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Calcium in PDB 6w7i: Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca

Enzymatic activity of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca

All present enzymatic activity of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca:
2.5.1.1; 2.5.1.10;

Protein crystallography data

The structure of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca, PDB code: 6w7i was solved by S.Maheshwari, Y.S.Kim, S.Aripirala, S.B.Gabelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.85 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.932, 79.977, 81.175, 90.00, 106.39, 90.00
R / Rfree (%) 18.4 / 23.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca (pdb code 6w7i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca, PDB code: 6w7i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6w7i

Go back to Calcium Binding Sites List in 6w7i
Calcium binding site 1 out of 6 in the Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:12.7
occ:1.00
 O11 A:476406 2.2 12.1 1.0
OD2 A:ASP250 2.2 13.0 1.0
O14 A:476406 2.3 13.6 1.0
O A:HOH540 2.4 12.7 1.0
O A:HOH504 2.5 15.1 1.0
O A:HOH599 2.5 13.8 1.0
CG A:ASP250 3.3 13.0 1.0
P10 A:476406 3.5 12.3 1.0
P9 A:476406 3.5 15.4 1.0
C8 A:476406 3.8 13.7 1.0
OD1 A:ASP250 3.8 11.8 1.0
C3 A:PEG407 3.9 21.6 1.0
O4 A:PEG407 4.1 21.5 1.0
O A:ASP250 4.1 13.6 1.0
O A:HOH553 4.2 9.9 1.0
NE2 A:GLN247 4.3 7.2 1.0
OD2 A:ASP268 4.3 16.7 1.0
C4 A:PEG407 4.3 25.2 1.0
O15 A:476406 4.4 14.8 1.0
NZ A:LYS264 4.4 16.5 1.0
CB A:ASP250 4.4 13.0 1.0
C A:ASP250 4.5 13.2 1.0
O13 A:476406 4.5 10.9 1.0
O12 A:476406 4.5 10.9 1.0
OD1 A:ASP268 4.6 15.9 1.0
CB A:ASP254 4.6 16.4 1.0
O16 A:476406 4.6 14.6 1.0
OD1 A:ASP251 4.7 11.8 1.0
O A:HOH669 4.8 16.6 1.0
CG A:ASP268 4.8 17.9 1.0
CE A:LYS264 4.8 16.9 1.0
OD2 A:ASP254 4.8 17.2 1.0
N A:ASP251 4.9 13.5 1.0

Calcium binding site 2 out of 6 in 6w7i

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Calcium binding site 2 out of 6 in the Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:18.0
occ:1.00
 O A:HOH531 2.2 12.6 1.0
O12 A:476406 2.2 10.9 1.0
OD2 A:ASP102 2.3 30.0 1.0
OD2 A:ASP98 2.4 11.4 1.0
O A:HOH669 2.4 16.6 1.0
O15 A:476406 2.5 14.8 1.0
CG A:ASP102 3.4 30.0 1.0
P10 A:476406 3.4 12.3 1.0
CG A:ASP98 3.5 12.3 1.0
CA A:CA403 3.6 13.6 1.0
P9 A:476406 3.6 15.4 1.0
C2 A:PEG407 3.7 24.7 1.0
C8 A:476406 3.8 13.7 1.0
C7 A:476406 3.9 14.1 1.0
CB A:ASP102 3.9 30.0 1.0
OD1 A:ASP98 4.0 12.6 1.0
O11 A:476406 4.1 12.1 1.0
OG A:SER104 4.2 17.3 1.0
NH2 A:ARG107 4.3 11.3 1.0
OD1 A:ASP99 4.4 13.2 1.0
O14 A:476406 4.4 13.6 1.0
O2 A:PEG407 4.4 26.4 1.0
C1 A:PEG407 4.4 24.6 1.0
OD1 A:ASP102 4.4 30.0 1.0
C3 A:PEG407 4.6 21.6 1.0
O A:ASP98 4.6 12.3 1.0
O A:HOH568 4.6 19.7 1.0
O13 A:476406 4.6 10.9 1.0
O A:HOH545 4.7 23.1 1.0
CB A:ASP98 4.7 12.5 1.0
O16 A:476406 4.8 14.6 1.0
O1 A:PEG407 4.9 20.8 1.0
C A:ASP98 4.9 12.8 1.0
O A:HOH665 4.9 8.6 1.0

