Magnesium in PDB 6h2n: Tarp-Udp-Glcnac-Mg

Protein crystallography data

The structure of Tarp-Udp-Glcnac-Mg, PDB code: 6h2n 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) 47.63 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.850, 95.270, 130.220, 90.00, 93.49, 90.00
R / Rfree (%) 17.8 / 22.6

Other elements in 6h2n:

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

Chlorine (Cl) 20 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tarp-Udp-Glcnac-Mg (pdb code 6h2n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Tarp-Udp-Glcnac-Mg, PDB code: 6h2n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6h2n

Go back to Magnesium Binding Sites List in 6h2n
Magnesium binding site 1 out of 5 in the Tarp-Udp-Glcnac-Mg


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-Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:50.8
occ:1.00
O A:HOH521 2.1 40.3 1.0
O2A A:UD1401 2.2 59.9 1.0
OD2 A:ASP94 2.3 59.7 1.0
O1B A:UD1401 2.4 56.0 1.0
OD1 A:ASP94 2.4 60.3 1.0
CG A:ASP94 2.7 59.5 1.0
PA A:UD1401 3.3 61.6 1.0
PB A:UD1401 3.6 71.1 1.0
OD1 A:ASP95 3.8 50.0 1.0
O1A A:UD1401 3.8 60.5 1.0
O A:VAL207 3.9 56.6 1.0
O3A A:UD1401 3.9 73.6 1.0
O1' A:UD1401 4.2 60.4 1.0
CB A:ASP94 4.2 59.0 1.0
OD2 A:ASP95 4.3 48.9 1.0
CG A:ASP95 4.3 49.6 1.0
CB A:ASP92 4.5 47.5 1.0
OD2 A:ASP92 4.6 44.4 1.0
O5B A:UD1401 4.7 45.4 1.0
O2B A:UD1401 4.9 57.7 1.0

Magnesium binding site 2 out of 5 in 6h2n

Go back to Magnesium Binding Sites List in 6h2n
Magnesium binding site 2 out of 5 in the Tarp-Udp-Glcnac-Mg


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-Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:69.9
occ:1.00
OD2 A:ASP316 4.2 23.9 1.0
OD2 B:ASP316 4.2 24.9 1.0
OD2 C:ASP316 4.4 27.4 1.0
OD1 A:ASP316 4.4 24.3 1.0
CB A:ALA319 4.6 23.2 1.0
OD1 C:ASP316 4.6 25.2 1.0
CD1 C:ILE322 4.7 24.2 1.0
CG A:ASP316 4.7 24.0 1.0
OD1 B:ASP316 4.7 23.1 1.0
CD1 A:ILE322 4.7 24.7 1.0
CG B:ASP316 4.8 22.6 1.0
N A:ALA319 4.8 23.7 1.0
CB C:LEU318 4.9 24.9 1.0
CB C:ALA319 4.9 21.7 1.0
CA A:ALA319 4.9 23.5 1.0
N C:ALA319 4.9 23.1 1.0
CG C:ASP316 4.9 25.0 1.0
CB A:LEU318 4.9 24.1 1.0
CB B:ALA319 4.9 20.0 1.0
CD1 B:ILE322 5.0 23.7 1.0

Magnesium binding site 3 out of 5 in 6h2n

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


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-Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:38.2
occ:1.00
O B:GLN27 2.2 23.8 1.0
O B:HOH633 2.4 23.9 1.0
O B:MET29 2.4 21.2 1.0
O B:HOH605 2.4 29.9 1.0
O B:HOH632 2.5 47.5 1.0
O B:HOH711 2.6 25.2 1.0
C B:GLN27 3.4 24.1 1.0
C B:MET29 3.4 22.6 1.0
C B:THR28 3.9 24.1 1.0
N B:SER31 3.9 24.8 1.0
O B:THR28 4.0 24.6 1.0
N B:LYS30 4.1 23.6 1.0
CA B:LYS30 4.1 25.8 1.0
N B:GLN27 4.2 23.2 1.0
N B:MET29 4.2 22.7 1.0
N B:THR28 4.3 23.5 1.0
C B:LYS30 4.3 24.9 1.0
CA B:THR28 4.3 24.1 1.0
CA B:GLN27 4.3 23.3 1.0
O B:HOH788 4.3 52.9 1.0
CA B:MET29 4.5 21.8 1.0
CA B:SER31 4.6 25.6 1.0
CB B:GLN27 4.7 21.6 1.0
CB B:SER31 4.8 27.7 1.0
OH B:TYR34 4.8 20.4 1.0
CE1 B:TYR34 4.9 20.2 1.0

