Manganese in PDB 5h63: Structure of Transferase Mutant-C23S,C199S

The structure of Structure of Transferase Mutant-C23S,C199S, PDB code: 5h63 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)	44.80 / 1.92
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	49.570, 52.280, 143.750, 90.00, 90.00, 108.00
R / Rfree (%)	18.4 / 22.8

The binding sites of Manganese atom in the Structure of Transferase Mutant-C23S,C199S (pdb code 5h63). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Structure of Transferase Mutant-C23S,C199S, PDB code: 5h63:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 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:Mn402 b:19.2 occ:1.00 O A:HOH542 2.1 17.1 1.0 O1B A:UD1401 2.2 17.1 1.0 OD2 A:ASP241 2.2 15.6 1.0 O2A A:UD1401 2.2 17.0 1.0 OD1 A:ASN338 2.3 19.3 1.0 OG A:SER340 2.5 14.8 1.0 CG A:ASP241 3.1 16.8 1.0 PB A:UD1401 3.3 18.7 1.0 CB A:SER340 3.3 18.6 1.0 PA A:UD1401 3.4 17.1 1.0 CG A:ASN338 3.4 19.9 1.0 OD1 A:ASP241 3.4 16.8 1.0 O3A A:UD1401 3.6 19.3 1.0 CA A:ASN338 4.0 18.5 1.0 O1' A:UD1401 4.1 22.1 1.0 N A:SER340 4.1 18.8 1.0 O A:HOH636 4.2 26.5 1.0 O A:HOH507 4.2 27.5 1.0 O1A A:UD1401 4.2 18.4 1.0 CA A:SER340 4.2 17.9 1.0 CB A:ASN338 4.3 19.9 1.0 ND2 A:ASN338 4.3 18.6 1.0 C A:ASN338 4.3 19.7 1.0 O A:HOH607 4.3 23.1 1.0 OD2 A:ASP239 4.4 14.3 1.0 CB A:ASP241 4.4 16.5 1.0 O2B A:UD1401 4.5 21.2 1.0 N2' A:UD1401 4.6 20.8 1.0 O7' A:UD1401 4.6 28.1 1.0 N A:SER341 4.6 23.8 1.0 O A:ASN338 4.6 16.1 1.0 O5B A:UD1401 4.7 14.7 1.0 OH A:TYR88 4.8 18.0 1.0 C7' A:UD1401 4.8 21.3 1.0 C A:SER340 4.8 19.9 1.0 C5B A:UD1401 4.8 14.5 1.0 N A:THR339 4.8 19.1 1.0

Manganese binding site 2 out of 6 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:Mn403 b:40.6 occ:1.00 OD1 D:ASN302 1.9 34.7 1.0 O D:HOH620 2.3 30.4 1.0 O A:HOH608 2.3 36.8 1.0 OD2 A:ASP326 2.3 35.1 1.0 OD1 A:ASP322 2.5 37.2 1.0 CG D:ASN302 2.9 32.5 1.0 CG A:ASP326 3.0 31.6 1.0 OD1 A:ASP326 3.1 30.6 1.0 ND2 D:ASN302 3.3 32.7 1.0 CG A:ASP322 3.4 41.2 1.0 OD2 A:ASP322 3.5 47.5 1.0 OD2 D:ASP299 4.0 42.2 1.0 CG D:ASP299 4.1 42.6 1.0 CB D:ASN302 4.2 33.7 1.0 OD1 D:ASP299 4.3 35.4 1.0 CD2 D:TYR301 4.4 39.8 1.0 O A:ASP322 4.4 29.8 1.0 CB A:ASP326 4.5 30.5 1.0 CB D:ASP299 4.7 42.7 1.0 CB A:ASP322 4.9 37.7 1.0 CE2 D:TYR301 5.0 36.5 1.0

Manganese binding site 3 out of 6 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:Mn402 b:19.0 occ:1.00 O B:HOH557 2.1 18.2 1.0 O1A B:UD1401 2.2 13.8 1.0 O2B B:UD1401 2.2 15.0 1.0 OD2 B:ASP241 2.2 16.5 1.0 OG B:SER340 2.3 16.0 1.0 OD1 B:ASN338 2.4 19.9 1.0 CG B:ASP241 3.2 16.8 1.0 PB B:UD1401 3.2 19.6 1.0 CB B:SER340 3.3 22.4 1.0 PA B:UD1401 3.3 16.8 1.0 CG B:ASN338 3.5 20.9 1.0 OD1 B:ASP241 3.5 15.0 1.0 O3A B:UD1401 3.6 17.4 1.0 O1' B:UD1401 4.0 21.7 1.0 CA B:ASN338 4.1 18.2 1.0 N B:SER340 4.1 19.1 1.0 O B:HOH519 4.1 26.7 1.0 O B:HOH610 4.2 26.3 1.0 O2A B:UD1401 4.2 18.2 1.0 CA B:SER340 4.2 18.5 1.0 O B:HOH584 4.3 25.9 1.0 OD2 B:ASP239 4.3 12.8 1.0 CB B:ASN338 4.3 19.9 1.0 ND2 B:ASN338 4.4 21.3 1.0 C B:ASN338 4.4 18.9 1.0 CB B:ASP241 4.4 17.1 1.0 O1B B:UD1401 4.5 22.1 1.0 N B:SER341 4.5 22.4 1.0 C8' B:UD1401 4.6 24.1 1.0 O5B B:UD1401 4.6 16.0 1.0 N2' B:UD1401 4.7 20.8 1.0 O B:ASN338 4.7 18.2 1.0 C B:SER340 4.7 22.4 1.0 C5B B:UD1401 4.8 15.0 1.0 OH B:TYR88 4.8 16.9 1.0 C7' B:UD1401 4.8 23.2 1.0 N B:THR339 4.9 18.2 1.0 C1' B:UD1401 4.9 23.9 1.0

