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Magnesium 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:

Iron (Fe) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2, PDB code: 3rur:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3rur

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Magnesium binding site 1 out of 5 in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg495

b:22.3
occ:1.00
 O D:HOH489 2.0 26.0 1.0
O D:HOH180 2.1 25.7 1.0
O A:HOH151 2.1 24.3 1.0
OE2 A:GLU354 2.1 19.8 1.0
O A:HOH526 2.1 22.3 1.0
O A:HOH185 2.2 24.2 1.0
CD A:GLU354 3.1 21.2 1.0
OE1 A:GLU354 3.4 22.7 1.0
O A:HOH92 4.0 27.1 1.0
O A:HOH110 4.0 25.0 1.0
O D:HOH510 4.1 38.3 1.0
OD1 A:ASN359 4.1 23.3 1.0
ND2 A:ASN359 4.3 19.4 1.0
OD2 D:ASP364 4.3 21.3 1.0
CG A:GLU354 4.4 18.2 1.0
O D:HOH131 4.5 29.5 1.0
CG A:GLU357 4.6 28.1 1.0
CG A:ASN359 4.6 18.6 1.0
CB A:GLU357 4.8 23.3 1.0
O D:ASP364 4.8 19.3 1.0

Magnesium binding site 2 out of 5 in 3rur

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Magnesium binding site 2 out of 5 in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg225

b:27.9
occ:1.00
 O C:HOH57 1.6 25.9 1.0
O B:HOH469 2.0 31.1 1.0
O C:HOH461 2.0 37.0 1.0
O B:HOH528 2.1 30.7 1.0
OE2 B:GLU354 2.2 22.7 1.0
O C:HOH75 2.4 24.7 1.0
CD B:GLU354 3.1 22.4 1.0
O C:HOH293 3.1 30.4 1.0
OE1 B:GLU354 3.4 24.1 1.0
O C:HOH28 3.7 27.2 1.0
O C:HOH462 3.8 41.1 1.0
O B:HOH508 3.9 26.0 1.0
OD1 B:ASN359 4.0 21.2 1.0
OD2 C:ASP364 4.1 19.1 1.0
ND2 B:ASN359 4.3 16.4 1.0
O B:HOH100 4.4 24.1 1.0
CG B:GLU354 4.5 19.9 1.0
CG B:ASN359 4.6 19.2 1.0
OE2 B:GLU357 4.7 40.3 1.0
O B:HOH462 4.9 36.6 1.0
CB B:GLU357 4.9 25.6 1.0
CG B:GLU357 5.0 30.3 1.0

Magnesium binding site 3 out of 5 in 3rur

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Magnesium binding site 3 out of 5 in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg95

b:20.2
occ:1.00
 O C:HOH96 2.0 22.5 1.0
OE2 C:GLU354 2.1 18.0 1.0
O B:HOH524 2.1 22.0 1.0
O C:HOH504 2.1 21.5 1.0
O C:HOH98 2.1 24.5 1.0
O B:HOH99 2.1 23.1 1.0
CD C:GLU354 3.0 20.5 1.0
OE1 C:GLU354 3.3 23.0 1.0
OE2 C:GLU357 4.0 33.1 1.0
O C:HOH55 4.0 22.9 1.0
O C:HOH148 4.0 30.5 1.0
O B:HOH102 4.0 24.4 1.0
ND2 C:ASN359 4.0 16.9 1.0
O C:HOH506 4.1 17.4 1.0
O B:HOH149 4.1 28.7 1.0
OD2 B:ASP364 4.1 21.1 1.0
OD1 C:ASN359 4.4 21.9 1.0
CG C:GLU354 4.4 17.7 1.0
CD C:GLU357 4.6 32.8 1.0
CG C:ASN359 4.7 19.4 1.0
CG C:GLU357 4.9 27.9 1.0
CB C:GLU357 4.9 22.6 1.0

Magnesium binding site 4 out of 5 in 3rur

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Magnesium binding site 4 out of 5 in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg166

b:21.6
occ:1.00
 OD2 D:ASP428 2.0 26.6 1.0
O C:HOH155 2.0 23.8 1.0
O C:HOH91 2.0 24.6 1.0
O D:HOH499 2.0 25.9 1.0
O C:HOH525 2.1 24.7 1.0
OD2 C:ASP428 2.1 24.5 1.0
CG D:ASP428 3.1 22.9 1.0
CG C:ASP428 3.3 20.4 1.0
CB D:ASP428 3.9 20.3 1.0
CB C:ASP428 4.0 18.6 1.0
OD1 D:ASP428 4.0 23.0 1.0
OE2 D:GLU398 4.1 25.2 1.0
OE1 D:GLU398 4.1 30.1 1.0
OE2 C:GLU398 4.1 23.3 1.0
O D:HOH171 4.2 32.8 1.0
OE1 C:GLU398 4.2 28.7 1.0
OD1 C:ASP428 4.2 21.1 1.0
O C:HOH85 4.2 35.6 1.0
O C:HOH517 4.3 39.1 1.0
O D:HOH129 4.4 31.4 1.0
CD D:GLU398 4.5 25.9 1.0
O C:HOH487 4.5 47.0 1.0
CD C:GLU398 4.6 24.8 1.0
O C:HOH274 4.6 36.7 1.0
CD2 C:LEU426 4.9 25.9 1.0
N D:ASP428 5.0 20.0 1.0

Magnesium binding site 5 out of 5 in 3rur

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Magnesium binding site 5 out of 5 in the Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Staphylococcus Aureus Heme-Bound Selenomethionine-Labeled Isdb-N2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg460

b:25.6
occ:1.00
 O D:HOH184 1.8 25.5 1.0
O A:HOH485 2.0 22.0 1.0
OE2 D:GLU354 2.0 18.9 1.0
O D:HOH498 2.1 29.2 1.0
O A:HOH527 2.1 27.7 1.0
O D:HOH54 2.4 20.8 1.0
CD D:GLU354 3.0 22.1 1.0
OE1 D:GLU354 3.4 20.4 1.0
O D:HOH507 3.8 22.9 1.0
OD2 A:ASP364 4.2 18.9 1.0
ND2 D:ASN359 4.2 18.0 1.0
O D:HOH513 4.2 38.8 1.0
CG D:GLU354 4.3 17.3 1.0
O A:HOH106 4.3 27.9 1.0
O A:ASP364 4.5 16.8 1.0
O2A D:HEM200 4.6 18.4 1.0
OG1 A:THR365 4.6 18.7 1.0
CA A:THR365 4.8 17.6 1.0
C A:ASP364 5.0 16.6 1.0
NE2 A:HIS369 5.0 27.5 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: Mon Aug 11 02:51:06 2025

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