Magnesium binding site 4 out of 5 in 6h2n

Go back to Magnesium Binding Sites List in 6h2n
Magnesium binding site 4 out of 5 in the Tarp-Udp-Glcnac-Mg


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-Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:31.8
occ:1.00
O2A B:UD1401 2.1 32.0 1.0
OD2 B:ASP94 2.2 40.5 1.0
OD1 B:ASP94 2.2 33.8 1.0
O B:HOH529 2.2 28.8 1.0
O1B B:UD1401 2.2 32.4 1.0
O B:HOH505 2.2 20.1 1.0
CG B:ASP94 2.5 34.6 1.0
PA B:UD1401 3.3 35.7 1.0
PB B:UD1401 3.4 33.2 1.0
OD1 B:ASP95 3.7 22.3 1.0
O3A B:UD1401 3.8 34.1 1.0
O1' B:UD1401 3.9 39.4 1.0
OD2 B:ASP95 3.9 20.9 1.0
CB B:ASP94 4.0 32.3 1.0
O1A B:UD1401 4.1 41.4 1.0
CG B:ASP95 4.1 21.0 1.0
CB B:ASP92 4.2 18.5 1.0
OD2 B:ASP92 4.2 17.4 1.0
O B:VAL207 4.5 31.4 1.0
O B:HOH628 4.6 46.0 1.0
O5B B:UD1401 4.6 26.1 1.0
O B:HOH718 4.7 46.6 1.0
CG B:ASP92 4.7 17.9 1.0
O2B B:UD1401 4.8 38.2 1.0
N B:ASP94 4.8 25.1 1.0
O B:HOH664 4.8 48.8 1.0
CA B:ASP94 4.9 28.4 1.0
C5B B:UD1401 4.9 24.5 1.0

Magnesium binding site 5 out of 5 in 6h2n

Go back to Magnesium Binding Sites List in 6h2n
Magnesium binding site 5 out of 5 in the Tarp-Udp-Glcnac-Mg


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-Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:40.5
occ:1.00
O2B C:UD1401 2.1 42.7 1.0
O2A C:UD1401 2.2 50.2 1.0
O C:HOH501 2.2 34.4 1.0
OD2 C:ASP94 2.2 41.9 1.0
OD1 C:ASP94 2.3 39.3 1.0
O C:HOH513 2.4 31.4 1.0
CG C:ASP94 2.5 40.0 1.0
PB C:UD1401 3.4 49.7 1.0
PA C:UD1401 3.5 47.8 1.0
OD1 C:ASP95 3.8 35.8 1.0
O3A C:UD1401 3.9 45.8 1.0
O1' C:UD1401 3.9 52.1 1.0
OD2 C:ASP95 4.0 34.8 1.0
CB C:ASP94 4.0 40.1 1.0
O C:VAL207 4.2 41.4 1.0
CG C:ASP95 4.2 35.5 1.0
CB C:ASP92 4.2 33.6 1.0
O1A C:UD1401 4.2 61.5 1.0
OD2 C:ASP92 4.3 32.8 1.0
O1B C:UD1401 4.7 53.6 1.0
O5B C:UD1401 4.7 43.3 1.0
CG C:ASP92 4.8 33.1 1.0
CA C:ASP94 4.9 38.6 1.0
N C:ASP94 4.9 37.0 1.0
C5B C:UD1401 5.0 43.3 1.0

Reference:

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
Page generated: Mon Dec 14 22:47:16 2020

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