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Calcium in PDB 6vjc: Lmfpps Mutant T164Y in Complex with 476A, Ipp & Ca

Enzymatic activity of Lmfpps Mutant T164Y in Complex with 476A, Ipp & Ca

All present enzymatic activity of Lmfpps Mutant T164Y in Complex with 476A, Ipp & Ca:
2.5.1.1; 2.5.1.10;

Protein crystallography data

The structure of Lmfpps Mutant T164Y in Complex with 476A, Ipp & Ca, PDB code: 6vjc 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) 42.98 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.525, 85.889, 107.202, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 19.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Lmfpps Mutant T164Y in Complex with 476A, Ipp & Ca (pdb code 6vjc). 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 T164Y in Complex with 476A, Ipp & Ca, PDB code: 6vjc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6vjc

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Calcium binding site 1 out of 6 in the Lmfpps Mutant T164Y 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 T164Y in Complex with 476A, Ipp & Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:19.4
occ:1.00
 O16 A:476405 2.3 20.4 1.0
OD2 A:ASP250 2.3 17.6 1.0
O A:HOH593 2.3 18.9 1.0
O12 A:476405 2.4 17.9 1.0
O A:HOH637 2.4 20.0 1.0
O A:HOH694 2.5 19.2 1.0
CG A:ASP250 3.4 19.8 1.0
P9 A:476405 3.5 19.8 1.0
P10 A:476405 3.6 19.3 1.0
C8 A:476405 3.8 17.6 1.0
O A:HOH674 3.8 18.8 1.0
OD1 A:ASP250 3.9 17.8 1.0
O A:HOH641 4.0 24.2 1.0
O A:ASP250 4.2 19.3 1.0
NE2 A:GLN247 4.3 20.6 1.0
O A:HOH787 4.3 23.9 1.0
O15 A:476405 4.4 18.1 1.0
OD2 A:ASP268 4.4 22.1 1.0
NZ A:LYS264 4.4 20.0 1.0
OD1 A:ASP268 4.5 22.3 1.0
O11 A:476405 4.5 17.7 1.0
O A:HOH784 4.6 20.8 1.0
CB A:ASP250 4.6 18.6 1.0
C A:ASP250 4.6 18.0 1.0
O13 A:476405 4.6 17.5 1.0
O14 A:476405 4.7 19.8 1.0
CE A:LYS264 4.7 20.1 1.0
CB A:ASP254 4.8 21.0 1.0
OD1 A:ASP251 4.8 18.9 1.0
OD2 A:ASP254 4.8 23.9 1.0
CG A:ASP268 4.8 24.9 1.0

Calcium binding site 2 out of 6 in 6vjc

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Calcium binding site 2 out of 6 in the Lmfpps Mutant T164Y 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 T164Y in Complex with 476A, Ipp & Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:21.1
occ:1.00
 OD2 A:ASP102 2.2 20.7 1.0
O13 A:476405 2.3 17.5 1.0
O A:HOH784 2.3 20.8 1.0
O A:HOH526 2.3 20.4 1.0
OD2 A:ASP98 2.3 18.2 1.0
O15 A:476405 2.4 18.1 1.0
CG A:ASP102 3.4 22.8 1.0
CG A:ASP98 3.4 19.4 1.0
P10 A:476405 3.4 19.3 1.0
CA A:CA403 3.5 20.1 1.0
P9 A:476405 3.6 19.8 1.0
C8 A:476405 3.9 17.6 1.0
OD1 A:ASP98 3.9 21.3 1.0
O12 A:476405 3.9 17.9 1.0
CB A:ASP102 3.9 19.8 1.0
C7 A:476405 4.0 19.0 1.0
O A:HOH789 4.2 27.3 1.0
NH2 A:ARG107 4.3 17.9 1.0
OG A:SER104 4.3 22.0 1.0
O16 A:476405 4.3 20.4 1.0
OD1 A:ASP102 4.4 23.6 1.0
OD1 A:ASP99 4.5 20.3 1.0
O A:HOH674 4.5 18.8 1.0
O A:ASP98 4.6 18.7 1.0
O A:HOH698 4.6 27.2 1.0
CB A:ASP98 4.7 18.9 1.0
O11 A:476405 4.7 17.7 1.0
O14 A:476405 4.8 19.8 1.0
O A:HOH578 4.8 28.5 1.0
C A:ASP98 4.9 18.3 1.0
O A:HOH752 4.9 18.1 1.0
O A:HOH629 5.0 24.6 1.0

