Magnesium in PDB 5nlm: Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate

The structure of Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate, PDB code: 5nlm was solved by D.H.Welner, T.Hsu, J.Dueber, P.D.Adams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.41 / 2.14
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	121.000, 172.820, 48.410, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 25.2

The binding sites of Magnesium atom in the Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate (pdb code 5nlm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate, PDB code: 5nlm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:88.2 occ:1.00 HA A:ALA393 2.8 54.2 1.0 O A:HOH1123 2.9 45.6 1.0 H A:ALA393 2.9 52.7 1.0 HB2 A:ASP189 3.0 56.1 1.0 HA A:IOS1000 3.0 0.2 1.0 OE2 A:GLU88 3.2 51.3 1.0 H1 A:IOS1000 3.5 0.9 1.0 N A:ALA393 3.5 43.8 1.0 C1 A:IOS1000 3.5 0.8 1.0 HB2 A:ALA393 3.5 52.2 1.0 CA A:ALA393 3.5 45.1 1.0 HD3 A:PRO190 3.6 51.4 1.0 HG22 A:ILE87 3.6 60.7 1.0 HB3 A:ASP189 3.7 56.1 1.0 OD2 A:ASP189 3.7 51.6 1.0 CB A:ASP189 3.7 46.7 1.0 N1 A:IOS1000 3.7 0.9 1.0 HB2 A:TYR392 3.7 55.0 1.0 HG21 A:ILE87 3.8 60.7 1.0 HD2 A:TYR392 3.9 56.6 1.0 CB A:ALA393 4.0 43.4 1.0 CG2 A:ILE87 4.1 50.5 1.0 CG A:ASP189 4.1 50.6 1.0 CD A:GLU88 4.2 48.3 1.0 O4 A:IOS1000 4.3 0.5 1.0 HG23 A:ILE87 4.4 60.7 1.0 OE1 A:GLU88 4.4 51.5 1.0 HB1 A:ALA393 4.4 52.2 1.0 CD A:PRO190 4.6 42.8 1.0 C2 A:IOS1000 4.6 1.0 1.0 CB A:TYR392 4.7 45.8 1.0 CD2 A:TYR392 4.7 47.1 1.0 C A:TYR392 4.7 40.9 1.0 O A:HOH1166 4.7 60.3 1.0 C A:ALA393 4.8 44.6 1.0 HB3 A:ALA393 4.8 52.2 1.0 H A:ASP189 4.9 49.0 1.0 C8 A:IOS1000 4.9 0.1 1.0 HD2 A:PRO190 4.9 51.4 1.0

Magnesium binding site 2 out of 5 in the Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:29.6 occ:1.00 H A:SER375 2.5 48.6 1.0 HB2 A:ASN374 2.7 42.5 1.0 HA3 A:GLY372 2.7 45.1 1.0 OG A:SER375 3.1 41.1 1.0 HE1 A:HIS370 3.1 44.0 1.0 N A:SER375 3.3 40.4 1.0 HG A:SER375 3.3 49.4 1.0 H A:ASN374 3.4 43.4 1.0 O A:HOH1168 3.4 40.5 1.0 HB2 A:SER375 3.5 46.8 1.0 CA A:GLY372 3.5 37.5 1.0 HE2 A:HIS370 3.6 47.9 1.0 CB A:ASN374 3.6 35.4 1.0 C A:GLY372 3.6 35.8 1.0 CE1 A:HIS370 3.7 36.6 1.0 CB A:SER375 3.7 38.9 1.0 O A:HOH1171 3.7 60.6 1.0 N A:ASN374 3.8 36.1 1.0 O A:GLY372 3.9 35.5 1.0 NE2 A:HIS370 3.9 39.9 1.0 CA A:ASN374 4.0 36.9 1.0 HB3 A:ASN374 4.1 42.5 1.0 HD22 A:ASN374 4.1 47.5 1.0 C A:ASN374 4.1 41.2 1.0 CA A:SER375 4.1 39.5 1.0 HA2 A:GLY372 4.1 45.1 1.0 N A:TRP373 4.1 33.9 1.0 H A:TRP373 4.2 40.7 1.0 H A:GLY372 4.4 42.2 1.0 N A:GLY372 4.4 35.1 1.0 HA A:SER375 4.5 47.4 1.0 CG A:ASN374 4.6 41.3 1.0 ND2 A:ASN374 4.6 39.5 1.0 HB3 A:SER375 4.6 46.8 1.0 C A:TRP373 4.7 35.2 1.0 ND1 A:HIS370 4.9 37.2 1.0 H A:THR376 4.9 40.8 1.0 HA A:ASN374 5.0 44.3 1.0

