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Iron in PDB 7t4h: Selenium-Incorporated Nitrogenase Fe Protein (AV2-Se) From A. Vinelandii (22 Mm Ksecn, with AV1)

Enzymatic activity of Selenium-Incorporated Nitrogenase Fe Protein (AV2-Se) From A. Vinelandii (22 Mm Ksecn, with AV1)

All present enzymatic activity of Selenium-Incorporated Nitrogenase Fe Protein (AV2-Se) From A. Vinelandii (22 Mm Ksecn, with AV1):
1.18.6.1;

Protein crystallography data

The structure of Selenium-Incorporated Nitrogenase Fe Protein (AV2-Se) From A. Vinelandii (22 Mm Ksecn, with AV1), PDB code: 7t4h 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) 37.38 / 1.51
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.82, 74.754, 74.801, 90, 90, 90
R / Rfree (%) 16.7 / 19.1

Other elements in 7t4h:

The structure of Selenium-Incorporated Nitrogenase Fe Protein (AV2-Se) From A. Vinelandii (22 Mm Ksecn, with AV1) 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 (22 Mm Ksecn, with AV1) (pdb code 7t4h). 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 (22 Mm Ksecn, with AV1), PDB code: 7t4h:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7t4h

Go back to Iron Binding Sites List in 7t4h
Iron binding site 1 out of 4 in the Selenium-Incorporated Nitrogenase Fe Protein (AV2-Se) From A. Vinelandii (22 Mm Ksecn, with AV1)


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 (22 Mm Ksecn, with AV1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:16.0
occ:0.49
 FE1 A:SF4301 0.0 16.0 0.5
FE1 A:SFS302 0.0 16.0 0.5
SG A:CYS97 2.3 17.8 1.0
S4 A:SF4301 2.3 16.0 0.6
S3 A:SF4301 2.3 16.0 0.5
SE4 A:SFS302 2.4 16.0 0.5
SE3 A:SFS302 2.5 16.0 0.5
FE2 A:SF4301 2.8 16.0 0.6
FE2 A:SFS302 2.8 16.0 0.5
CB A:CYS97 3.3 20.4 1.0
CA A:CYS97 3.8 18.5 1.0
N A:ALA98 4.2 14.8 1.0
C A:CYS97 4.3 15.3 1.0
CA A:GLY133 4.4 18.7 1.0
N A:GLY133 4.8 16.9 1.0
N A:GLY99 4.8 14.9 1.0
SG A:CYS132 4.9 17.6 1.0

Iron binding site 2 out of 4 in 7t4h

Go back to Iron Binding Sites List in 7t4h
Iron binding site 2 out of 4 in the Selenium-Incorporated Nitrogenase Fe Protein (AV2-Se) From A. Vinelandii (22 Mm Ksecn, with AV1)


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 (22 Mm Ksecn, with AV1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:16.0
occ:0.55
 FE2 A:SF4301 0.0 16.0 0.6
FE2 A:SFS302 0.0 16.0 0.5
SG A:CYS132 2.3 17.6 1.0
S3 A:SF4301 2.3 16.0 0.5
S4 A:SF4301 2.3 16.0 0.6
SE3 A:SFS302 2.4 16.0 0.5
SE4 A:SFS302 2.5 16.0 0.5
FE1 A:SF4301 2.8 16.0 0.5
FE1 A:SFS302 2.8 16.0 0.5
CB A:CYS132 3.4 18.5 1.0
C A:CYS132 4.0 16.8 1.0
O A:CYS132 4.2 17.4 1.0
CA A:CYS132 4.3 18.1 1.0
CG2 A:VAL130 4.3 18.3 1.0
N A:GLY133 4.3 16.9 1.0
CA A:GLY133 4.8 18.7 1.0
SG A:CYS97 4.8 17.8 1.0
N A:CYS132 4.9 14.9 1.0
CB A:VAL130 4.9 20.4 1.0

Iron binding site 3 out of 4 in 7t4h

Go back to Iron Binding Sites List in 7t4h
Iron binding site 3 out of 4 in the Selenium-Incorporated Nitrogenase Fe Protein (AV2-Se) From A. Vinelandii (22 Mm Ksecn, with AV1)


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 (22 Mm Ksecn, with AV1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:16.0
occ:0.51
 FE1 A:SF4301 0.0 16.0 0.5
FE1 A:SFS302 0.0 16.0 0.5
SG A:CYS97 2.3 17.8 1.0
S4 A:SF4301 2.3 16.0 0.6
S3 A:SF4301 2.3 16.0 0.5
SE4 A:SFS302 2.4 16.0 0.5
SE3 A:SFS302 2.5 16.0 0.5
FE2 A:SF4301 2.8 16.0 0.6
FE2 A:SFS302 2.8 16.0 0.5
CB A:CYS97 3.3 20.4 1.0
CA A:CYS97 3.8 18.5 1.0
N A:ALA98 4.2 14.8 1.0
C A:CYS97 4.3 15.3 1.0
CA A:GLY133 4.4 18.7 1.0
N A:GLY133 4.8 16.9 1.0
N A:GLY99 4.8 14.9 1.0
SG A:CYS132 4.9 17.6 1.0

Iron binding site 4 out of 4 in 7t4h

Go back to Iron Binding Sites List in 7t4h
Iron binding site 4 out of 4 in the Selenium-Incorporated Nitrogenase Fe Protein (AV2-Se) From A. Vinelandii (22 Mm Ksecn, with AV1)


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 (22 Mm Ksecn, with AV1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:16.0
occ:0.45
 FE2 A:SF4301 0.0 16.0 0.6
FE2 A:SFS302 0.0 16.0 0.5
SG A:CYS132 2.3 17.6 1.0
S3 A:SF4301 2.3 16.0 0.5
S4 A:SF4301 2.3 16.0 0.6
SE3 A:SFS302 2.4 16.0 0.5
SE4 A:SFS302 2.5 16.0 0.5
FE1 A:SF4301 2.8 16.0 0.5
FE1 A:SFS302 2.8 16.0 0.5
CB A:CYS132 3.4 18.5 1.0
C A:CYS132 4.0 16.8 1.0
O A:CYS132 4.2 17.4 1.0
CA A:CYS132 4.3 18.1 1.0
CG2 A:VAL130 4.3 18.3 1.0
N A:GLY133 4.3 16.9 1.0
CA A:GLY133 4.8 18.7 1.0
SG A:CYS97 4.8 17.8 1.0
N A:CYS132 4.9 14.9 1.0
CB A:VAL130 4.9 20.4 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 01:01:55 2024

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