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

Go back to Calcium Binding Sites List in 6vjc
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

Go back to Calcium Binding Sites List in 6vjc
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

Go back to Calcium Binding Sites List in 6vjc
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

Go back to Calcium Binding Sites List in 6vjc
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: Sat Dec 12 07:50:24 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy