Magnesium in PDB 6h4m: Tarp-Udp-Glcnac-3RBOP

The structure of Tarp-Udp-Glcnac-3RBOP, PDB code: 6h4m was solved by Y.Guo, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.44 / 2.73
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	95.170, 210.750, 123.200, 90.00, 91.92, 90.00
R / Rfree (%)	18.9 / 23.3

The structure of Tarp-Udp-Glcnac-3RBOP also contains other interesting chemical elements:

Chlorine

(Cl)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Magnesium atom in the Tarp-Udp-Glcnac-3RBOP (pdb code 6h4m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the Tarp-Udp-Glcnac-3RBOP, PDB code: 6h4m:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in the Tarp-Udp-Glcnac-3RBOP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tarp-Udp-Glcnac-3RBOP within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:55.7 occ:1.00 OD2 B:ASP316 3.3 58.4 1.0 OD2 C:ASP316 3.3 58.8 1.0 OD2 F:ASP316 4.0 76.5 1.0 CG B:ASP316 4.2 46.0 1.0 CG C:ASP316 4.3 48.6 1.0 OD1 B:ASP316 4.4 56.7 1.0 OD1 C:ASP316 4.5 67.5 1.0 CB B:ALA319 4.6 34.6 1.0 CB C:LEU318 4.8 36.5 1.0 CB B:LEU318 4.8 34.2 1.0 N B:ALA319 4.8 31.7 1.0 CA B:ALA319 5.0 31.4 1.0

Magnesium binding site 2 out of 15 in the Tarp-Udp-Glcnac-3RBOP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tarp-Udp-Glcnac-3RBOP within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:40.7 occ:1.00 O2B B:UD1402 2.4 51.5 1.0 O2A B:UD1402 2.5 69.3 1.0 O B:HOH570 3.2 43.6 1.0 OD1 B:ASP95 3.5 45.6 1.0 PA B:UD1402 3.7 54.6 1.0 PB B:UD1402 3.8 71.8 1.0 OD2 B:ASP95 4.1 38.9 1.0 CG B:ASP95 4.1 41.3 1.0 O B:VAL207 4.2 54.4 1.0 O3A B:UD1402 4.2 57.9 1.0 CB B:ASP92 4.3 39.5 1.0 O1' B:UD1402 4.3 0.9 1.0 CB B:ASP94 4.3 71.0 1.0 O1A B:UD1402 4.3 80.4 1.0 OD2 B:ASP92 4.4 44.7 1.0 CG B:ASP92 4.8 47.4 1.0 N B:ASP94 4.9 45.0 1.0 N2' B:UD1402 5.0 0.1 1.0

Magnesium binding site 3 out of 15 in the Tarp-Udp-Glcnac-3RBOP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tarp-Udp-Glcnac-3RBOP within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:55.1 occ:1.00 O2A C:UD1402 2.6 73.6 1.0 O2B C:UD1402 2.8 63.6 1.0 OD1 C:ASP95 3.4 58.1 1.0 PA C:UD1402 3.6 82.5 1.0 O C:VAL207 3.7 72.1 1.0 O1A C:UD1402 3.9 92.0 1.0 OD2 C:ASP95 4.0 61.4 1.0 CG C:ASP95 4.1 61.9 1.0 PB C:UD1402 4.1 72.8 1.0 O3A C:UD1402 4.3 70.0 1.0 OD2 C:ASP92 4.6 66.9 1.0 CB C:ASP94 4.6 96.0 1.0 CB C:ASP92 4.6 57.0 1.0 CG1 C:VAL206 4.7 59.9 1.0 C C:VAL207 4.8 66.4 1.0 C8' C:UD1402 4.9 69.4 1.0 O1' C:UD1402 4.9 0.8 1.0 N2' C:UD1402 5.0 83.7 1.0

