:GLY134 4.2 44.9 1.0
SG B:CYS97 4.4 49.9 1.0
SG A:CYS132 4.5 39.3 1.0
N A:GLY134 4.5 44.8 1.0
SG B:CYS132 4.5 45.8 1.0
N A:GLY99 4.8 53.7 1.0
N A:CYS97 4.8 56.8 1.0
CA A:ALA98 5.0 53.6 1.0
CB B:CYS132 5.0 49.2 1.0

Iron binding site 3 out of 4 in 1xd9

Go back to Iron Binding Sites List in 1xd9
Iron binding site 3 out of 4 in the Crystal Structure of the Nitrogenase Fe Protein ASP39ASN with Mgadp Bound


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 the Nitrogenase Fe Protein ASP39ASN with Mgadp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe290

b:37.8
occ:1.00
 FE3 A:SF4290 0.0 37.8 1.0
SG A:CYS132 2.1 39.3 1.0
S4 A:SF4290 2.2 42.2 1.0
S2 A:SF4290 2.3 35.0 1.0
FE1 A:SF4290 2.5 39.6 1.0
S1 A:SF4290 2.5 38.9 1.0
FE4 A:SF4290 2.6 37.9 1.0
FE2 A:SF4290 2.8 38.1 1.0
CB A:CYS132 3.1 48.2 1.0
S3 A:SF4290 3.9 34.5 1.0
N A:GLY134 4.1 44.8 1.0
CA A:GLY134 4.3 44.9 1.0
SG B:CYS97 4.5 49.9 1.0
CA A:CYS132 4.5 48.4 1.0
SG B:CYS132 4.6 45.8 1.0
N B:ALA98 4.6 52.7 1.0
SG A:CYS97 4.6 39.9 1.0
CA B:CYS97 4.7 55.2 1.0
CG1 A:VAL130 4.8 66.6 1.0
N A:GLY133 4.8 47.6 1.0
C A:CYS132 4.8 50.5 1.0
CD1 A:PHE135 4.8 49.6 1.0
O B:GLY96 5.0 63.5 1.0
CE1 A:PHE135 5.0 49.6 1.0

Iron binding site 4 out of 4 in 1xd9

Go back to Iron Binding Sites List in 1xd9
Iron binding site 4 out of 4 in the Crystal Structure of the Nitrogenase Fe Protein ASP39ASN with Mgadp Bound


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 the Nitrogenase Fe Protein ASP39ASN with Mgadp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe290

b:37.9
occ:1.00
 FE4 A:SF4290 0.0 37.9 1.0
SG B:CYS132 2.1 45.8 1.0
S1 A:SF4290 2.3 38.9 1.0
S3 A:SF4290 2.3 34.5 1.0
S2 A:SF4290 2.4 35.0 1.0
FE3 A:SF4290 2.6 37.8 1.0
FE2 A:SF4290 2.6 38.1 1.0
FE1 A:SF4290 2.6 39.6 1.0
CB B:CYS132 3.2 49.2 1.0
S4 A:SF4290 3.8 42.2 1.0
N B:GLY134 4.2 53.1 1.0
CA B:GLY134 4.3 48.5 1.0
SG A:CYS132 4.5 39.3 1.0
SG A:CYS97 4.5 39.9 1.0
CA B:CYS132 4.6 49.6 1.0
N A:ALA98 4.6 52.1 1.0
SG B:CYS97 4.6 49.9 1.0
CA A:CYS97 4.7 51.8 1.0
CG1 B:VAL130 4.7 66.8 1.0
CD1 B:PHE135 4.8 62.2 1.0
C B:CYS132 4.9 52.0 1.0
N B:GLY133 4.9 52.4 1.0
CE1 B:PHE135 4.9 61.0 1.0

Reference:

S.B.Jang, M.S.Jeong, L.C.Seefeldt, J.W.Peters. Structural and Biochemical Implications of Single Amino Acid Substitutions in the Nucleotide-Dependent Switch Regions of the Nitrogenase Fe Protein From Azotobacter Vinelandii J.Biol.Inorg.Chem. V. 9 1028 2004.
ISSN: ISSN 0949-8257
PubMed: 15549494
DOI: 10.1007/S00775-004-0605-5
Page generated: Sat Aug 3 16:52:13 2024

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