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Iron in PDB 3rur: Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2

Protein crystallography data

The structure of Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2, PDB code: 3rur was solved by C.F.M.Gaudin, J.C.Grigg, A.L.Arrieta, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.814, 79.378, 113.869, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.2

Other elements in 3rur:

The structure of Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2 also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2 (pdb code 3rur). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2, PDB code: 3rur:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3rur

Go back to Iron Binding Sites List in 3rur
Iron binding site 1 out of 4 in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:23.2
occ:1.00
 FE A:HEM200 0.0 23.2 1.0
NA A:HEM200 2.0 23.6 1.0
NC A:HEM200 2.0 23.7 1.0
ND A:HEM200 2.0 20.4 1.0
NB A:HEM200 2.1 23.9 1.0
OH A:TYR440 2.4 29.5 1.0
SE A:MSE362 2.7 21.4 0.8
C1A A:HEM200 3.0 24.9 1.0
C1D A:HEM200 3.0 18.3 1.0
C4D A:HEM200 3.0 21.5 1.0
C4C A:HEM200 3.0 20.7 1.0
C4A A:HEM200 3.0 26.0 1.0
C1C A:HEM200 3.0 22.7 1.0
C4B A:HEM200 3.1 23.3 1.0
C1B A:HEM200 3.1 23.8 1.0
CZ A:TYR440 3.3 29.4 1.0
CHA A:HEM200 3.4 23.9 1.0
CHD A:HEM200 3.4 18.0 1.0
CHC A:HEM200 3.4 24.8 1.0
CHB A:HEM200 3.5 23.1 1.0
CG A:MSE362 3.6 19.5 0.2
CG A:MSE362 3.8 16.4 0.8
CE A:MSE362 3.8 17.0 0.8
CE2 A:TYR440 4.0 29.1 1.0
CE1 A:TYR440 4.1 31.0 1.0
OH A:TYR444 4.1 24.1 1.0
C3C A:HEM200 4.3 24.2 1.0
C3A A:HEM200 4.3 28.7 1.0
C2D A:HEM200 4.3 19.1 1.0
C2C A:HEM200 4.3 24.6 1.0
C2A A:HEM200 4.3 30.4 1.0
C3D A:HEM200 4.3 18.8 1.0
C2B A:HEM200 4.3 24.9 1.0
C3B A:HEM200 4.4 28.1 1.0
CE2 A:TYR444 4.4 20.2 1.0
CB A:MSE362 4.4 18.0 0.2
CB A:MSE362 4.5 16.8 0.8
CZ A:TYR444 4.6 21.0 1.0
CE A:MSE362 4.8 23.6 0.2

Iron binding site 2 out of 4 in 3rur

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Iron binding site 2 out of 4 in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe200

b:20.6
occ:1.00
 FE B:HEM200 0.0 20.6 1.0
NB B:HEM200 2.0 20.5 1.0
ND B:HEM200 2.0 20.3 1.0
NA B:HEM200 2.0 17.2 1.0
NC B:HEM200 2.0 19.8 1.0
OH B:TYR440 2.2 19.3 1.0
SE B:MSE362 2.7 19.2 0.2
C4A B:HEM200 3.0 15.7 1.0
C4C B:HEM200 3.0 21.6 1.0
C1B B:HEM200 3.0 18.3 1.0
C1A B:HEM200 3.1 17.7 1.0
C4B B:HEM200 3.1 21.4 1.0
CZ B:TYR440 3.1 19.6 1.0
C4D B:HEM200 3.1 18.2 1.0
C1C B:HEM200 3.1 23.4 1.0
C1D B:HEM200 3.1 20.7 1.0
CHB B:HEM200 3.4 18.0 1.0
CHD B:HEM200 3.4 19.9 1.0
CHC B:HEM200 3.4 22.0 1.0
CHA B:HEM200 3.4 16.2 1.0
CG B:MSE362 3.5 18.8 0.2
CG B:MSE362 3.5 21.1 0.8
CE2 B:TYR440 3.6 20.5 1.0
CE1 B:TYR440 3.9 20.8 1.0
OH B:TYR444 4.1 20.8 1.0
CE B:MSE362 4.1 25.6 0.8
C3A B:HEM200 4.2 16.9 1.0
C3C B:HEM200 4.2 23.3 1.0
C2A B:HEM200 4.3 16.3 1.0
C3B B:HEM200 4.3 21.2 1.0
C2C B:HEM200 4.3 24.6 1.0
C2B B:HEM200 4.3 20.0 1.0
C3D B:HEM200 4.3 19.8 1.0
C2D B:HEM200 4.3 21.2 1.0
CB B:MSE362 4.3 19.1 0.8
CE2 B:TYR444 4.4 18.7 1.0
CB B:MSE362 4.5 17.8 0.2
CZ B:TYR444 4.5 15.9 1.0
CE B:MSE362 4.6 21.3 0.2
SE B:MSE362 4.8 25.1 0.8
CD2 B:TYR440 4.8 22.7 1.0

Iron binding site 3 out of 4 in 3rur

Go back to Iron Binding Sites List in 3rur
Iron binding site 3 out of 4 in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe200

b:19.9
occ:1.00
 FE C:HEM200 0.0 19.9 1.0
ND C:HEM200 2.0 19.2 1.0
NB C:HEM200 2.0 19.3 1.0
NC C:HEM200 2.0 21.4 1.0
NA C:HEM200 2.1 17.4 1.0
OH C:TYR440 2.3 19.6 1.0
SE C:MSE362 2.6 22.4 0.8
C1D C:HEM200 3.0 20.6 1.0
C4A C:HEM200 3.0 17.5 1.0
C4C C:HEM200 3.0 23.4 1.0
C1B C:HEM200 3.1 17.1 1.0
C4D C:HEM200 3.1 17.9 1.0
C4B C:HEM200 3.1 20.7 1.0
C1C C:HEM200 3.1 23.0 1.0
C1A C:HEM200 3.1 18.4 1.0
CZ C:TYR440 3.2 23.1 1.0
CHD C:HEM200 3.4 18.6 1.0
CHB C:HEM200 3.4 15.8 1.0
CHC C:HEM200 3.5 21.9 1.0
CG C:MSE362 3.5 18.4 0.2
CHA C:HEM200 3.5 18.3 1.0
CE C:MSE362 3.6 19.0 0.8
CG C:MSE362 3.7 17.8 0.8
CE2 C:TYR440 3.9 24.9 1.0
CE1 C:TYR440 4.0 23.3 1.0
OH C:TYR444 4.2 18.5 1.0
C3A C:HEM200 4.3 16.3 1.0
C3C C:HEM200 4.3 23.6 1.0
C2D C:HEM200 4.3 21.1 1.0
C3D C:HEM200 4.3 21.8 1.0
C2A C:HEM200 4.3 18.0 1.0
C3B C:HEM200 4.3 21.3 1.0
C2C C:HEM200 4.3 23.8 1.0
C2B C:HEM200 4.3 19.0 1.0
CE C:MSE362 4.3 20.2 0.2
CB C:MSE362 4.4 16.4 0.2
CB C:MSE362 4.4 16.1 0.8
CE2 C:TYR444 4.6 16.7 1.0
CZ C:TYR444 4.7 18.4 1.0
SE C:MSE362 4.7 21.9 0.2

Iron binding site 4 out of 4 in 3rur

Go back to Iron Binding Sites List in 3rur
Iron binding site 4 out of 4 in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe200

b:21.5
occ:1.00
 FE D:HEM200 0.0 21.5 1.0
ND D:HEM200 2.0 20.2 1.0
NC D:HEM200 2.0 22.9 1.0
NB D:HEM200 2.1 22.8 1.0
NA D:HEM200 2.1 19.7 1.0
OH D:TYR440 2.2 22.4 1.0
SE D:MSE362 2.5 27.3 0.2
C4C D:HEM200 3.0 23.8 1.0
C4A D:HEM200 3.0 17.5 1.0
CZ D:TYR440 3.0 22.9 1.0
C1D D:HEM200 3.1 22.8 1.0
C4D D:HEM200 3.1 19.4 1.0
C1C D:HEM200 3.1 23.3 1.0
C1A D:HEM200 3.1 16.8 1.0
C1B D:HEM200 3.1 19.7 1.0
C4B D:HEM200 3.1 19.0 1.0
CHD D:HEM200 3.4 22.4 1.0
CHB D:HEM200 3.4 19.1 1.0
CG D:MSE362 3.5 20.0 0.2
CHA D:HEM200 3.5 19.4 1.0
CHC D:HEM200 3.5 22.1 1.0
CG D:MSE362 3.5 14.9 0.8
CE2 D:TYR440 3.7 25.9 1.0
CE1 D:TYR440 3.9 24.6 1.0
OH D:TYR444 4.1 22.4 1.0
CE D:MSE362 4.1 23.5 0.2
CE D:MSE362 4.2 20.5 0.8
C3A D:HEM200 4.3 16.9 1.0
C3C D:HEM200 4.3 24.7 1.0
C2C D:HEM200 4.3 24.0 1.0
C2A D:HEM200 4.3 15.5 1.0
C2D D:HEM200 4.3 21.8 1.0
C3B D:HEM200 4.3 21.8 1.0
C3D D:HEM200 4.3 21.6 1.0
CB D:MSE362 4.3 18.7 0.2
CB D:MSE362 4.3 17.8 0.8
CE2 D:TYR444 4.3 20.3 1.0
C2B D:HEM200 4.3 19.9 1.0
CZ D:TYR444 4.5 19.1 1.0
SE D:MSE362 4.8 22.3 0.8
CD2 D:TYR440 4.9 28.5 1.0
CG2 D:VAL433 4.9 24.7 1.0

Reference:

C.F.Gaudin, J.C.Grigg, A.L.Arrieta, M.E.Murphy. Unique Heme-Iron Coordination By the Hemoglobin Receptor Isdb of Staphylococcus Aureus. Biochemistry V. 50 5443 2011.
ISSN: ISSN 0006-2960
PubMed: 21574663
DOI: 10.1021/BI200369P
Page generated: Sun Aug 4 19:45:57 2024

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