Magnesium binding site 4 out of 15 in the Tarp-Udp-Glcnac-3RBOP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tarp-Udp-Glcnac-3RBOP within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg403 b:50.7 occ:1.00 O2B F:UD1402 2.4 47.8 1.0 O2A F:UD1402 2.5 65.5 1.0 OD1 F:ASP95 3.4 45.6 1.0 C8' F:UD1402 3.6 90.0 1.0 PB F:UD1402 3.7 60.3 1.0 PA F:UD1402 3.8 66.6 1.0 OD2 F:ASP95 3.8 42.5 1.0 CG F:ASP95 4.0 44.4 1.0 O F:VAL207 4.0 49.5 1.0 O3A F:UD1402 4.2 73.9 1.0 OD2 F:ASP92 4.2 53.4 1.0 CB F:ASP92 4.3 37.6 1.0 O1' F:UD1402 4.3 0.8 1.0 O1A F:UD1402 4.4 82.2 1.0 N2' F:UD1402 4.4 0.7 1.0 CB F:ASP94 4.6 69.1 1.0 C7' F:UD1402 4.6 93.2 1.0 CG F:ASP92 4.7 42.0 1.0 CG1 F:VAL206 4.9 48.5 1.0

Magnesium binding site 5 out of 15 in the Tarp-Udp-Glcnac-3RBOP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tarp-Udp-Glcnac-3RBOP within 5.0Å range: probe atom residue distance (Å) B Occ O:Mg403 b:45.7 occ:1.00 O2A O:UD1402 2.4 87.0 1.0 O2B O:UD1402 2.5 56.4 1.0 OD1 O:ASP95 3.5 41.0 1.0 PA O:UD1402 3.6 62.6 1.0 PB O:UD1402 3.8 71.8 1.0 OD2 O:ASP95 3.8 35.2 1.0 CG O:ASP95 4.0 37.6 1.0 OD2 O:ASP92 4.1 41.9 1.0 O3A O:UD1402 4.1 84.8 1.0 O1A O:UD1402 4.2 94.3 1.0 O O:VAL207 4.2 44.9 1.0 CB O:ASP92 4.2 34.7 1.0 C8' O:UD1402 4.2 82.9 1.0 N2' O:UD1402 4.3 0.3 1.0 O1' O:UD1402 4.4 0.9 1.0 CG O:ASP92 4.6 37.9 1.0 CB O:ASP94 4.8 68.6 1.0 C7' O:UD1402 4.8 0.1 1.0 CG1 O:VAL206 4.9 41.9 1.0 O5B O:UD1402 4.9 52.7 1.0

Magnesium binding site 6 out of 15 in the Tarp-Udp-Glcnac-3RBOP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Tarp-Udp-Glcnac-3RBOP within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg403 b:56.4 occ:1.00 OAF P:FQ8401 3.6 95.5 1.0 O2B P:UDP402 4.0 0.9 1.0

Magnesium binding site 7 out of 15 in the Tarp-Udp-Glcnac-3RBOP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Tarp-Udp-Glcnac-3RBOP within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg403 b:44.4 occ:1.00 O2A E:UD1402 2.3 54.5 1.0 O2B E:UD1402 3.1 0.8 1.0 OD1 E:ASP95 3.4 53.1 1.0 PA E:UD1402 3.6 56.0 1.0 OD2 E:ASP95 3.9 52.7 1.0 CG E:ASP95 3.9 45.0 1.0 O1A E:UD1402 4.0 48.5 1.0 O E:VAL207 4.1 53.8 1.0 CB E:ASP92 4.2 47.8 1.0 PB E:UD1402 4.2 95.5 1.0 OD2 E:ASP92 4.3 63.8 1.0 CB E:ASP94 4.3 62.7 1.0 O3A E:UD1402 4.4 79.6 1.0 O1' E:UD1402 4.6 0.2 1.0 CG E:ASP92 4.7 49.1 1.0 O5B E:UD1402 4.8 43.5 1.0 N E:ASP94 4.9 40.3 1.0

