Calcium in PDB 7lce: Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase

All present enzymatic activity of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase:
2.9.1.1;

The structure of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase, PDB code: 7lce 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)	60.37 / 2.58
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	60.374, 171.569, 195.054, 90, 90, 90
R / Rfree (%)	19.3 / 22.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase (pdb code 7lce). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase, PDB code: 7lce:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca404 b:87.7 occ:1.00 O A:GLY198 4.1 81.7 1.0 C A:GLY198 4.3 71.8 1.0 CZ2 A:TRP199 4.3 62.6 1.0 CH2 A:TRP199 4.4 60.5 1.0 CE2 A:TRP199 4.4 67.9 1.0 CZ3 A:TRP199 4.4 67.9 1.0 OD2 A:ASP195 4.4 97.3 1.0 CD2 A:TRP199 4.5 56.4 1.0 CE3 A:TRP199 4.5 57.0 1.0 CA A:GLY198 4.5 75.6 1.0 N A:TRP199 4.9 78.0 1.0 NE1 A:TRP199 5.0 73.3 1.0

Calcium binding site 2 out of 16 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:79.9 occ:1.00 O A:HOH514 2.4 60.6 1.0 OE1 A:GLU310 2.5 109.6 1.0 OE2 A:GLU310 2.7 92.3 1.0 CD A:GLU310 3.0 107.4 1.0 CG A:GLU310 4.5 95.0 1.0 N A:GLY285 4.8 79.3 1.0

Calcium binding site 3 out of 16 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:94.1 occ:1.00 O A:THR228 4.1 76.9 1.0 CD2 A:HIS87 4.3 68.4 1.0 CZ3 A:TRP229 4.4 62.9 1.0 CH2 A:TRP229 4.4 55.0 1.0 O A:HIS87 4.5 79.5 1.0 CE3 A:TRP229 4.5 51.2 1.0 CB A:THR228 4.6 51.4 1.0 CZ2 A:TRP229 4.6 64.6 1.0 C A:THR228 4.7 71.3 1.0 CB A:HIS87 4.7 54.8 1.0 CD2 A:TRP229 4.7 58.8 1.0 CE2 A:TRP229 4.7 66.1 1.0 CG A:HIS87 4.9 71.0 1.0 CA A:HIS87 4.9 61.7 1.0 OG1 A:THR228 4.9 91.1 1.0

Calcium binding site 4 out of 16 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:108.4 occ:1.00 O A:HOH510 3.1 62.0 1.0 O A:ASN150 4.1 90.0 1.0 OD1 A:ASN182 4.3 74.9 1.0 C A:ASN150 4.3 70.5 1.0 CA A:GLU151 4.5 75.3 1.0 N A:GLU151 4.6 70.4 1.0 O A:ASN182 4.7 68.6 1.0 CG2 A:ILE149 4.8 79.9 1.0 CB A:ASN182 4.9 67.2 1.0

Calcium binding site 5 out of 16 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca408 b:125.4 occ:0.83 O A:HOH533 2.9 95.8 1.0 O A:ILE290 3.7 86.9 1.0 OD2 A:ASP289 4.3 82.3 1.0 C A:ILE290 4.9 77.8 1.0 CB A:ASP289 5.0 70.3 1.0

Calcium binding site 6 out of 16 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca409 b:97.5 occ:1.00 CD2 D:LEU9 4.0 91.0 1.0 CG1 A:VAL255 4.3 69.6 1.0 CZ A:TYR256 4.4 81.6 1.0 CE1 A:TYR256 4.4 88.7 1.0 OH A:TYR256 4.7 86.4 1.0 CE2 A:TYR256 4.8 89.6 1.0 CD1 A:TYR256 4.8 75.4 1.0 CD1 A:LEU57 4.8 65.9 1.0

Calcium binding site 7 out of 16 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:142.0 occ:1.00 O B:HOH501 2.6 139.1 1.0 OE1 B:GLU326 4.6 130.7 1.0 O B:HOH510 4.8 73.0 1.0

Calcium binding site 8 out of 16 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:86.2 occ:1.00 CD2 B:HIS87 3.8 67.7 1.0 CZ3 B:TRP229 4.0 60.7 1.0 CH2 B:TRP229 4.1 61.0 1.0 CE3 B:TRP229 4.2 53.6 1.0 CZ2 B:TRP229 4.3 66.2 1.0 OG1 B:THR228 4.3 83.2 1.0 O B:THR228 4.3 72.8 1.0 CD2 B:TRP229 4.5 58.8 1.0 CE2 B:TRP229 4.5 65.1 1.0 CG B:HIS87 4.5 58.9 1.0 CB B:HIS87 4.5 51.3 1.0 O B:HIS87 4.7 85.0 1.0 CB B:THR228 4.8 56.9 1.0 C B:THR228 4.8 63.9 1.0 CA B:HIS87 4.8 61.7 1.0 NE2 B:HIS87 4.8 76.2 1.0

Calcium binding site 9 out of 16 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:115.9 occ:1.00 ND2 B:ASN314 3.6 117.5 1.0 OD2 B:ASP317 3.8 111.8 1.0 OD1 B:ASP317 4.3 124.9 1.0 CG B:ASP317 4.5 123.7 1.0 CG B:ASN314 4.8 121.3 1.0

Calcium binding site 10 out of 16 in the Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of D-Glucosaminate-6-Phosphate Ammonia-Lyase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca405 b:102.5 occ:1.00 O B:GLY198 4.0 84.7 1.0 C B:GLY198 4.3 72.0 1.0 CD2 B:TRP199 4.6 81.8 1.0 CE2 B:TRP199 4.6 81.0 1.0 CE3 B:TRP199 4.6 76.7 1.0 CZ2 B:TRP199 4.6 75.1 1.0 CA B:GLY198 4.6 68.1 1.0 CZ3 B:TRP199 4.6 69.9 1.0 CH2 B:TRP199 4.6 70.6 1.0 OD2 B:ASP195 4.8 115.1 1.0 N B:TRP199 4.9 89.4 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