Manganese in PDB 6h21: Tarp-Udp-Glcnac-Mn

The structure of Tarp-Udp-Glcnac-Mn, PDB code: 6h21 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)	47.68 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.860, 95.360, 130.550, 90.00, 93.51, 90.00
R / Rfree (%)	17.6 / 21.1

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

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	10 atoms

The binding sites of Manganese atom in the Tarp-Udp-Glcnac-Mn (pdb code 6h21). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Tarp-Udp-Glcnac-Mn, PDB code: 6h21:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in the Tarp-Udp-Glcnac-Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Tarp-Udp-Glcnac-Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:42.6 occ:1.00 O A:HOH505 2.1 41.7 1.0 OD2 A:ASP94 2.1 49.3 1.0 O2A A:UD1402 2.2 46.3 1.0 O2B A:UD1402 2.3 41.7 1.0 O A:HOH501 2.3 46.9 1.0 OD1 A:ASP94 2.3 49.0 1.0 CG A:ASP94 2.5 49.5 1.0 PA A:UD1402 3.3 47.9 1.0 O A:HOH588 3.4 48.3 1.0 PB A:UD1402 3.5 50.7 1.0 MN A:MN404 3.8 60.5 1.0 O1A A:UD1402 3.8 42.7 1.0 O3A A:UD1402 3.8 52.7 1.0 O A:HOH562 3.9 51.0 1.0 OD1 A:ASP95 3.9 47.3 1.0 O1' A:UD1402 4.0 51.7 1.0 O A:HOH503 4.0 48.3 1.0 CB A:ASP94 4.0 50.8 1.0 OD2 A:ASP95 4.1 46.2 1.0 O A:VAL207 4.2 54.0 1.0 CG A:ASP95 4.3 46.8 1.0 CB A:ASP92 4.4 48.2 1.0 OD2 A:ASP92 4.5 46.6 1.0 O5B A:UD1402 4.7 37.3 1.0 O1B A:UD1402 4.8 51.8 1.0 CA A:ASP94 4.9 50.9 1.0 CG A:ASP92 4.9 47.8 1.0 N A:ASP94 5.0 51.0 1.0

Manganese binding site 2 out of 7 in the Tarp-Udp-Glcnac-Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Tarp-Udp-Glcnac-Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn404 b:60.5 occ:1.00 OD2 A:ASP94 2.2 49.3 1.0 O A:HOH503 2.2 48.3 1.0 O A:HOH588 2.4 48.3 1.0 CG A:ASP94 3.3 49.5 1.0 CB A:ASP94 3.7 50.8 1.0 MN A:MN403 3.8 42.6 1.0 O A:VAL207 4.1 54.0 1.0 O1A A:UD1402 4.1 42.7 1.0 O2B A:UD1402 4.2 41.7 1.0 O A:HOH501 4.3 46.9 1.0 CB A:ASP209 4.3 74.3 1.0 OD1 A:ASP94 4.4 49.0 1.0 N A:ASP209 4.4 70.4 1.0 O2A A:UD1402 5.0 46.3 1.0 CA A:ASP209 5.0 75.0 1.0

Manganese binding site 3 out of 7 in the Tarp-Udp-Glcnac-Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Tarp-Udp-Glcnac-Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn409 b:25.5 occ:1.00 O2A B:UD1408 2.2 27.7 1.0 O2B B:UD1408 2.2 28.9 1.0 OD2 B:ASP94 2.3 24.3 1.0 O B:HOH508 2.3 21.6 1.0 O B:HOH597 2.3 24.9 1.0 OD1 B:ASP94 2.3 22.9 1.0 CG B:ASP94 2.6 23.7 1.0 PA B:UD1408 3.3 27.7 1.0 PB B:UD1408 3.3 27.1 1.0 O3A B:UD1408 3.6 27.1 1.0 O B:HOH608 3.7 37.5 1.0 O1' B:UD1408 3.7 28.1 1.0 OD2 B:ASP95 3.8 21.4 1.0 OD1 B:ASP95 3.9 23.1 1.0 O1A B:UD1408 3.9 29.1 1.0 O B:HOH605 4.0 36.8 1.0 MN B:MN410 4.0 42.8 1.0 CB B:ASP92 4.1 21.4 1.0 OD2 B:ASP92 4.1 21.1 1.0 CB B:ASP94 4.1 24.2 1.0 CG B:ASP95 4.2 22.1 1.0 O B:HOH501 4.2 42.9 1.0 O5B B:UD1408 4.5 23.1 1.0 O B:HOH744 4.6 49.2 1.0 O B:HOH737 4.6 39.6 1.0 CG B:ASP92 4.6 21.1 1.0 O1B B:UD1408 4.6 29.2 1.0 O B:VAL207 4.7 31.2 1.0 O B:HOH546 4.9 40.9 1.0 N B:ASP94 4.9 23.1 1.0 C5B B:UD1408 4.9 25.4 1.0 CA B:ASP94 5.0 23.7 1.0

