Magnesium in PDB 7lc0: Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase

The structure of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase, PDB code: 7lc0 was solved by R.S.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.02 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.089, 205.572, 164.026, 90, 95.19, 90
R / Rfree (%)	19.3 / 22.8

The structure of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase (pdb code 7lc0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase, PDB code: 7lc0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:57.2 occ:1.00 CG1 A:VAL255 4.2 59.0 1.0 CE2 A:TYR256 4.4 65.5 1.0 CZ A:TYR256 4.4 74.5 1.0 CB A:GLU259 4.5 71.4 1.0 OH A:TYR61 4.6 76.5 1.0 CD2 A:TYR256 4.6 73.4 1.0 CG A:GLU259 4.6 76.8 1.0 CE1 A:TYR256 4.7 69.2 1.0 OH A:TYR256 4.8 88.4 1.0 OE1 A:GLU259 4.9 86.6 1.0 CG A:TYR256 4.9 70.5 1.0 CD1 A:TYR256 5.0 61.9 1.0

Magnesium binding site 2 out of 11 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:62.0 occ:1.00 O B:SER281 2.2 68.9 1.0 C B:SER281 3.1 62.0 1.0 CB B:SER281 3.8 60.8 1.0 N B:ALA282 3.9 56.0 1.0 CA B:SER281 4.0 55.9 1.0 CA B:ALA282 4.1 67.1 1.0 O B:LEU286 4.5 58.5 1.0 C B:ALA282 4.7 69.2 1.0 O B:ILE283 4.9 77.7 1.0

Magnesium binding site 3 out of 11 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:53.4 occ:1.00 ND1 C:HIS87 4.1 55.5 1.0 O C:HOH505 4.1 51.2 1.0 O C:HIS87 4.4 51.3 1.0 CB C:HIS87 4.4 41.6 1.0 O C:THR228 4.5 39.2 1.0 CZ3 C:TRP229 4.7 36.4 1.0 CH2 C:TRP229 4.7 37.6 1.0 CG C:HIS87 4.7 53.7 1.0 CB C:THR228 4.7 37.9 1.0 CA C:HIS87 4.8 41.4 1.0 CE3 C:TRP229 4.9 33.2 1.0 C C:HIS87 4.9 45.7 1.0 CZ2 C:TRP229 5.0 42.9 1.0

Magnesium binding site 4 out of 11 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg407 b:55.8 occ:1.00 O E:GLY198 3.9 76.9 1.0 C E:GLY198 4.3 63.5 1.0 CE2 E:TRP199 4.4 59.2 1.0 CZ2 E:TRP199 4.4 60.4 1.0 CA E:GLY198 4.5 63.6 1.0 CH2 E:TRP199 4.6 55.5 1.0 CD2 E:TRP199 4.6 56.7 1.0 CZ3 E:TRP199 4.7 49.1 1.0 CE3 E:TRP199 4.8 54.0 1.0 NE1 E:TRP199 4.8 50.1 1.0 OD2 E:ASP195 4.9 86.7 1.0

Magnesium binding site 5 out of 11 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg405 b:52.2 occ:1.00 CZ2 F:TRP199 3.8 56.0 1.0 CE2 F:TRP199 3.8 48.1 1.0 CH2 F:TRP199 3.9 55.0 1.0 CD2 F:TRP199 4.0 46.8 1.0 CZ3 F:TRP199 4.1 57.3 1.0 CE3 F:TRP199 4.1 46.8 1.0 O F:GLY198 4.2 62.3 1.0 C F:GLY198 4.3 49.9 1.0 NE1 F:TRP199 4.4 43.8 1.0 CA F:GLY198 4.5 42.6 1.0 OD2 F:ASP195 4.7 61.0 1.0 CG F:TRP199 4.7 43.2 1.0 N F:TRP199 4.7 55.0 1.0 CD1 F:TRP199 4.9 42.0 1.0

Magnesium binding site 6 out of 11 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg404 b:46.6 occ:1.00 O G:HOH519 3.3 36.9 1.0 NH2 G:ARG110 3.4 56.0 1.0 ND2 C:ASN113 3.6 48.3 1.0 OG1 C:THR121 3.8 53.3 1.0 CG2 C:THR121 4.1 44.1 1.0 CZ G:ARG110 4.1 50.4 1.0 OD1 C:ASN113 4.2 60.2 1.0 CG C:ASN113 4.3 49.4 1.0 NE G:ARG110 4.5 59.9 1.0 CB C:THR121 4.5 40.0 1.0 O G:GLY135 4.7 37.0 1.0 NH1 G:ARG110 5.0 41.0 1.0