Calcium binding site 3 out of 6 in 6w7i

Go back to Calcium Binding Sites List in 6w7i
Calcium binding site 3 out of 6 in the Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:13.6
occ:1.00
 OD2 A:ASP102 2.3 30.0 1.0
O15 A:476406 2.4 14.8 1.0
O A:HOH536 2.4 11.6 1.0
O A:HOH665 2.4 8.6 1.0
OD1 A:ASP98 2.5 12.6 1.0
O A:HOH526 2.5 12.3 1.0
OD1 A:ASP102 3.0 30.0 1.0
CG A:ASP102 3.0 30.0 1.0
CG A:ASP98 3.3 12.3 1.0
OD2 A:ASP98 3.3 11.4 1.0
CA A:CA402 3.6 18.0 1.0
P9 A:476406 3.6 15.4 1.0
O16 A:476406 3.7 14.6 1.0
OD1 A:ASP170 4.0 16.0 1.0
O A:HOH509 4.2 19.9 1.0
NE2 A:GLN167 4.2 13.2 1.0
OE1 A:GLN167 4.4 15.2 1.0
CG A:ASP170 4.5 14.8 1.0
O A:HOH553 4.5 9.9 1.0
CB A:ASP102 4.5 30.0 1.0
OD2 A:ASP170 4.6 14.2 1.0
O14 A:476406 4.6 13.6 1.0
C7 A:476406 4.6 14.1 1.0
CB A:ASP98 4.7 12.5 1.0
CD A:GLN167 4.7 14.3 1.0
NZ A:LYS273 4.8 26.0 1.0
C8 A:476406 4.8 13.7 1.0
O A:HOH669 4.9 16.6 1.0
C1 A:476406 5.0 14.7 1.0
O A:HOH505 5.0 29.2 1.0
O A:ASP98 5.0 12.3 1.0
N2 A:476406 5.0 14.4 1.0

Calcium binding site 4 out of 6 in 6w7i

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Calcium binding site 4 out of 6 in the Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:15.6
occ:1.00
 O16 B:476405 2.2 16.3 1.0
OD2 B:ASP250 2.3 16.2 1.0
O12 B:476405 2.3 16.5 1.0
O B:HOH595 2.3 13.1 1.0
O B:HOH527 2.5 12.8 1.0
O B:HOH573 2.6 13.4 1.0
CG B:ASP250 3.3 15.8 1.0
P9 B:476405 3.5 15.8 1.0
P10 B:476405 3.5 14.3 1.0
C8 B:476405 3.8 15.9 1.0
OD1 B:ASP250 3.8 16.1 1.0
O B:HOH600 3.9 15.5 1.0
O B:HOH569 4.1 12.4 1.0
O B:HOH695 4.2 23.3 1.0
O B:ASP250 4.2 15.1 1.0
OD2 B:ASP268 4.3 16.7 1.0
O14 B:476405 4.3 16.6 1.0
NE2 B:GLN247 4.4 11.2 1.0
OD1 B:ASP268 4.4 16.5 1.0
CB B:ASP250 4.5 15.1 1.0
NZ B:LYS264 4.5 15.2 1.0
O13 B:476405 4.5 15.4 1.0
O11 B:476405 4.5 14.8 1.0
O B:HOH682 4.5 21.0 1.0
O15 B:476405 4.5 15.8 1.0
C B:ASP250 4.6 15.5 1.0
CE B:LYS264 4.6 17.6 1.0
CB B:ASP254 4.7 19.4 1.0
OD1 B:ASP251 4.7 16.3 1.0
OD2 B:ASP254 4.8 19.8 1.0
CG B:ASP268 4.8 18.4 1.0

