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Calcium in PDB 6o9f: The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form

Enzymatic activity of The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form

All present enzymatic activity of The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form:
3.1.1.3;

Protein crystallography data

The structure of The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form, PDB code: 6o9f was solved by A.Mcpherson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.27 / 2.48
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.185, 91.366, 124.316, 90, 94.71, 90
R / Rfree (%) 17.5 / 21.5

Calcium Binding Sites:

The binding sites of Calcium atom in the The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form (pdb code 6o9f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form, PDB code: 6o9f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6o9f

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Calcium binding site 1 out of 8 in the The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:60.8
occ:1.00
 O A:GLU45 2.6 32.8 1.0
O A:ALA47 2.6 39.4 1.0
H A:ALA49 3.5 58.9 1.0
HA A:GLU45 3.6 41.2 1.0
HA A:ASP48 3.6 52.1 1.0
C A:GLU45 3.7 34.7 1.0
C A:ALA47 3.8 34.9 1.0
HB3 A:ASN33 3.9 67.1 1.0
O6 A:NAG303 4.1 79.8 1.0
HD22 A:ASN33 4.1 90.5 1.0
HD21 A:ASN33 4.1 90.5 1.0
O5 A:NAG303 4.2 97.4 1.0
CA A:GLU45 4.2 34.3 1.0
ND2 A:ASN33 4.3 75.4 1.0
N A:ALA49 4.3 49.1 1.0
HO6 A:NAG303 4.3 95.8 1.0
O A:VAL44 4.4 32.6 1.0
CA A:ASP48 4.4 43.4 1.0
O A:ALA49 4.5 39.2 1.0
CG A:ASN33 4.5 62.5 1.0
N A:ASP48 4.6 39.0 1.0
C A:LYS46 4.6 40.5 1.0
CB A:ASN33 4.6 55.9 1.0
O A:LYS46 4.7 45.8 1.0
N A:ALA47 4.7 38.5 1.0
HB3 A:GLU45 4.8 40.4 1.0
N A:LYS46 4.8 35.9 1.0
HB3 A:ALA49 4.8 41.8 1.0
C1 A:NAG303 4.8 86.2 1.0
CA A:ALA47 4.9 35.7 1.0
C A:ASP48 4.9 42.7 1.0
O A:ILE34 4.9 40.3 1.0
H A:ILE34 4.9 56.9 1.0
H A:ALA47 4.9 46.2 1.0

Calcium binding site 2 out of 8 in 6o9f

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Calcium binding site 2 out of 8 in the The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:29.7
occ:1.00
 O B:HOH414 2.2 37.2 1.0
O B:HOH446 2.4 27.7 1.0
O B:ALA47 2.5 20.9 1.0
O B:GLU45 2.5 22.5 1.0
O B:HOH421 2.7 22.8 1.0
O B:HOH452 2.7 24.7 1.0
HA B:ASP48 3.6 33.1 1.0
H B:ALA49 3.6 26.8 1.0
C B:GLU45 3.6 23.9 1.0
C B:ALA47 3.7 23.7 1.0
HA B:GLU45 3.7 30.7 1.0
HB3 B:ASN33 3.9 41.0 1.0
CA B:GLU45 4.2 25.5 1.0
CA B:ASP48 4.4 27.5 1.0
N B:ALA49 4.4 22.3 1.0
O B:VAL44 4.4 21.0 1.0
N B:ASP48 4.4 22.2 1.0
C B:LYS46 4.5 23.7 1.0
N B:ALA47 4.5 21.8 1.0
O B:LYS46 4.5 26.4 1.0
N B:LYS46 4.7 25.2 1.0
H B:ALA47 4.7 26.1 1.0
CA B:ALA47 4.7 22.7 1.0
HB3 B:GLU45 4.8 30.4 1.0
O B:ALA49 4.8 20.9 1.0
CB B:ASN33 4.8 34.1 1.0
O B:ILE34 4.9 29.9 1.0
CG B:ASN33 4.9 35.3 1.0
HA B:LYS46 4.9 28.9 1.0
O5 B:NAG305 4.9 55.9 1.0
H B:ILE34 5.0 28.4 1.0
C B:ASP48 5.0 21.4 1.0
CA B:LYS46 5.0 24.1 1.0

Calcium binding site 3 out of 8 in 6o9f

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Calcium binding site 3 out of 8 in the The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:53.5
occ:1.00
 O B:HOH401 2.3 21.3 1.0
O B:HOH468 2.3 24.3 1.0
O B:HOH406 2.4 26.6 1.0
O B:HOH404 2.5 38.5 1.0
HH22 B:ARG81 2.8 29.6 1.0
HH12 B:ARG81 3.0 29.4 1.0
HB3 B:SER85 3.1 24.8 1.0
OD2 B:ASP62 3.1 16.9 1.0
O B:HOH463 3.5 29.5 1.0
O B:HOH460 3.5 35.7 1.0
NH2 B:ARG81 3.5 24.6 1.0
NH1 B:ARG81 3.7 24.4 1.0
OD1 B:ASP57 3.8 32.4 1.0
CG B:ASP62 4.0 21.8 1.0
CB B:SER85 4.0 20.6 1.0
OD1 B:ASP62 4.0 23.0 1.0
CZ B:ARG81 4.1 21.8 1.0
HG B:SER85 4.2 25.6 1.0
HH21 B:ARG81 4.2 29.6 1.0
HB2 B:SER85 4.2 24.8 1.0
HH11 B:ARG81 4.4 29.4 1.0
OG B:SER85 4.5 21.3 1.0
HB2 B:GLU56 4.8 29.2 1.0
CG B:ASP57 4.9 33.0 1.0
H B:SER85 5.0 30.1 1.0
OG1 B:THR64 5.0 21.4 1.0