Magnesium binding site 7 out of 11 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg405 b:55.2 occ:1.00 O G:GLY198 4.0 58.3 1.0 C G:GLY198 4.2 42.4 1.0 CE2 G:TRP199 4.2 53.8 1.0 CZ2 G:TRP199 4.3 44.0 1.0 CA G:GLY198 4.3 53.9 1.0 OD2 G:ASP195 4.4 66.6 1.0 CD2 G:TRP199 4.4 48.4 1.0 CH2 G:TRP199 4.5 48.8 1.0 CE3 G:TRP199 4.6 43.4 1.0 CZ3 G:TRP199 4.6 40.2 1.0 NE1 G:TRP199 4.7 53.0 1.0 N G:TRP199 4.8 49.2 1.0 CG G:TRP199 4.9 45.0 1.0

Magnesium binding site 8 out of 11 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg406 b:49.6 occ:1.00 ND1 G:HIS87 3.7 41.8 1.0 CH2 G:TRP229 4.2 40.4 1.0 CZ3 G:TRP229 4.2 40.4 1.0 CZ2 G:TRP229 4.3 44.4 1.0 O G:HOH510 4.3 39.9 1.0 CB G:HIS87 4.4 40.5 1.0 CE2 G:TRP229 4.4 35.6 1.0 CE3 G:TRP229 4.4 34.8 1.0 O G:THR228 4.5 49.8 1.0 CD2 G:TRP229 4.5 39.6 1.0 CG G:HIS87 4.5 41.8 1.0 O G:HIS87 4.6 37.7 1.0 CA G:HIS87 4.6 44.8 1.0 CE1 G:HIS87 4.8 50.9 1.0 CB G:THR228 4.9 35.4 1.0 OG1 G:THR228 4.9 47.7 1.0 C G:THR228 4.9 41.9 1.0 C G:HIS87 5.0 38.7 1.0

Magnesium binding site 9 out of 11 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg401 b:56.1 occ:1.00 CE2 H:TRP199 3.7 56.9 1.0 CZ2 H:TRP199 3.8 56.9 1.0 OD2 H:ASP195 4.0 69.7 1.0 CD2 H:TRP199 4.0 48.6 1.0 NE1 H:TRP199 4.1 53.9 1.0 CH2 H:TRP199 4.1 42.8 1.0 O H:GLY198 4.2 53.8 1.0 C H:GLY198 4.2 50.5 1.0 CA H:GLY198 4.4 53.3 1.0 CE3 H:TRP199 4.4 49.2 1.0 CZ3 H:TRP199 4.4 50.2 1.0 CD1 H:TRP199 4.6 48.9 1.0 CG H:TRP199 4.6 43.9 1.0 N H:TRP199 4.7 47.5 1.0

Magnesium binding site 10 out of 11 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg402 b:57.8 occ:1.00 CB H:THR228 4.0 46.3 1.0 OG1 H:THR228 4.0 60.4 1.0 ND1 H:HIS87 4.1 57.3 1.0 O H:THR228 4.2 51.4 1.0 CZ3 H:TRP229 4.2 40.1 1.0 CH2 H:TRP229 4.2 44.5 1.0 CE3 H:TRP229 4.3 38.1 1.0 CZ2 H:TRP229 4.3 43.8 1.0 CE2 H:TRP229 4.3 45.5 1.0 CD2 H:TRP229 4.3 42.5 1.0 C H:THR228 4.4 41.6 1.0 O H:HIS87 4.8 53.0 1.0 CA H:THR228 4.8 47.3 1.0 CB H:HIS87 4.8 45.8 1.0 CG H:HIS87 4.9 44.0 1.0 N H:TRP229 4.9 38.1 1.0 CE1 H:HIS87 5.0 59.1 1.0 NE1 H:TRP229 5.0 48.3 1.0

R.S.Phillips, S.C.Ting, K.Anderson. Structure and Mechanism of D-Glucosaminate-6-Phosphate Ammonia-Lyase: A Novel Octameric Assembly For A Pyridoxal 5'-Phosphate-Dependent Enzyme, and Unprecedented Stereochemical Inversion in the Elimination Reaction of A D-Amino Acid. Biochemistry V. 60 1609 2021.
ISSN: ISSN 0006-2960
PubMed: 33949189
DOI: 10.1021/ACS.BIOCHEM.1C00106