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Magnesium in PDB 3rtl: Staphylococcus Aureus Heme-Bound Isdb-N2

Protein crystallography data

The structure of Staphylococcus Aureus Heme-Bound Isdb-N2, PDB code: 3rtl 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) 67.42 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.527, 82.608, 116.888, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.7

Other elements in 3rtl:

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

Iron (Fe) 4 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Staphylococcus Aureus Heme-Bound Isdb-N2 (pdb code 3rtl). 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 Isdb-N2, PDB code: 3rtl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3rtl

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Magnesium binding site 1 out of 5 in the Staphylococcus Aureus Heme-Bound 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 Isdb-N2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg50

b:15.3
occ:1.00
 O B:HOH503 2.0 13.8 1.0
O B:HOH606 2.1 17.3 1.0
OE2 A:GLU354 2.1 13.1 1.0
O A:HOH614 2.1 15.9 1.0
O A:HOH87 2.1 15.9 1.0
O A:HOH229 2.1 15.8 1.0
CD A:GLU354 3.1 14.0 1.0
OE1 A:GLU354 3.4 14.8 1.0
O A:HOH51 4.0 15.6 1.0
OD1 A:ASN359 4.0 14.4 1.0
O B:HOH193 4.0 19.8 1.0
O A:HOH33 4.1 14.6 1.0
O A:HOH117 4.1 21.7 1.0
O B:HOH68 4.1 18.1 1.0
OE1 A:GLU357 4.1 27.0 1.0
OD2 B:ASP364 4.2 12.9 1.0
ND2 A:ASN359 4.3 13.0 1.0
CG A:GLU354 4.4 11.6 1.0
CG A:ASN359 4.6 13.6 1.0
O B:HOH461 4.7 29.1 1.0
CD A:GLU357 4.8 25.0 1.0

Magnesium binding site 2 out of 5 in 3rtl

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Magnesium binding site 2 out of 5 in the Staphylococcus Aureus Heme-Bound 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 Isdb-N2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:18.8
occ:0.80
 O B:HOH624 1.5 13.0 0.8
O B:HOH622 1.9 18.8 0.8
O A:HOH625 2.0 19.7 0.8
O A:HOH623 2.1 12.1 0.8
OE2 B:GLU354 2.1 13.0 1.0
O B:HOH626 2.5 13.9 0.8
CD B:GLU354 3.1 10.6 1.0
OE1 B:GLU354 3.3 14.2 1.0
O B:HOH14 4.0 17.7 1.0
O B:HOH478 4.1 29.7 1.0
OD2 A:ASP364 4.3 12.4 1.0
O A:HOH318 4.3 24.4 1.0
CG B:GLU354 4.4 9.8 1.0
O A:HOH165 4.4 20.5 1.0
OD1 B:ASN359 4.4 14.2 1.0
O2D B:HEM200 4.5 17.2 0.5
O1A B:HEM200 4.7 7.9 0.5
O A:ASP364 4.8 12.2 1.0
OG1 A:THR365 4.8 12.4 1.0
OE2 B:GLU357 5.0 29.9 1.0
CA A:THR365 5.0 11.8 1.0

Magnesium binding site 3 out of 5 in 3rtl

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Magnesium binding site 3 out of 5 in the Staphylococcus Aureus Heme-Bound 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 Isdb-N2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg56

b:15.4
occ:1.00
 O B:HOH615 2.0 16.4 1.0
OD2 B:ASP428 2.0 17.5 1.0
O B:HOH504 2.1 17.7 1.0
OD2 C:ASP428 2.1 16.6 1.0
O C:HOH29 2.1 16.6 1.0
O C:HOH605 2.1 16.4 1.0
CG B:ASP428 3.2 15.1 1.0
CG C:ASP428 3.3 14.7 1.0
O C:HOH80 4.0 18.8 1.0
OD1 B:ASP428 4.0 15.3 1.0
OD1 C:ASP428 4.1 16.2 1.0
CB B:ASP428 4.1 13.9 1.0
OE2 B:GLU398 4.1 15.9 1.0
O B:HOH16 4.1 18.6 1.0
CB C:ASP428 4.1 13.1 1.0
O B:HOH217 4.1 27.5 1.0
OE1 B:GLU398 4.2 19.5 1.0
OE2 C:GLU398 4.2 14.9 1.0
O C:HOH530 4.2 36.0 1.0
O C:HOH249 4.2 25.7 1.0
O B:HOH619 4.2 34.1 1.0
OE1 C:GLU398 4.2 18.8 1.0
CD B:GLU398 4.6 17.8 1.0
CD C:GLU398 4.7 16.6 1.0

Magnesium binding site 4 out of 5 in 3rtl

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Magnesium binding site 4 out of 5 in the Staphylococcus Aureus Heme-Bound 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 Isdb-N2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg18

b:19.9
occ:1.00
 O C:HOH595 1.6 19.1 1.0
O D:HOH608 1.9 23.3 1.0
O C:HOH510 2.0 20.3 1.0
O C:HOH617 2.1 20.1 1.0
OE2 C:GLU354 2.2 13.8 1.0
O D:HOH486 2.3 16.3 1.0
CD C:GLU354 3.2 12.6 1.0
OE1 C:GLU354 3.4 14.9 1.0
O D:HOH131 3.6 22.9 1.0
O C:HOH66 3.9 19.9 1.0
O C:HOH498 3.9 28.9 1.0
O D:HOH293 4.0 25.3 1.0
OD2 D:ASP364 4.1 13.3 1.0
OE2 C:GLU357 4.1 28.3 1.0
OD1 C:ASN359 4.1 14.6 1.0
ND2 C:ASN359 4.3 12.5 1.0
O C:HOH37 4.5 18.1 1.0
CG C:GLU354 4.6 11.5 1.0
CD C:GLU357 4.6 26.1 1.0
CG C:ASN359 4.7 11.8 1.0
O D:HOH464 4.8 26.9 1.0
CG C:GLU357 4.8 22.0 1.0
CB C:GLU357 4.9 17.2 1.0
CE1 D:HIS369 5.0 16.6 1.0
O C:HOH163 5.0 23.6 1.0
O C:HOH513 5.0 32.6 1.0

Magnesium binding site 5 out of 5 in 3rtl

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Magnesium binding site 5 out of 5 in the Staphylococcus Aureus Heme-Bound 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 Isdb-N2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4

b:16.0
occ:1.00
 O C:HOH607 2.0 18.1 1.0
O C:HOH127 2.1 15.7 1.0
O D:HOH22 2.1 16.6 1.0
OE2 D:GLU354 2.1 13.5 1.0
O D:HOH616 2.1 16.4 1.0
O D:HOH602 2.1 16.5 1.0
CD D:GLU354 3.1 14.3 1.0
OE1 D:GLU354 3.4 16.1 1.0
O D:HOH65 4.0 17.3 1.0
OD1 D:ASN359 4.0 16.2 1.0
O D:HOH45 4.1 14.5 1.0
OE2 D:GLU357 4.1 24.2 1.0
O D:HOH144 4.1 21.4 1.0
O C:HOH39 4.1 20.6 1.0
O C:HOH111 4.1 17.9 1.0
OD2 C:ASP364 4.2 12.9 1.0
ND2 D:ASN359 4.2 13.4 1.0
CG D:GLU354 4.5 13.3 1.0
CG D:ASN359 4.6 13.6 1.0
O D:HOH296 4.7 28.9 1.0
CD D:GLU357 4.7 24.5 1.0
O C:HOH326 4.8 33.1 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 02:50:36 2025

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