Manganese in PDB 5h62: Structure of Transferase Mutant-C23S,C199S

The structure of Structure of Transferase Mutant-C23S,C199S, PDB code: 5h62 was solved by J.B.Park, Y.Yoo, J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.29 / 1.66
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.590, 143.630, 52.730, 90.00, 108.24, 90.00
R / Rfree (%)	18.1 / 21.3

The binding sites of Manganese atom in the Structure of Transferase Mutant-C23S,C199S (pdb code 5h62). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Structure of Transferase Mutant-C23S,C199S, PDB code: 5h62:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Structure of Transferase Mutant-C23S,C199S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Transferase Mutant-C23S,C199S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:19.0 occ:1.00 O2B A:UDP404 2.1 17.6 1.0 O A:HOH572 2.1 18.4 1.0 O1A A:UDP404 2.2 18.4 1.0 OD1 A:ASN338 2.2 19.6 1.0 OD2 A:ASP241 2.2 17.8 1.0 OG A:SER340 2.3 18.8 1.0 CG A:ASP241 3.1 17.4 1.0 CG A:ASN338 3.3 21.6 1.0 CB A:SER340 3.3 18.2 1.0 PA A:UDP404 3.4 19.8 1.0 PB A:UDP404 3.4 20.7 1.0 OD1 A:ASP241 3.5 19.1 1.0 O3A A:UDP404 3.6 22.4 1.0 O A:HOH657 4.0 26.1 1.0 O A:HOH507 4.0 24.2 1.0 N A:SER340 4.1 18.5 1.0 CA A:ASN338 4.1 18.3 1.0 ND2 A:ASN338 4.2 22.7 1.0 CB A:ASN338 4.3 20.7 1.0 O A:HOH580 4.3 20.7 1.0 O2A A:UDP404 4.3 18.9 1.0 CA A:SER340 4.3 19.1 1.0 O1B A:UDP404 4.3 21.6 1.0 OD2 A:ASP239 4.3 15.8 1.0 O3B A:UDP404 4.4 26.5 1.0 CB A:ASP241 4.4 19.0 1.0 C A:ASN338 4.4 20.4 1.0 O5' A:UDP404 4.6 17.6 1.0 O A:ASN338 4.6 20.4 1.0 N A:SER341 4.6 21.1 1.0 C5' A:UDP404 4.6 15.6 1.0 C1 A:EDO401 4.7 40.7 1.0 C2 A:EDO401 4.7 40.8 1.0 C A:SER340 4.8 20.7 1.0 OH A:TYR88 4.8 22.0 1.0 O2 A:EDO401 4.9 35.7 1.0 N A:THR339 4.9 20.6 1.0

Manganese binding site 2 out of 3 in the Structure of Transferase Mutant-C23S,C199S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Transferase Mutant-C23S,C199S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn405 b:39.8 occ:1.00 O B:HOH566 2.1 33.2 1.0 NE2 B:HIS267 2.3 38.7 1.0 OD1 A:ASP322 2.3 39.2 1.0 OG B:SER269 2.3 34.7 1.0 CB B:SER269 3.1 31.8 1.0 CG A:ASP322 3.2 37.2 1.0 CD2 B:HIS267 3.2 43.3 1.0 CE1 B:HIS267 3.3 42.9 1.0 OD2 A:ASP322 3.4 42.8 1.0 O B:HOH656 3.8 42.4 1.0 O B:HOH528 4.0 47.0 1.0 OE1 B:GLU271 4.1 47.1 1.0 OD1 A:ASP320 4.3 34.7 1.0 CG B:HIS267 4.4 40.5 1.0 ND1 B:HIS267 4.4 41.5 1.0 O A:HOH742 4.4 35.9 1.0 OG B:SER262 4.4 47.3 1.0 CB A:ASP322 4.5 33.0 1.0 CA B:SER269 4.5 27.3 1.0 N B:SER269 4.7 28.1 1.0 CD B:LYS264 4.9 97.9 1.0 N A:ASP322 4.9 34.6 1.0 OD2 A:ASP320 5.0 40.5 1.0

Manganese binding site 3 out of 3 in the Structure of Transferase Mutant-C23S,C199S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Transferase Mutant-C23S,C199S within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:24.3 occ:1.00 O1B B:UDP402 1.8 23.4 1.0 O B:HOH511 2.1 28.0 1.0 O1A B:UDP402 2.1 23.4 1.0 O B:HOH540 2.2 25.6 1.0 OD2 B:ASP241 2.3 20.1 1.0 OG B:SER340 2.4 23.8 1.0 CG B:ASP241 3.1 19.7 1.0 PB B:UDP402 3.2 33.4 1.0 PA B:UDP402 3.4 25.2 1.0 CB B:SER340 3.4 25.9 1.0 OD1 B:ASP241 3.4 20.4 1.0 O3A B:UDP402 3.7 28.5 1.0 O B:HOH515 3.9 38.7 1.0 OD1 B:ASN338 4.0 41.1 1.0 O B:HOH532 4.1 26.1 1.0 O2B B:UDP402 4.1 40.5 1.0 O3B B:UDP402 4.1 37.8 1.0 N B:SER340 4.3 22.8 1.0 OD2 B:ASP239 4.4 16.8 1.0 CA B:ASN338 4.4 22.6 1.0 O2A B:UDP402 4.4 22.3 1.0 CA B:SER340 4.4 23.4 1.0 O B:HOH505 4.4 40.0 1.0 CB B:ASP241 4.4 18.5 1.0 OG B:SER341 4.5 45.5 1.0 O5' B:UDP402 4.5 23.3 1.0 C5' B:UDP402 4.6 21.8 1.0 C B:ASN338 4.7 24.6 1.0 OH B:TYR88 4.8 20.9 1.0 CB B:ASN338 4.8 28.8 1.0 CG B:ASN338 4.9 33.6 1.0 O B:ASN338 4.9 27.1 1.0 C B:SER340 5.0 29.2 1.0

J.B.Park, Y.H.Kim, Y.Yoo, J.Kim, S.H.Jun, J.W.Cho, S.El Qaidi, S.Walpole, S.Monaco, A.A.Garcia-Garcia, M.Wu, M.P.Hays, R.Hurtado-Guerrero, J.Angulo, P.R.Hardwidge, J.S.Shin, H.S.Cho. Structural Basis For Arginine Glycosylation of Host Substrates By Bacterial Effector Proteins. Nat Commun V. 9 4283 2018.
ISSN: ESSN 2041-1723
PubMed: 30327479
DOI: 10.1038/S41467-018-06680-6