Calcium binding site 5 out of 6 in 6w7i

Go back to Calcium Binding Sites List in 6w7i
Calcium binding site 5 out of 6 in the Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:18.0
occ:1.00
 O11 B:476405 2.1 14.8 1.0
O B:HOH550 2.2 15.7 1.0
OD2 B:ASP102 2.3 17.2 1.0
OD2 B:ASP98 2.3 16.1 1.0
O B:HOH682 2.4 21.0 1.0
O14 B:476405 2.5 16.6 1.0
CG B:ASP102 3.4 18.3 1.0
P10 B:476405 3.4 14.3 1.0
CG B:ASP98 3.4 12.5 1.0
CA B:CA403 3.6 17.5 1.0
P9 B:476405 3.7 15.8 1.0
OD1 B:ASP98 3.7 13.0 1.0
C8 B:476405 3.8 15.9 1.0
CB B:ASP102 3.9 18.6 1.0
O12 B:476405 4.0 16.5 1.0
O B:HOH690 4.0 20.6 1.0
C7 B:476405 4.0 14.4 1.0
NH2 B:ARG107 4.2 12.8 1.0
OG B:SER104 4.3 20.1 1.0
O16 B:476405 4.4 16.3 1.0
OD1 B:ASP102 4.4 19.8 1.0
O B:HOH621 4.4 21.7 1.0
OD1 B:ASP99 4.4 13.7 1.0
O B:HOH600 4.4 15.5 1.0
O B:ASP98 4.6 12.3 1.0
O13 B:476405 4.6 15.4 1.0
O B:HOH506 4.6 24.2 1.0
CB B:ASP98 4.7 13.2 1.0
O B:HOH583 4.8 17.8 1.0
C B:ASP98 4.9 13.0 1.0
O15 B:476405 4.9 15.8 1.0
O B:HOH647 4.9 14.8 1.0

Calcium binding site 6 out of 6 in 6w7i

Go back to Calcium Binding Sites List in 6w7i
Calcium binding site 6 out of 6 in the Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:17.5
occ:1.00
 O B:HOH588 2.4 14.1 1.0
O B:HOH647 2.4 14.8 1.0
OD1 B:ASP98 2.4 13.0 1.0
OD2 B:ASP102 2.4 17.2 1.0
O14 B:476405 2.5 16.6 1.0
O B:HOH517 2.5 9.2 1.0
OD1 B:ASP102 2.8 19.8 1.0
CG B:ASP102 3.0 18.3 1.0
CG B:ASP98 3.4 12.5 1.0
OD2 B:ASP98 3.6 16.1 1.0
CA B:CA402 3.6 18.0 1.0
P9 B:476405 3.7 15.8 1.0
O15 B:476405 3.8 15.8 1.0
OD1 B:ASP170 3.8 16.1 1.0
NE2 B:GLN167 4.2 12.5 1.0
O B:HOH510 4.2 22.6 1.0
OE1 B:GLN167 4.4 14.8 1.0
O B:HOH569 4.4 12.4 1.0
CB B:ASP102 4.4 18.6 1.0
CG B:ASP170 4.5 15.9 1.0
O16 B:476405 4.6 16.3 1.0
OD2 B:ASP170 4.7 15.8 1.0
CD B:GLN167 4.7 13.4 1.0
CB B:ASP98 4.8 13.2 1.0
NZ B:LYS273 4.8 27.4 1.0
C7 B:476405 4.8 14.4 1.0
C8 B:476405 4.9 15.9 1.0
O B:HOH682 4.9 21.0 1.0
O B:ASP98 5.0 12.3 1.0

Reference:

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
Page generated: Tue Jul 16 17:21:45 2024

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