Magnesium binding site 3 out of 5 in the Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:70.4 occ:1.00 HH11 A:ARG442 2.0 97.3 1.0 HD2 A:ARG442 2.3 95.1 1.0 NH1 A:ARG442 2.7 81.0 1.0 O A:GLY365 2.9 47.1 1.0 HG3 A:PRO385 2.9 56.9 1.0 HH12 A:ARG442 3.1 97.3 1.0 CD A:ARG442 3.2 79.2 1.0 HB2 A:ARG442 3.3 84.3 1.0 HG2 A:PRO385 3.4 56.9 1.0 HG3 A:ARG442 3.4 90.0 1.0 CG A:PRO385 3.5 47.4 1.0 CZ A:ARG442 3.6 84.6 1.0 CG A:ARG442 3.7 74.9 1.0 HD2 A:PRO385 3.8 57.2 1.0 NE A:ARG442 3.8 84.4 1.0 HD3 A:ARG442 3.8 95.1 1.0 C A:GLY365 3.8 45.3 1.0 HA2 A:GLY365 3.9 57.6 1.0 CB A:ARG442 4.0 70.2 1.0 CD A:PRO385 4.0 47.6 1.0 HA3 A:GLY365 4.0 57.6 1.0 HD3 A:PRO385 4.1 57.2 1.0 CA A:GLY365 4.2 48.0 1.0 HE1 A:MET433 4.5 62.4 1.0 HB3 A:ARG442 4.6 84.3 1.0 HE A:ARG442 4.6 0.4 1.0 HG2 A:ARG442 4.6 90.0 1.0 HA A:MET433 4.6 68.7 1.0 HG A:LEU432 4.7 59.5 1.0 O A:LEU432 4.7 57.9 1.0 HA A:ARG442 4.7 81.1 1.0 NH2 A:ARG442 4.8 88.7 1.0 O A:GLY273 4.8 65.3 1.0 CB A:PRO385 4.9 45.2 1.0 HD11 A:LEU432 4.9 61.6 1.0 HE3 A:MET433 5.0 62.4 1.0 CA A:ARG442 5.0 67.5 1.0

Magnesium binding site 4 out of 5 in the Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1004 b:0.7 occ:1.00 HE A:ARG58 2.2 72.0 1.0 HH21 A:ARG58 2.3 72.3 1.0 HD2 A:PRO53 2.8 80.5 1.0 O A:PRO53 2.9 72.3 1.0 NE A:ARG58 3.0 60.0 1.0 NH2 A:ARG58 3.1 60.2 1.0 CZ A:ARG58 3.5 59.4 1.0 HB3 A:PRO52 3.5 93.2 1.0 CD A:PRO53 3.6 67.0 1.0 N A:PRO53 3.8 68.3 1.0 HB2 A:PRO53 3.8 76.6 1.0 HH22 A:ARG58 3.8 72.3 1.0 C A:PRO53 3.9 67.5 1.0 HD2 A:ARG58 4.1 73.4 1.0 CD A:ARG58 4.2 61.1 1.0 HB2 A:PRO52 4.2 93.2 1.0 CB A:PRO52 4.2 77.6 1.0 C A:PRO52 4.2 69.9 1.0 CA A:PRO53 4.3 66.3 1.0 HA A:PRO52 4.3 86.3 1.0 CB A:PRO53 4.3 63.8 1.0 HD3 A:PRO53 4.3 80.5 1.0 HG2 A:PRO53 4.3 77.6 1.0 CG A:PRO53 4.4 64.6 1.0 CA A:PRO52 4.4 71.9 1.0 HG3 A:ARG58 4.5 70.1 1.0 NH1 A:ARG58 4.8 55.0 1.0 HD3 A:ARG58 4.9 73.4 1.0 CG A:ARG58 4.9 58.3 1.0 O A:PRO52 4.9 69.5 1.0

Magnesium binding site 5 out of 5 in the Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Complex Between A Udp-Glucosyltransferase From Polygonum Tinctorium Capable of Glucosylating Indoxyl and Indoxyl Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:52.3 occ:0.50 HH11 B:ARG36 1.9 100.0 1.0 HH12 B:ARG36 2.1 100.0 1.0 NH1 B:ARG36 2.2 83.3 1.0 HB3 B:GLU32 2.4 67.9 1.0 OE1 B:GLU32 2.6 60.8 1.0 HG3 B:ARG36 2.9 78.6 1.0 O B:GLU32 3.1 52.4 1.0 HA B:GLU32 3.1 65.3 1.0 CB B:GLU32 3.2 56.5 1.0 CZ B:ARG36 3.3 81.5 1.0 CA B:GLU32 3.5 54.4 1.0 CD B:GLU32 3.6 62.5 1.0 C B:GLU32 3.6 51.7 1.0 CG B:ARG36 3.6 65.5 1.0 HG2 B:ARG36 3.7 78.6 1.0 HB2 B:LYS35 3.8 64.5 1.0 HD2 B:ARG36 3.8 84.5 1.0 CG B:GLU32 3.9 60.2 1.0 HD22 B:LEU247 3.9 77.0 1.0 HB2 B:GLU32 3.9 67.9 1.0 CD B:ARG36 4.0 70.4 1.0 NE B:ARG36 4.1 77.0 1.0 HH22 B:ARG36 4.1 0.3 1.0 HG3 B:GLU32 4.2 72.3 1.0 NH2 B:ARG36 4.2 85.2 1.0 HD3 B:LYS35 4.4 66.4 1.0 HE2 B:LYS35 4.4 69.6 1.0 O B:ILE248 4.5 69.1 1.0 H B:ARG36 4.5 64.9 1.0 CB B:LYS35 4.7 53.7 1.0 OE2 B:GLU32 4.7 63.8 1.0 HB3 B:LYS35 4.7 64.5 1.0 HG2 B:GLU32 4.7 72.3 1.0 CD2 B:LEU247 4.8 64.2 1.0 N B:PHE33 4.8 50.0 1.0 HD23 B:LEU247 4.8 77.0 1.0 HB3 B:LEU247 4.8 73.7 1.0 HZ3 B:LYS35 4.8 72.2 1.0 HE B:ARG36 4.8 92.5 1.0 N B:ARG36 4.9 54.0 1.0 CB B:ARG36 4.9 58.7 1.0 N B:GLU32 4.9 53.1 1.0 H B:ILE248 4.9 77.6 1.0 HH21 B:ARG36 4.9 0.3 1.0 HA B:LEU247 5.0 74.8 1.0

T.M.Hsu, D.H.Welner, Z.N.Russ, B.Cervantes, R.L.Prathuri, P.D.Adams, J.E.Dueber. Employing A Biochemical Protecting Group For A Sustainable Indigo Dyeing Strategy. Nat. Chem. Biol. V. 14 256 2018.
ISSN: ESSN 1552-4469
PubMed: 29309053
DOI: 10.1038/NCHEMBIO.2552