Atomistry » Magnesium » PDB 3rr5-3rv4 » 3rtl
Atomistry »
  Magnesium »
    PDB 3rr5-3rv4 »
      3rtl »

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

Go back to Magnesium Binding Sites List in 3rtl
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

Go back to Magnesium Binding Sites List in 3rtl
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

Go back to Magnesium Binding Sites List in 3rtl
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

Go back to Magnesium Binding Sites List in 3rtl
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

Go back to Magnesium Binding Sites List in 3rtl
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: Thu Aug 15 10:38:32 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy