Calcium in PDB 6ww1: Crystal Structure of the Lmfpps Mutant E97Y

All present enzymatic activity of Crystal Structure of the Lmfpps Mutant E97Y:
2.5.1.1; 2.5.1.10;

The structure of Crystal Structure of the Lmfpps Mutant E97Y, PDB code: 6ww1 was solved by S.Maheshwari, Y.S.Kim, S.B.Gabelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.699, 86.078, 107.425, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 29.5

The binding sites of Calcium atom in the Crystal Structure of the Lmfpps Mutant E97Y (pdb code 6ww1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Lmfpps Mutant E97Y, PDB code: 6ww1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of the Lmfpps Mutant E97Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Lmfpps Mutant E97Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:13.1 occ:1.00 O12 A:476405 2.2 11.8 1.0 O16 A:476405 2.2 13.8 1.0 O A:HOH542 2.5 12.7 1.0 O A:HOH521 2.5 13.5 1.0 O A:HOH529 2.5 10.8 1.0 OD2 A:ASP250 2.7 10.0 1.0 CG A:ASP250 3.5 10.7 1.0 P9 A:476405 3.5 15.5 1.0 P10 A:476405 3.5 12.7 1.0 C8 A:476405 3.7 12.6 1.0 OD1 A:ASP250 3.8 10.3 1.0 O A:ASP250 3.8 13.7 1.0 O A:HOH678 3.9 17.7 1.0 O A:HOH578 4.1 14.7 1.0 O A:HOH736 4.3 22.0 1.0 OD2 A:ASP268 4.4 16.1 1.0 O15 A:476405 4.4 12.4 1.0 O A:HOH731 4.4 13.9 1.0 OD1 A:ASP268 4.4 14.1 1.0 NZ A:LYS264 4.4 10.0 1.0 C A:ASP250 4.5 13.0 1.0 O13 A:476405 4.5 10.2 1.0 O11 A:476405 4.5 11.5 1.0 O14 A:476405 4.6 13.4 1.0 CB A:ASP250 4.6 11.0 1.0 OD1 A:ASP251 4.6 30.0 1.0 CE A:LYS264 4.7 10.7 1.0 CB A:ASP254 4.7 14.2 1.0 NE2 A:GLN247 4.7 10.1 1.0 CG A:ASP268 4.8 15.6 1.0 OD2 A:ASP254 4.8 14.5 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of the Lmfpps Mutant E97Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Lmfpps Mutant E97Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:20.9 occ:1.00 OD2 A:ASP102 2.2 14.7 1.0 O13 A:476405 2.2 10.2 1.0 O A:HOH505 2.2 11.2 1.0 OD2 A:ASP98 2.3 15.9 1.0 O A:HOH731 2.4 13.9 1.0 O15 A:476405 2.5 12.4 1.0 CG A:ASP102 3.3 15.6 1.0 CG A:ASP98 3.4 15.2 1.0 P10 A:476405 3.4 12.7 1.0 CA A:CA403 3.5 14.7 1.0 P9 A:476405 3.6 15.5 1.0 OD1 A:ASP98 3.8 14.2 1.0 C8 A:476405 3.8 12.6 1.0 CB A:ASP102 3.9 15.2 1.0 C7 A:476405 3.9 13.4 1.0 O12 A:476405 4.0 11.8 1.0 O A:HOH739 4.1 23.3 1.0 NH2 A:ARG107 4.2 8.5 1.0 OG A:SER104 4.2 14.7 1.0 OD1 A:ASP102 4.4 16.9 1.0 O16 A:476405 4.4 13.8 1.0 O A:HOH678 4.4 17.7 1.0 OD1 A:ASP99 4.5 10.2 1.0 O A:ASP98 4.5 13.5 1.0 O A:HOH685 4.6 15.0 1.0 CB A:ASP98 4.6 13.3 1.0 O11 A:476405 4.7 11.5 1.0 O A:HOH556 4.7 20.6 1.0 C A:ASP98 4.8 13.3 1.0 O14 A:476405 4.8 13.4 1.0 O A:HOH579 5.0 12.3 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of the Lmfpps Mutant E97Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Lmfpps Mutant E97Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:14.7 occ:1.00 O15 A:476405 2.3 12.4 1.0 O A:HOH648 2.3 8.8 1.0 O A:HOH579 2.3 12.3 1.0 OD2 A:ASP102 2.4 14.7 1.0 OD1 A:ASP98 2.4 14.2 1.0 O A:HOH565 2.5 11.9 1.0 OD1 A:ASP102 2.9 16.9 1.0 CG A:ASP102 3.0 15.6 1.0 CG A:ASP98 3.2 15.2 1.0 OD2 A:ASP98 3.3 15.9 1.0 CA A:CA402 3.5 20.9 1.0 P9 A:476405 3.5 15.5 1.0 O14 A:476405 3.8 13.4 1.0 OD1 A:ASP170 4.0 17.2 1.0 NE2 A:GLN167 4.3 11.3 1.0 O A:HOH536 4.3 17.6 1.0 OD2 A:ASP170 4.4 17.7 1.0 CG A:ASP170 4.5 16.0 1.0 CB A:ASP102 4.5 15.2 1.0 O A:HOH578 4.5 14.7 1.0 O16 A:476405 4.6 13.8 1.0 OE1 A:GLN167 4.6 12.6 1.0 C7 A:476405 4.7 13.4 1.0 CB A:ASP98 4.7 13.3 1.0 C8 A:476405 4.8 12.6 1.0 O A:HOH534 4.9 22.5 1.0 CD A:GLN167 4.9 12.8 1.0 O A:HOH731 4.9 13.9 1.0 NZ A:LYS273 4.9 21.5 1.0 C1 A:476405 4.9 13.5 1.0 O A:ASP98 5.0 13.5 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of the Lmfpps Mutant E97Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Lmfpps Mutant E97Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:14.6 occ:1.00 O B:HOH501 2.2 13.7 1.0 O16 B:476405 2.2 15.6 1.0 OD2 B:ASP250 2.3 11.8 1.0 O12 B:476405 2.4 12.8 1.0 O B:HOH683 2.4 10.7 1.0 O B:HOH590 2.4 14.8 1.0 CG B:ASP250 3.3 12.8 1.0 P9 B:476405 3.6 15.0 1.0 P10 B:476405 3.6 13.6 1.0 C8 B:476405 3.8 13.5 1.0 OD1 B:ASP251 3.9 30.0 1.0 OD1 B:ASP250 3.9 11.8 1.0 O B:HOH604 3.9 13.4 1.0 O B:HOH592 3.9 17.9 1.0 NE2 B:GLN247 4.3 11.0 1.0 O B:ASP250 4.3 13.5 1.0 O B:HOH696 4.3 12.4 1.0 CB B:ASP254 4.4 17.8 1.0 OD2 B:ASP268 4.4 14.2 1.0 NZ B:LYS264 4.4 13.6 1.0 CB B:ASP250 4.4 12.0 1.0 OD1 B:ASP268 4.5 15.4 1.0 O15 B:476405 4.5 14.0 1.0 C B:ASP250 4.5 14.0 1.0 O B:HOH703 4.5 9.4 1.0 O11 B:476405 4.6 12.4 1.0 O14 B:476405 4.6 13.4 1.0 O13 B:476405 4.6 11.3 1.0 CG B:ASP254 4.7 19.2 1.0 CE B:LYS264 4.8 12.8 1.0 OD2 B:ASP254 4.8 20.5 1.0 CG B:ASP268 4.8 15.8 1.0 N B:ASP251 4.9 13.7 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of the Lmfpps Mutant E97Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Lmfpps Mutant E97Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:21.4 occ:1.00 O13 B:476405 2.1 11.3 1.0 O B:HOH516 2.2 16.5 1.0 OD2 B:ASP98 2.3 11.6 1.0 O B:HOH703 2.3 9.4 1.0 O15 B:476405 2.4 14.0 1.0 OD2 B:ASP102 2.4 14.4 1.0 P10 B:476405 3.2 13.6 1.0 P9 B:476405 3.4 15.0 1.0 CG B:ASP98 3.4 11.2 1.0 CA B:CA403 3.5 13.4 1.0 C8 B:476405 3.5 13.5 1.0 CG B:ASP102 3.6 14.5 1.0 C7 B:476405 3.7 13.3 1.0 OD1 B:ASP98 3.8 10.7 1.0 O12 B:476405 3.9 12.8 1.0 CB B:ASP102 4.1 14.0 1.0 O B:HOH697 4.1 18.8 1.0 O16 B:476405 4.2 15.6 1.0 NH2 B:ARG107 4.2 9.2 1.0 O B:HOH604 4.3 13.4 1.0 OG B:SER104 4.4 13.3 1.0 O B:HOH672 4.4 19.7 1.0 O11 B:476405 4.5 12.4 1.0 OD1 B:ASP99 4.5 11.0 1.0 O B:ASP98 4.6 11.5 1.0 OD1 B:ASP102 4.6 13.5 1.0 O14 B:476405 4.7 13.4 1.0 CB B:ASP98 4.7 11.0 1.0 C B:ASP98 4.9 11.6 1.0 N2 B:476405 4.9 14.2 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of the Lmfpps Mutant E97Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Lmfpps Mutant E97Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:13.4 occ:1.00 O15 B:476405 2.2 14.0 1.0 OD1 B:ASP98 2.3 10.7 1.0 O B:HOH577 2.3 9.3 1.0 OD2 B:ASP102 2.3 14.4 1.0 O B:HOH556 2.5 10.4 1.0 O B:HOH562 2.6 17.6 1.0 CG B:ASP102 3.0 14.5 1.0 OD1 B:ASP102 3.0 13.5 1.0 CG B:ASP98 3.2 11.2 1.0 OD2 B:ASP98 3.4 11.6 1.0 P9 B:476405 3.5 15.0 1.0 CA B:CA402 3.5 21.4 1.0 O14 B:476405 3.7 13.4 1.0 OD1 B:ASP170 4.0 15.7 1.0 NE2 B:GLN167 4.2 12.2 1.0 O B:HOH509 4.3 17.0 1.0 CG B:ASP170 4.5 14.3 1.0 OD2 B:ASP170 4.5 15.8 1.0 CB B:ASP102 4.5 14.0 1.0 OE1 B:GLN167 4.5 11.9 1.0 O16 B:476405 4.5 15.6 1.0 O B:HOH592 4.6 17.9 1.0 CB B:ASP98 4.6 11.0 1.0 C7 B:476405 4.6 13.3 1.0 CD B:GLN167 4.7 12.3 1.0 C8 B:476405 4.7 13.5 1.0 O B:ASP98 4.8 11.5 1.0 N2 B:476405 4.9 14.2 1.0 O B:HOH703 4.9 9.4 1.0 O B:HOH522 5.0 24.3 1.0 C1 B:476405 5.0 15.7 1.0

S.Maheshwari, Y.S.Kim, S.Aripirala, M.Murphy, L.M.Amzel, S.B.Gabelli. Identifying Structural Determinants of Product Specificity in Leishmania Major Farnesyl Diphosphate Synthase. Biochemistry V. 59 2751 2020.
ISSN: ISSN 0006-2960
PubMed: 32584028
DOI: 10.1021/ACS.BIOCHEM.0C00432