Manganese binding site 4 out of 7 in the Tarp-Udp-Glcnac-Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Tarp-Udp-Glcnac-Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn410 b:42.8 occ:1.00 O B:HOH752 2.2 33.6 1.0 O B:HOH546 2.2 40.9 1.0 OD2 B:ASP94 2.2 24.3 1.0 O B:HOH501 2.3 42.9 1.0 O B:HOH608 2.4 37.5 1.0 OD2 B:ASP209 2.5 51.6 1.0 CG B:ASP94 3.3 23.7 1.0 CG B:ASP209 3.5 50.3 1.0 CB B:ASP94 3.7 24.2 1.0 O B:HOH771 3.9 42.4 1.0 MN B:MN409 4.0 25.5 1.0 O2B B:UD1408 4.1 28.9 1.0 CB B:ASP209 4.1 51.3 1.0 O B:VAL207 4.1 31.2 1.0 O1A B:UD1408 4.2 29.1 1.0 OD1 B:ASP94 4.4 22.9 1.0 O B:HOH597 4.4 24.9 1.0 OD1 B:ASP209 4.4 50.5 1.0 O B:HOH737 4.5 39.6 1.0 O B:HOH693 4.6 42.8 1.0 N B:ASP209 4.8 44.8 1.0 O2A B:UD1408 4.8 27.7 1.0 PA B:UD1408 5.0 27.7 1.0

Manganese binding site 5 out of 7 in the Tarp-Udp-Glcnac-Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Tarp-Udp-Glcnac-Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn411 b:84.5 occ:1.00 OD2 C:ASP316 2.7 31.5 1.0 O B:HOH684 2.9 57.1 1.0 O A:HOH657 3.0 44.4 1.0 OD2 B:ASP316 3.4 29.8 1.0 CG C:ASP316 3.7 29.1 1.0 OD2 A:ASP316 3.8 31.8 1.0 OD1 C:ASP316 3.9 30.0 1.0 CG B:ASP316 4.2 27.9 1.0 OD1 B:ASP316 4.2 28.9 1.0 CG A:ASP316 4.7 31.9 1.0 OD1 A:ASP316 4.9 32.1 1.0

Manganese binding site 6 out of 7 in the Tarp-Udp-Glcnac-Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Tarp-Udp-Glcnac-Mn within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn404 b:35.8 occ:1.00 O2A C:UD1403 2.1 34.8 1.0 O C:HOH517 2.2 33.5 1.0 O2B C:UD1403 2.2 35.2 1.0 OD2 C:ASP94 2.2 38.3 1.0 O C:HOH524 2.3 32.8 1.0 OD1 C:ASP94 2.3 37.2 1.0 CG C:ASP94 2.6 38.2 1.0 PA C:UD1403 3.3 37.6 1.0 PB C:UD1403 3.4 37.3 1.0 O3A C:UD1403 3.7 38.4 1.0 OD1 C:ASP95 3.7 36.5 1.0 O1' C:UD1403 3.8 41.2 1.0 OD2 C:ASP95 4.0 35.2 1.0 MN C:MN405 4.1 74.9 1.0 CB C:ASP94 4.1 38.9 1.0 CB C:ASP92 4.1 36.1 1.0 CG C:ASP95 4.2 36.0 1.0 O1A C:UD1403 4.2 41.6 1.0 OD2 C:ASP92 4.2 35.5 1.0 O C:VAL207 4.5 43.2 1.0 O5B C:UD1403 4.6 40.2 1.0 O C:HOH626 4.7 50.1 1.0 CG C:ASP92 4.7 35.7 1.0 O1B C:UD1403 4.7 40.7 1.0 C5B C:UD1403 4.9 41.3 1.0 CA C:ASP94 5.0 38.7 1.0 N C:ASP94 5.0 38.1 1.0

Manganese binding site 7 out of 7 in the Tarp-Udp-Glcnac-Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Tarp-Udp-Glcnac-Mn within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn405 b:74.9 occ:1.00 OD2 C:ASP94 2.4 38.3 1.0 CG C:ASP209 3.4 60.2 1.0 CG C:ASP94 3.5 38.2 1.0 CB C:ASP94 3.9 38.9 1.0 O2B C:UD1403 4.0 35.2 1.0 O1A C:UD1403 4.1 41.6 1.0 MN C:MN404 4.1 35.8 1.0 CB C:ASP209 4.2 60.7 1.0 O2A C:UD1403 4.4 34.8 1.0 OD1 C:ASP94 4.6 37.2 1.0 O C:HOH517 4.6 33.5 1.0 O C:VAL207 4.6 43.2 1.0 PA C:UD1403 4.7 37.6 1.0 N C:ASP209 4.9 57.8 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