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Calcium in PDB 4llt: Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site

Enzymatic activity of Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site

All present enzymatic activity of Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site:
2.5.1.10;

Protein crystallography data

The structure of Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site, PDB code: 4llt was solved by J.Kim, R.Toro, R.Bhosle, N.F.Al Obaidi, L.L.Morisco, S.R.Wasserman, S.Sojitra, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, M.Stead, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.46 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.899, 83.117, 71.332, 90.00, 108.95, 90.00
R / Rfree (%) 17.4 / 20.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site (pdb code 4llt). 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 A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site, PDB code: 4llt:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4llt

Go back to Calcium Binding Sites List in 4llt
Calcium binding site 1 out of 6 in the Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site


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 A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:16.9
occ:1.00
 OD1 A:ASP216 2.2 15.9 1.0
O2B A:IPE302 2.3 18.0 1.0
O A:HOH489 2.3 22.6 1.0
O A:HOH472 2.4 25.0 1.0
O A:HOH458 2.5 17.4 1.0
O1A A:IPE302 2.5 20.4 1.0
CG A:ASP216 3.3 16.2 1.0
PB A:IPE302 3.6 17.0 1.0
PA A:IPE302 3.6 20.4 1.0
OD2 A:ASP216 3.7 17.8 1.0
O3A A:IPE302 3.8 16.8 1.0
NZ A:LYS230 4.3 16.3 1.0
O A:ASP216 4.3 16.0 1.0
O2A A:IPE302 4.4 17.6 1.0
O A:HOH490 4.4 24.5 1.0
O3B A:IPE302 4.4 17.4 1.0
OD1 A:ASP235 4.5 26.7 1.0
OD2 A:ASP235 4.5 20.8 1.0
O A:HOH537 4.5 30.1 1.0
CB A:ASP216 4.6 15.9 1.0
NE2 A:GLN213 4.6 26.8 1.0
O1B A:IPE302 4.7 16.1 1.0
CE A:LYS230 4.7 16.3 1.0
OD1 A:ASP217 4.7 18.8 1.0
C A:ASP216 4.8 17.0 1.0
O1 A:IPE302 4.9 23.6 1.0
CG A:ASP235 4.9 25.5 1.0

Calcium binding site 2 out of 6 in 4llt

Go back to Calcium Binding Sites List in 4llt
Calcium binding site 2 out of 6 in the Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site


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 A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:15.1
occ:0.90
 OD2 A:ASP80 2.3 20.2 1.0
O A:HOH538 2.3 25.3 1.0
O2A A:IPE302 2.3 17.6 1.0
O1B A:IPE302 2.3 16.1 1.0
OD2 A:ASP86 2.3 19.4 1.0
O A:HOH462 2.5 23.6 1.0
CG A:ASP86 3.4 20.7 1.0
CG A:ASP80 3.4 15.7 1.0
PB A:IPE302 3.5 17.0 1.0
PA A:IPE302 3.5 20.4 1.0
O3A A:IPE302 3.7 16.8 1.0
CB A:ASP86 3.7 19.0 1.0
O A:HOH464 3.8 24.5 1.0
OD1 A:ASP80 4.0 19.6 1.0
O A:HOH457 4.0 28.7 1.0
O2B A:IPE302 4.1 18.0 1.0
O A:HOH540 4.1 24.2 1.0
NH1 A:ARG91 4.2 17.3 1.0
OD1 A:ASP88 4.3 24.5 1.0
C1 A:IPE302 4.4 21.9 1.0
OD1 A:ASP86 4.5 25.5 1.0
O1 A:IPE302 4.5 23.6 1.0
CB A:ASP80 4.5 14.8 1.0
CA A:CA305 4.6 22.5 0.8
O1A A:IPE302 4.7 20.4 1.0
O3B A:IPE302 4.7 17.4 1.0
OD2 A:ASP81 4.8 17.5 1.0
O A:ASP80 4.8 15.0 1.0
O A:HOH527 4.9 26.4 1.0

Calcium binding site 3 out of 6 in 4llt

Go back to Calcium Binding Sites List in 4llt
Calcium binding site 3 out of 6 in the Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site


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 A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:22.5
occ:0.80
 O A:HOH457 2.3 28.7 1.0
O A:HOH527 2.4 26.4 1.0
OD2 A:ASP156 2.4 30.3 1.0
O A:HOH464 2.4 24.5 1.0
O A:HOH528 2.5 33.1 1.0
OE1 A:GLU160 2.6 49.6 1.0
OD1 A:ASP86 2.6 25.5 1.0
OD2 A:ASP86 2.8 19.4 1.0
CG A:ASP86 3.1 20.7 1.0
CG A:ASP156 3.6 28.6 1.0
CD A:GLU160 3.7 46.5 1.0
O2A A:IPE302 4.2 17.6 1.0
OD1 A:ASP80 4.2 19.6 1.0
NZ A:LYS178 4.3 37.9 1.0
OE2 A:GLU160 4.4 50.9 1.0
OD1 A:ASP156 4.4 29.4 1.0
CE A:LYS240 4.4 56.7 1.0
CD A:LYS240 4.5 55.4 1.0
CA A:CA304 4.6 15.1 0.9
CE A:LYS178 4.6 43.4 1.0
CB A:ASP156 4.6 21.8 1.0
CB A:ASP86 4.6 19.0 1.0
CG A:GLU160 4.7 40.0 1.0
OE1 A:GLN153 4.7 22.1 1.0
OD2 A:ASP80 4.9 20.2 1.0
NZ A:LYS240 5.0 58.6 1.0
CG A:ASP80 5.0 15.7 1.0