Calcium binding site 3 out of 6 in 6vjc

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Calcium binding site 3 out of 6 in the Lmfpps Mutant T164Y 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 T164Y in Complex with 476A, Ipp & Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:20.1
occ:1.00
 O A:HOH719 2.4 18.3 1.0
O A:HOH557 2.4 21.2 1.0
OD1 A:ASP98 2.4 21.3 1.0
O15 A:476405 2.4 18.1 1.0
OD2 A:ASP102 2.4 20.7 1.0
O A:HOH752 2.5 18.1 1.0
OD1 A:ASP102 3.0 23.6 1.0
CG A:ASP102 3.0 22.8 1.0
CG A:ASP98 3.1 19.4 1.0
OD2 A:ASP98 3.2 18.2 1.0
CA A:CA402 3.5 21.1 1.0
P9 A:476405 3.6 19.8 1.0
O14 A:476405 3.7 19.8 1.0
NE2 A:GLN167 4.2 18.4 1.0
OD1 A:ASP170 4.2 23.6 1.0
O A:HOH553 4.3 22.4 1.0
OE1 A:GLN167 4.4 26.6 1.0
CB A:ASP102 4.5 19.8 1.0
O16 A:476405 4.6 20.4 1.0
OD2 A:ASP170 4.6 25.4 1.0
CG A:ASP170 4.6 20.8 1.0
O A:HOH641 4.6 24.2 1.0
CB A:ASP98 4.6 18.9 1.0
NZ A:LYS273 4.7 38.6 1.0
CD A:GLN167 4.7 21.0 1.0
O A:HOH784 4.8 20.8 1.0
C7 A:476405 4.9 19.0 1.0
C8 A:476405 4.9 17.6 1.0
O A:HOH556 4.9 35.1 1.0
O A:ASP98 4.9 18.7 1.0

Calcium binding site 4 out of 6 in 6vjc

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Calcium binding site 4 out of 6 in the Lmfpps Mutant T164Y 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 T164Y in Complex with 476A, Ipp & Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:19.2
occ:1.00
 OD2 B:ASP250 2.3 19.6 1.0
O16 B:476405 2.3 21.7 1.0
O12 B:476405 2.3 19.7 1.0
O B:HOH775 2.4 18.9 1.0
O B:HOH644 2.4 16.8 1.0
O B:HOH711 2.5 20.5 1.0
CG B:ASP250 3.3 21.6 1.0
P9 B:476405 3.5 19.9 1.0
P10 B:476405 3.5 18.5 1.0
C8 B:476405 3.8 17.7 1.0
O B:HOH760 3.8 20.3 1.0
OD1 B:ASP250 3.8 19.3 1.0
O B:HOH713 4.0 21.8 1.0
NE2 B:GLN247 4.3 16.2 1.0
O B:ASP250 4.3 20.9 1.0
NZ B:LYS264 4.3 20.6 1.0
O B:HOH872 4.3 21.6 1.0
O15 B:476405 4.4 18.2 1.0
OD2 B:ASP268 4.4 25.5 1.0
CB B:ASP250 4.5 20.6 1.0
O13 B:476405 4.5 16.7 1.0
O11 B:476405 4.5 18.1 1.0
C B:ASP250 4.6 20.7 1.0
OD1 B:ASP268 4.6 22.4 1.0
O B:HOH864 4.6 21.3 1.0
O14 B:476405 4.7 18.2 1.0
CE B:LYS264 4.7 22.1 1.0
CB B:ASP254 4.7 24.9 1.0
OD1 B:ASP251 4.8 19.7 1.0
OD2 B:ASP254 4.8 24.7 1.0
CG B:ASP268 4.9 24.1 1.0

