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Iron in PDB 7tpo: Selenium-Incorporated Nitrogenase Fe-Protein (AV2-Se) From A. Vinelandii (1 Mm Ksecn)

Enzymatic activity of Selenium-Incorporated Nitrogenase Fe-Protein (AV2-Se) From A. Vinelandii (1 Mm Ksecn)

All present enzymatic activity of Selenium-Incorporated Nitrogenase Fe-Protein (AV2-Se) From A. Vinelandii (1 Mm Ksecn):
1.18.6.1;

Protein crystallography data

The structure of Selenium-Incorporated Nitrogenase Fe-Protein (AV2-Se) From A. Vinelandii (1 Mm Ksecn), PDB code: 7tpo was solved by T.M.Buscagan, J.T.Kaiser, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.16 / 1.35
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.883, 74.757, 75.144, 90, 90, 90
R / Rfree (%) 17.9 / 20.3

Other elements in 7tpo:

The structure of Selenium-Incorporated Nitrogenase Fe-Protein (AV2-Se) From A. Vinelandii (1 Mm Ksecn) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Selenium-Incorporated Nitrogenase Fe-Protein (AV2-Se) From A. Vinelandii (1 Mm Ksecn) (pdb code 7tpo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Selenium-Incorporated Nitrogenase Fe-Protein (AV2-Se) From A. Vinelandii (1 Mm Ksecn), PDB code: 7tpo:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7tpo

Go back to Iron Binding Sites List in 7tpo
Iron binding site 1 out of 4 in the Selenium-Incorporated Nitrogenase Fe-Protein (AV2-Se) From A. Vinelandii (1 Mm Ksecn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Selenium-Incorporated Nitrogenase Fe-Protein (AV2-Se) From A. Vinelandii (1 Mm Ksecn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:16.3
occ:1.00
 FE1 A:SF4301 0.0 16.3 1.0
FE1 A:SFS302 0.0 16.3 0.0
S4 A:SF4301 2.3 16.3 1.0
SG A:CYS97 2.3 18.7 1.0
S3 A:SF4301 2.3 16.3 1.0
SE4 A:SFS302 2.4 16.3 0.0
SE3 A:SFS302 2.4 16.3 0.0
FE2 A:SF4301 2.7 16.3 1.0
FE2 A:SFS302 2.7 16.3 0.0
CB A:CYS97 3.3 21.6 1.0
CA A:CYS97 3.8 19.1 1.0
N A:ALA98 4.2 15.4 1.0
C A:CYS97 4.3 16.4 1.0
CA A:GLY133 4.5 18.6 1.0
N A:GLY99 4.8 13.5 1.0
N A:GLY133 4.8 17.0 1.0
SG A:CYS132 4.9 18.4 1.0
O A:HOH491 4.9 20.1 1.0

Iron binding site 2 out of 4 in 7tpo

Go back to Iron Binding Sites List in 7tpo
Iron binding site 2 out of 4 in the Selenium-Incorporated Nitrogenase Fe-Protein (AV2-Se) From A. Vinelandii (1 Mm Ksecn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Selenium-Incorporated Nitrogenase Fe-Protein (AV2-Se) From A. Vinelandii (1 Mm Ksecn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:16.3
occ:1.00
 FE2 A:SF4301 0.0 16.3 1.0
FE2 A:SFS302 0.0 16.3 0.0
S3 A:SF4301 2.3 16.3 1.0
S4 A:SF4301 2.3 16.3 1.0
SG A:CYS132 2.3 18.4 1.0
SE3 A:SFS302 2.4 16.3 0.0
SE4 A:SFS302 2.4 16.3 0.0
FE1 A:SF4301 2.7 16.3 1.0
FE1 A:SFS302 2.7 16.3 0.0
CB A:CYS132 3.4 18.2 1.0
C A:CYS132 4.1 17.6 1.0
O A:CYS132 4.3 16.7 1.0
CG2 A:VAL130 4.3 18.7 1.0
CA A:CYS132 4.3 16.1 1.0
N A:GLY133 4.4 17.0 1.0
SG A:CYS97 4.8 18.7 1.0
CB A:VAL130 4.8 18.8 1.0
CA A:GLY133 4.9 18.6 1.0
N A:CYS132 4.9 15.3 1.0

Iron binding site 3 out of 4 in 7tpo

Go back to Iron Binding Sites List in 7tpo
Iron binding site 3 out of 4 in the Selenium-Incorporated Nitrogenase Fe-Protein (AV2-Se) From A. Vinelandii (1 Mm Ksecn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Selenium-Incorporated Nitrogenase Fe-Protein (AV2-Se) From A. Vinelandii (1 Mm Ksecn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:16.3
occ:0.00
 FE1 A:SF4301 0.0 16.3 1.0
FE1 A:SFS302 0.0 16.3 0.0
S4 A:SF4301 2.3 16.3 1.0
SG A:CYS97 2.3 18.7 1.0
S3 A:SF4301 2.3 16.3 1.0
SE4 A:SFS302 2.4 16.3 0.0
SE3 A:SFS302 2.4 16.3 0.0
FE2 A:SF4301 2.7 16.3 1.0
FE2 A:SFS302 2.7 16.3 0.0
CB A:CYS97 3.3 21.6 1.0
CA A:CYS97 3.8 19.1 1.0
N A:ALA98 4.2 15.4 1.0
C A:CYS97 4.3 16.4 1.0
CA A:GLY133 4.5 18.6 1.0
N A:GLY99 4.8 13.5 1.0
N A:GLY133 4.8 17.0 1.0
SG A:CYS132 4.9 18.4 1.0
O A:HOH491 4.9 20.1 1.0

Iron binding site 4 out of 4 in 7tpo

Go back to Iron Binding Sites List in 7tpo
Iron binding site 4 out of 4 in the Selenium-Incorporated Nitrogenase Fe-Protein (AV2-Se) From A. Vinelandii (1 Mm Ksecn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Selenium-Incorporated Nitrogenase Fe-Protein (AV2-Se) From A. Vinelandii (1 Mm Ksecn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:16.3
occ:0.00
 FE2 A:SF4301 0.0 16.3 1.0
FE2 A:SFS302 0.0 16.3 0.0
S3 A:SF4301 2.3 16.3 1.0
S4 A:SF4301 2.3 16.3 1.0
SG A:CYS132 2.3 18.4 1.0
SE3 A:SFS302 2.4 16.3 0.0
SE4 A:SFS302 2.4 16.3 0.0
FE1 A:SF4301 2.7 16.3 1.0
FE1 A:SFS302 2.7 16.3 0.0
CB A:CYS132 3.4 18.2 1.0
C A:CYS132 4.1 17.6 1.0
O A:CYS132 4.3 16.7 1.0
CG2 A:VAL130 4.3 18.7 1.0
CA A:CYS132 4.3 16.1 1.0
N A:GLY133 4.4 17.0 1.0
SG A:CYS97 4.8 18.7 1.0
CB A:VAL130 4.8 18.8 1.0
CA A:GLY133 4.9 18.6 1.0
N A:CYS132 4.9 15.3 1.0

Reference:

T.M.Buscagan, J.T.Kaiser, D.C.Rees. Selenocyanate Derived Se-Incorporation Into the Nitrogenase Fe Protein Cluster. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 35904245
DOI: 10.7554/ELIFE.79311
Page generated: Fri Aug 9 02:03:54 2024

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