Calcium binding site 4 out of 6 in 4llt

Go back to Calcium Binding Sites List in 4llt
Calcium binding site 4 out of 6 in the Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site


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 A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:16.6
occ:0.80
 O2B B:IPE302 2.3 18.1 1.0
O1A B:IPE302 2.3 23.4 1.0
O B:HOH537 2.3 29.6 1.0
OD2 B:ASP80 2.3 21.9 1.0
OD2 B:ASP86 2.4 25.1 1.0
O B:HOH497 2.4 23.9 1.0
CG B:ASP86 3.4 22.4 1.0
CG B:ASP80 3.5 17.8 1.0
PA B:IPE302 3.5 23.7 1.0
PB B:IPE302 3.5 20.2 1.0
CB B:ASP86 3.7 20.7 1.0
O3A B:IPE302 3.7 21.2 1.0
O B:HOH519 3.9 29.4 1.0
OD1 B:ASP80 4.0 19.0 1.0
O1B B:IPE302 4.1 21.1 1.0
O B:HOH546 4.2 33.3 1.0
O B:HOH538 4.2 27.6 1.0
O B:HOH539 4.2 32.6 1.0
NH1 B:ARG91 4.2 19.2 1.0
OD2 B:ASP88 4.3 27.6 1.0
C1 B:IPE302 4.4 26.4 1.0
O1 B:IPE302 4.5 24.7 1.0
OD1 B:ASP86 4.5 21.9 1.0
O2A B:IPE302 4.6 24.9 1.0
CB B:ASP80 4.6 14.2 1.0
CA B:CA305 4.7 25.3 0.8
O B:HOH520 4.7 27.4 1.0
O3B B:IPE302 4.7 19.7 1.0
OD2 B:ASP81 4.7 20.6 1.0
O B:ASP80 4.8 14.1 1.0

Calcium binding site 5 out of 6 in 4llt

Go back to Calcium Binding Sites List in 4llt
Calcium binding site 5 out of 6 in the Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site


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 A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:16.7
occ:0.80
 O1B B:IPE302 2.2 21.1 1.0
O B:HOH514 2.3 27.6 1.0
OD2 B:ASP216 2.4 19.6 1.0
O B:HOH443 2.4 21.8 1.0
O B:HOH451 2.4 19.4 1.0
O2A B:IPE302 2.4 24.9 1.0
CG B:ASP216 3.4 20.5 1.0
PB B:IPE302 3.6 20.2 1.0
PA B:IPE302 3.6 23.7 1.0
O B:HOH546 3.7 33.3 1.0
O3A B:IPE302 3.8 21.2 1.0
OD1 B:ASP216 3.8 20.5 1.0
NZ B:LYS230 4.3 20.1 1.0
O B:ASP216 4.4 17.6 1.0
O1A B:IPE302 4.4 23.4 1.0
O B:HOH475 4.4 24.7 1.0
O3B B:IPE302 4.5 19.7 1.0
OD1 B:ASP235 4.5 35.2 1.0
OD2 B:ASP235 4.5 32.4 1.0
O2B B:IPE302 4.6 18.1 1.0
NE2 B:GLN213 4.6 30.8 1.0
CB B:ASP216 4.6 18.2 1.0
CE B:LYS230 4.7 19.2 1.0
O B:HOH545 4.7 31.4 1.0
C B:ASP216 4.8 17.9 1.0
OD1 B:ASP217 4.8 23.7 1.0
O1 B:IPE302 4.9 24.7 1.0
CG B:ASP235 5.0 35.0 1.0

Calcium binding site 6 out of 6 in 4llt

Go back to Calcium Binding Sites List in 4llt
Calcium binding site 6 out of 6 in the Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site


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 A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:25.3
occ:0.80
 O B:HOH520 2.1 27.4 1.0
O B:HOH521 2.3 36.6 1.0
O B:HOH519 2.3 29.4 1.0
OD2 B:ASP156 2.4 33.7 1.0
O B:HOH539 2.5 32.6 1.0
OD1 B:ASP86 2.6 21.9 1.0
OD2 B:ASP86 2.7 25.1 1.0
CG B:ASP86 3.0 22.4 1.0
CG B:ASP156 3.6 34.5 1.0
NZ B:LYS178 3.8 43.0 1.0
OD1 B:ASP80 4.1 19.0 1.0
OE2 B:GLU160 4.1 64.8 1.0
O1A B:IPE302 4.2 23.4 1.0
OD1 B:ASP156 4.4 39.7 1.0
CB B:ASP156 4.5 28.6 1.0
CB B:ASP86 4.6 20.7 1.0
O B:HOH551 4.6 42.4 1.0
CA B:CA303 4.7 16.6 0.8
OE1 B:GLN153 4.7 27.0 1.0
OD2 B:ASP80 4.9 21.9 1.0
CG B:ASP80 4.9 17.8 1.0

Reference:

J.Kim, R.Toro, R.Bhosle, N.F.Al Obaidi, L.L.Morisco, S.R.Wasserman, S.Sojitra, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, M.Stead, J.A.Gerlt, S.C.Almo. Crystal Structure of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, with Two Ipp and Calcium Bound in Active Site To Be Published.
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