Calcium binding site 5 out of 6 in 6vjc

Go back to Calcium Binding Sites List in 6vjc
Calcium binding site 5 out of 6 in the Lmfpps Mutant T164Y 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 T164Y in Complex with 476A, Ipp & Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:22.1
occ:1.00
 O13 B:476405 2.2 16.7 1.0
OD2 B:ASP102 2.2 21.7 1.0
O B:HOH864 2.3 21.3 1.0
OD2 B:ASP98 2.3 17.2 1.0
O B:HOH634 2.3 21.6 1.0
O15 B:476405 2.4 18.2 1.0
CG B:ASP102 3.4 22.1 1.0
P10 B:476405 3.4 18.5 1.0
CG B:ASP98 3.4 18.4 1.0
CA B:CA403 3.5 19.3 1.0
P9 B:476405 3.5 19.9 1.0
C8 B:476405 3.8 17.7 1.0
OD1 B:ASP98 3.9 21.9 1.0
C7 B:476405 3.9 18.7 1.0
CB B:ASP102 3.9 19.8 1.0
O12 B:476405 4.0 19.7 1.0
O B:HOH875 4.2 24.6 1.0
NH2 B:ARG107 4.2 19.0 1.0
O16 B:476405 4.2 21.7 1.0
OG B:SER104 4.3 21.5 1.0
OD1 B:ASP102 4.4 22.4 1.0
OD1 B:ASP99 4.5 18.8 1.0
O B:HOH760 4.5 20.3 1.0
O11 B:476405 4.6 18.1 1.0
O B:HOH747 4.6 26.8 1.0
CB B:ASP98 4.6 18.8 1.0
O B:ASP98 4.7 17.7 1.0
O14 B:476405 4.7 18.2 1.0
O B:HOH851 4.8 21.1 1.0
O B:HOH684 4.9 24.6 1.0
O B:HOH707 4.9 31.2 1.0
C B:ASP98 5.0 19.1 1.0

Calcium binding site 6 out of 6 in 6vjc

Go back to Calcium Binding Sites List in 6vjc
Calcium binding site 6 out of 6 in the Lmfpps Mutant T164Y 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 T164Y in Complex with 476A, Ipp & Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:19.3
occ:1.00
 O B:HOH697 2.3 19.6 1.0
OD2 B:ASP102 2.4 21.7 1.0
OD1 B:ASP98 2.4 21.9 1.0
O B:HOH624 2.4 23.6 1.0
O B:HOH851 2.4 21.1 1.0
O15 B:476405 2.4 18.2 1.0
OD1 B:ASP102 2.9 22.4 1.0
CG B:ASP102 3.0 22.1 1.0
CG B:ASP98 3.1 18.4 1.0
OD2 B:ASP98 3.3 17.2 1.0
CA B:CA402 3.5 22.1 1.0
P9 B:476405 3.6 19.9 1.0
O14 B:476405 3.7 18.2 1.0
OD1 B:ASP170 4.1 25.4 1.0
NE2 B:GLN167 4.2 20.9 1.0
O A:HOH517 4.3 25.0 1.0
OE1 B:GLN167 4.4 23.5 1.0
CB B:ASP102 4.5 19.8 1.0
CG B:ASP170 4.5 20.2 1.0
OD2 B:ASP170 4.5 25.0 1.0
CB B:ASP98 4.6 18.8 1.0
O16 B:476405 4.6 21.7 1.0
O B:HOH713 4.7 21.8 1.0
NZ B:LYS273 4.7 40.7 1.0
CD B:GLN167 4.7 22.0 1.0
C7 B:476405 4.8 18.7 1.0
O B:HOH864 4.8 21.3 1.0
C8 B:476405 4.9 17.7 1.0
O B:HOH604 4.9 35.4 1.0
O B:ASP98 4.9 17.7 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 17:12:32 2024

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