Magnesium binding site 8 out of 15 in the Tarp-Udp-Glcnac-3RBOP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Tarp-Udp-Glcnac-3RBOP within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg403 b:46.5 occ:1.00 O2B G:UD1402 2.3 81.2 1.0 O2A G:UD1402 2.9 89.4 1.0 OD1 G:ASP95 3.1 52.8 1.0 OD2 G:ASP95 3.7 49.8 1.0 PB G:UD1402 3.8 82.5 1.0 CG G:ASP95 3.8 57.7 1.0 O G:VAL207 3.8 75.9 1.0 PA G:UD1402 3.9 77.5 1.0 O G:HOH551 4.2 58.5 1.0 O3A G:UD1402 4.2 98.7 1.0 CB G:ASP92 4.4 52.5 1.0 OD2 G:ASP92 4.5 51.5 1.0 O1' G:UD1402 4.5 0.6 1.0 O1A G:UD1402 4.5 87.0 1.0 CB G:ASP94 4.5 85.7 1.0 CG1 G:VAL206 4.6 52.1 1.0 N2' G:UD1402 4.9 0.6 1.0 C G:VAL207 4.9 59.2 1.0 O1B G:UD1402 4.9 0.2 1.0 CG G:ASP92 5.0 47.6 1.0

Magnesium binding site 9 out of 15 in the Tarp-Udp-Glcnac-3RBOP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Tarp-Udp-Glcnac-3RBOP within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg403 b:53.8 occ:1.00 OD2 E:ASP316 3.7 60.2 1.0 OD2 G:ASP316 3.7 68.2 1.0 OD2 Q:ASP316 3.7 52.7 1.0 CG Q:ASP316 4.6 47.3 1.0 CG E:ASP316 4.6 50.4 1.0 CG G:ASP316 4.7 56.2 1.0 OD1 Q:ASP316 4.8 67.7 1.0 OD1 E:ASP316 4.8 52.7 1.0 CB G:ALA319 4.8 44.9 1.0 CB Q:LEU318 4.9 34.6 1.0 CB Q:ALA319 4.9 36.3 1.0 CD1 Q:ILE322 4.9 45.2 1.0 OD1 G:ASP316 5.0 70.2 1.0

Magnesium binding site 10 out of 15 in the Tarp-Udp-Glcnac-3RBOP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Tarp-Udp-Glcnac-3RBOP within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:52.4 occ:1.00 O2B A:UD1402 2.1 72.5 1.0 OD2 A:ASP94 2.4 72.8 1.0 OD1 A:ASP94 2.8 71.2 1.0 O2A A:UD1402 2.9 70.6 1.0 CG A:ASP94 3.0 80.5 1.0 OD1 A:ASP95 3.2 40.3 1.0 PB A:UD1402 3.5 67.2 1.0 OD2 A:ASP95 3.8 40.3 1.0 CG A:ASP95 3.9 43.2 1.0 PA A:UD1402 4.0 72.1 1.0 O A:VAL207 4.0 47.0 1.0 O1' A:UD1402 4.1 93.7 1.0 O3A A:UD1402 4.2 83.7 1.0 OD2 A:ASP92 4.4 43.7 1.0 CB A:ASP92 4.5 36.7 1.0 CB A:ASP94 4.5 69.0 1.0 N2' A:UD1402 4.5 0.6 1.0 O1A A:UD1402 4.6 72.0 1.0 O1B A:UD1402 4.7 87.3 1.0 CG1 A:VAL206 4.7 53.8 1.0 CG A:ASP92 4.9 42.0 1.0 C8' A:UD1402 4.9 84.8 1.0

D.Gerlach, Y.Guo, C.De Castro, S.H.Kim, K.Schlatterer, F.F.Xu, C.Pereira, P.H.Seeberger, S.Ali, J.Codee, W.Sirisarn, B.Schulte, C.Wolz, J.Larsen, A.Molinaro, B.L.Lee, G.Xia, T.Stehle, A.Peschel. Methicillin-Resistant Staphylococcus Aureus Alters Cell Wall Glycosylation to Evade Immunity. Nature V. 563 705 2018.
ISSN: ESSN 1476-4687
PubMed: 30464342
DOI: 10.1038/S41586-018-0730-X