Magnesium in PDB 3w7w: Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose

The structure of Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose, PDB code: 3w7w was solved by T.Miyazaki, M.Ichikawa, G.Yokoi, M.Kitaoka, H.Mori, Y.Kitano, A.Nishikawa, T.Tonozuka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.88 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.884, 138.136, 82.547, 90.00, 99.03, 90.00
R / Rfree (%)	17.4 / 22.6

The structure of Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose (pdb code 3w7w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose, PDB code: 3w7w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:39.9 occ:1.00 O A:HOH1321 2.0 22.7 1.0 O A:HOH1341 2.1 25.7 1.0 O A:HOH1557 2.1 42.8 1.0 O A:HOH1198 2.3 21.7 1.0 O A:HOH1558 2.5 33.4 1.0 O A:TRP385 4.0 15.1 1.0 OD1 A:ASP445 4.1 24.5 1.0 O A:HOH1242 4.1 17.5 1.0 OD2 A:ASP445 4.4 22.4 1.0 N A:GLU387 4.4 15.7 1.0 O A:HOH1105 4.4 17.6 1.0 O A:HOH1313 4.5 37.6 1.0 OE1 A:GLU377 4.5 31.1 1.0 OD1 A:ASN386 4.6 16.1 1.0 O A:HOH1165 4.7 20.8 1.0 CG A:ASP445 4.7 23.1 1.0 CA A:ASN386 4.7 16.0 1.0 CG A:ARG388 4.8 16.0 1.0 CD A:GLU377 4.9 30.6 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:34.8 occ:1.00 O A:HOH1556 2.0 37.4 1.0 O A:HOH1555 2.0 34.6 1.0 O A:HOH1308 2.0 32.4 1.0 OD2 A:ASP501 2.1 23.4 1.0 O A:HOH1234 2.2 24.2 1.0 O A:HOH1470 2.2 21.9 1.0 CG A:ASP501 3.2 21.3 1.0 CB A:ASP501 3.6 20.0 1.0 O A:HOH1503 4.1 35.8 1.0 O2 A:GLA1006 4.1 19.7 1.0 O1 A:GLA1006 4.2 23.7 1.0 OD1 A:ASP501 4.3 21.6 1.0 NE1 A:TRP496 4.3 20.4 1.0 O A:HOH1481 4.3 33.4 1.0 O A:HOH1163 4.5 21.7 1.0 C3 A:GLA1006 4.8 18.0 1.0 O2 A:GLC1007 4.9 20.8 1.0 C2 A:GLA1006 5.0 18.9 1.0 CD1 A:TRP496 5.0 20.4 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1004 b:23.0 occ:1.00 O A:HOH1554 2.0 19.5 1.0 O A:HOH1325 2.0 18.6 1.0 O A:HOH1509 2.0 15.8 1.0 O A:HOH1553 2.1 19.5 1.0 O A:HOH1552 2.2 22.4 1.0 O A:HOH1147 2.2 18.1 1.0 O A:HOH1133 3.9 21.5 1.0 O A:HOH1441 4.1 25.4 1.0 NE2 A:GLN585 4.1 22.4 1.0 OH A:TYR558 4.2 17.0 1.0 O A:HOH1525 4.2 31.9 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1005 b:29.3 occ:1.00 O A:HOH1413 1.9 23.4 1.0 O A:HOH1205 2.0 20.7 1.0 O A:HOH1396 2.0 22.1 1.0 O A:HOH1546 2.1 24.7 1.0 OE1 A:GLU566 2.1 20.9 1.0 O A:HOH1311 2.2 23.0 1.0 CD A:GLU566 3.1 20.7 1.0 OE2 A:GLU566 3.4 20.2 1.0 OD1 A:ASN404 4.3 26.2 1.0 O A:HOH1416 4.3 31.8 1.0 ND2 A:ASN404 4.4 23.2 1.0 CG A:GLU566 4.5 19.4 1.0 CG A:ASN404 4.8 22.0 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:41.6 occ:1.00 O B:HOH1171 2.0 26.6 1.0 O A:HOH1293 2.1 28.7 1.0 O B:HOH1233 2.4 39.0 1.0 O B:HOH1070 2.5 32.2 1.0 OE2 B:GLU465 3.9 38.6 1.0 OG1 B:THR467 4.0 31.1 1.0 O A:HOH1211 4.1 24.5 1.0 OG1 A:THR458 4.2 24.8 1.0 OE1 A:GLU487 4.3 32.2 1.0 O A:HOH1159 4.4 20.9 1.0 O B:HOH1147 4.4 21.8 1.0 CD B:GLU465 4.8 35.5 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg803 b:36.4 occ:1.00 O B:HOH1131 1.8 38.9 1.0 O B:HOH1098 2.1 26.8 1.0 O B:HOH1256 2.1 27.3 1.0 O B:HOH1181 2.1 35.5 1.0 O B:HOH1286 2.2 29.3 1.0 O B:HOH1308 2.2 31.5 1.0 O B:HOH1201 4.1 34.3 1.0 O B:ALA145 4.1 29.8 1.0 O B:HOH1021 4.2 26.0 1.0 O B:ASP22 4.3 26.4 1.0 O B:HOH1112 4.4 30.5 1.0 OE2 B:GLU144 4.4 29.2 1.0 O B:TYR21 4.5 22.5 1.0 OD1 B:ASP25 4.6 26.4 1.0 CB B:TYR21 4.6 20.6 1.0 OE1 B:GLU147 4.7 40.2 1.0 CB B:GLU147 5.0 35.3 1.0 C B:ASP22 5.0 26.3 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg804 b:28.0 occ:1.00 O B:HOH1295 2.0 30.3 1.0 O B:HOH1282 2.1 24.1 1.0 O B:HOH1296 2.2 27.2 1.0 O B:HOH1072 2.2 24.2 1.0 OD1 B:ASP501 2.2 19.7 1.0 O B:HOH1018 2.3 24.2 1.0 CG B:ASP501 3.3 20.4 1.0 CB B:ASP501 3.7 20.1 1.0 O1 B:GLA805 3.7 20.4 1.0 O B:HOH1234 4.1 31.9 1.0 NE1 B:TRP496 4.1 19.6 1.0 O2 B:GLA805 4.3 16.8 1.0 OD2 B:ASP501 4.3 17.8 1.0 O B:HOH1251 4.4 24.9 1.0 O B:HOH998 4.5 21.9 1.0 CE2 B:TYR679 4.6 18.8 1.0 O B:HOH1042 4.6 25.7 1.0 CD2 B:TYR679 4.7 21.5 1.0 C3 B:GLA805 4.7 16.8 1.0 C2 B:GLA805 4.9 17.4 1.0 CD1 B:TRP496 4.9 19.6 1.0 C1 B:GLA805 4.9 17.5 1.0

T.Miyazaki, M.Ichikawa, G.Yokoi, M.Kitaoka, H.Mori, Y.Kitano, A.Nishikawa, T.Tonozuka. Structure of A Bacterial Glycoside Hydrolase Family 63 Enzyme in Complex with Its Glycosynthase Product, and Insights Into the Substrate Specificity. Febs J. V. 280 4560 2013.
ISSN: ISSN 1742-464X
PubMed: 23826932
DOI: 10.1111/FEBS.12424