Manganese binding site 4 out of 6 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 4 of Structure of Transferase Mutant-C23S,C199S within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:42.0 occ:1.00 OD1 C:ASN302 1.9 35.0 1.0 OD2 B:ASP326 2.1 32.3 1.0 O C:HOH572 2.3 29.1 1.0 OD1 B:ASP322 2.6 43.1 1.0 CG C:ASN302 2.9 32.2 1.0 CG B:ASP326 3.0 30.9 1.0 OD1 B:ASP326 3.1 28.9 1.0 ND2 C:ASN302 3.3 31.3 1.0 OD2 B:ASP322 3.3 47.4 1.0 CG B:ASP322 3.4 42.0 1.0 OD2 C:ASP299 3.9 38.9 1.0 CG C:ASP299 4.2 41.2 1.0 CB C:ASN302 4.2 30.5 1.0 OD1 C:ASP299 4.4 40.8 1.0 CB B:ASP326 4.4 29.0 1.0 O B:ASP322 4.4 30.9 1.0 CD2 C:TYR301 4.5 37.5 1.0 CB C:ASP299 4.9 39.6 1.0 CB B:ASP322 4.9 39.3 1.0 C B:ASP322 4.9 34.6 1.0 CE2 C:TYR301 5.0 34.8 1.0

Manganese binding site 5 out of 6 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 5 of Structure of Transferase Mutant-C23S,C199S within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn402 b:19.8 occ:1.00 O2B C:UD1401 1.9 17.8 1.0 O2A C:UD1401 2.1 17.4 1.0 O C:HOH520 2.2 16.2 1.0 OG C:SER340 2.2 19.4 1.0 OD2 C:ASP241 2.3 15.4 1.0 OD1 C:ASN338 2.3 21.8 1.0 CG C:ASP241 3.1 15.9 1.0 PB C:UD1401 3.2 23.7 1.0 CB C:SER340 3.3 21.6 1.0 PA C:UD1401 3.4 21.0 1.0 OD1 C:ASP241 3.4 14.4 1.0 CG C:ASN338 3.5 23.8 1.0 O3A C:UD1401 3.7 19.4 1.0 O1' C:UD1401 4.0 23.4 1.0 O C:HOH505 4.1 32.2 1.0 N C:SER340 4.2 18.4 1.0 CA C:ASN338 4.2 18.7 1.0 CA C:SER340 4.3 20.0 1.0 OD2 C:ASP239 4.3 13.3 1.0 O1A C:UD1401 4.3 16.4 1.0 O1B C:UD1401 4.4 24.9 1.0 CB C:ASN338 4.4 21.9 1.0 CB C:ASP241 4.4 14.9 1.0 ND2 C:ASN338 4.4 25.5 1.0 N2' C:UD1401 4.5 25.3 1.0 C C:ASN338 4.5 20.1 1.0 O5B C:UD1401 4.6 18.8 1.0 O7' C:UD1401 4.6 29.6 1.0 C5B C:UD1401 4.6 16.8 1.0 N C:SER341 4.7 29.7 1.0 OH C:TYR88 4.7 17.0 1.0 C7' C:UD1401 4.8 27.8 1.0 O C:ASN338 4.8 17.7 1.0 C C:SER340 4.8 24.4 1.0 N C:THR339 4.9 17.1 1.0

Manganese binding site 6 out of 6 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 6 of Structure of Transferase Mutant-C23S,C199S within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn402 b:19.9 occ:1.00 O2B D:UD1401 1.9 20.8 1.0 O D:HOH533 2.1 18.9 1.0 O1A D:UD1401 2.2 16.2 1.0 OD1 D:ASN338 2.2 24.2 1.0 OD2 D:ASP241 2.3 14.9 1.0 OG D:SER340 2.3 17.3 1.0 CG D:ASP241 3.1 14.9 1.0 PB D:UD1401 3.2 24.7 1.0 OD1 D:ASP241 3.4 14.9 1.0 CG D:ASN338 3.4 25.3 1.0 CB D:SER340 3.4 20.7 1.0 PA D:UD1401 3.4 20.6 1.0 O3A D:UD1401 3.7 21.9 1.0 O D:HOH583 3.9 30.8 1.0 O1' D:UD1401 4.0 25.6 1.0 O D:HOH528 4.1 33.1 1.0 O D:HOH543 4.1 32.5 1.0 CA D:ASN338 4.1 19.1 1.0 N D:SER340 4.2 18.1 1.0 ND2 D:ASN338 4.3 26.1 1.0 CA D:SER340 4.3 20.0 1.0 OD2 D:ASP239 4.3 15.0 1.0 CB D:ASN338 4.3 23.1 1.0 O2A D:UD1401 4.4 18.3 1.0 O1B D:UD1401 4.4 24.3 1.0 CB D:ASP241 4.4 15.2 1.0 C D:ASN338 4.4 20.1 1.0 N2' D:UD1401 4.5 26.6 1.0 N D:SER341 4.6 32.8 1.0 O5B D:UD1401 4.6 20.3 1.0 C8' D:UD1401 4.7 23.2 1.0 OH D:TYR88 4.7 15.9 1.0 C5B D:UD1401 4.7 18.6 1.0 O D:ASN338 4.8 17.9 1.0 C D:SER340 4.8 25.9 1.0 N D:THR339 4.9 16.9 1.0 C7' D:UD1401 4.9 28.6 1.0 C1' D:UD1401 5.0 28.8 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