Calcium binding site 4 out of 8 in 6o9f

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Calcium binding site 4 out of 8 in the The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:48.0
occ:1.00
 O C:HOH471 2.4 36.5 1.0
O C:HOH450 2.5 34.6 1.0
O C:GLU45 2.6 24.6 1.0
O C:HOH433 2.6 39.3 1.0
O C:ALA47 2.6 29.8 1.0
O C:HOH408 3.1 47.6 1.0
HA C:GLU45 3.6 30.8 1.0
H C:ALA49 3.6 34.7 1.0
C C:GLU45 3.7 26.0 1.0
HA C:ASP48 3.7 46.2 1.0
C C:ALA47 3.8 28.9 1.0
HB3 C:ASN33 3.9 36.3 1.0
CA C:GLU45 4.2 25.6 1.0
O5 C:NAG304 4.3 90.5 1.0
O C:HOH402 4.3 56.0 1.0
O C:LYS46 4.3 28.8 1.0
HO6 C:NAG304 4.4 114.2 1.0
O C:VAL44 4.4 22.8 1.0
C C:LYS46 4.4 28.6 1.0
N C:ALA49 4.5 28.9 1.0
CA C:ASP48 4.5 38.5 1.0
N C:ASP48 4.6 33.8 1.0
N C:ALA47 4.6 28.0 1.0
CG C:ASN33 4.7 43.1 1.0
CB C:ASN33 4.7 30.2 1.0
HB3 C:GLU45 4.7 34.1 1.0
C1 C:NAG304 4.8 77.4 1.0
N C:LYS46 4.8 29.0 1.0
O C:ALA49 4.8 28.2 1.0
CA C:ALA47 4.9 30.7 1.0
OD1 C:ASN33 4.9 55.2 1.0
O C:ILE34 4.9 26.6 1.0
H C:ALA47 4.9 33.6 1.0
O6 C:NAG304 5.0 95.1 1.0
HB3 C:ALA49 5.0 29.0 1.0

Calcium binding site 5 out of 8 in 6o9f

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Calcium binding site 5 out of 8 in the The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:58.8
occ:1.00
 HH12 C:ARG81 2.6 21.1 1.0
O C:HOH475 2.8 33.4 1.0
O C:HOH478 2.8 38.4 1.0
O C:HOH404 2.8 13.6 1.0
HH22 C:ARG81 3.1 26.6 1.0
O C:HOH459 3.1 39.4 1.0
HB3 C:SER85 3.2 31.0 1.0
NH1 C:ARG81 3.4 17.6 1.0
O C:HOH462 3.5 19.0 0.6
O C:HOH462 3.7 18.5 0.4
NH2 C:ARG81 3.8 22.1 1.0
HH11 C:ARG81 4.0 21.1 1.0
OD2 C:ASP62 4.1 27.7 1.0
CZ C:ARG81 4.1 19.9 1.0
CB C:SER85 4.1 25.8 1.0
O C:HOH466 4.2 30.8 1.0
HG2 C:ARG84 4.2 31.9 1.0
O C:HOH405 4.2 37.9 1.0
HB2 C:SER85 4.4 31.0 1.0
HH21 C:ARG81 4.6 26.6 1.0
O B:HOH449 4.6 35.5 1.0
HD2 C:ARG84 4.6 30.7 1.0
HB3 C:ARG84 4.7 28.1 1.0
HG C:SER85 4.7 26.7 1.0
HA C:SER85 4.7 30.0 1.0
CA C:SER85 4.9 25.0 1.0
H C:SER85 4.9 30.4 1.0
OG C:SER85 4.9 22.2 1.0
OD1 C:ASP57 4.9 45.8 1.0
CG C:ARG84 5.0 26.5 1.0

Calcium binding site 6 out of 8 in 6o9f

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Calcium binding site 6 out of 8 in the The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca302

b:66.7
occ:1.00
 O E:GLU45 2.8 48.8 1.0
O E:ALA47 3.0 50.9 1.0
OD1 E:ASN33 3.3 82.5 1.0
HO6 E:NAG303 3.3 105.3 1.0
HA E:GLU45 3.4 66.7 1.0
H E:ALA49 3.6 62.8 1.0
HB3 E:ASN33 3.6 75.9 1.0
C E:GLU45 3.8 54.2 1.0
O6 E:NAG303 4.0 87.8 1.0
HA E:ASP48 4.1 67.6 1.0
CA E:GLU45 4.1 55.6 1.0
CG E:ASN33 4.1 77.3 1.0
O E:ILE34 4.2 55.3 1.0
C E:ALA47 4.2 50.6 1.0
O E:ALA49 4.3 52.3 1.0
CB E:ASN33 4.3 63.2 1.0
O E:VAL44 4.3 48.4 1.0
N E:ALA49 4.4 52.3 1.0
H E:ILE34 4.4 74.1 1.0
HB3 E:ALA49 4.5 63.4 1.0
O5 E:NAG303 4.6 103.8 1.0
HB3 E:GLU45 4.7 66.5 1.0
HG22 E:THR35 4.7 71.9 1.0
CA E:ASP48 4.9 56.3 1.0
C E:LYS46 4.9 51.7 1.0
N E:ILE34 4.9 61.8 1.0
N E:LYS46 5.0 51.8 1.0
CB E:GLU45 5.0 55.4 1.0
N E:ALA47 5.0 51.8 1.0
O E:LYS46 5.0 52.9 1.0
N E:ASP48 5.0 52.0 1.0

Calcium binding site 7 out of 8 in 6o9f

Go back to Calcium Binding Sites List in 6o9f
Calcium binding site 7 out of 8 in the The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:50.7
occ:1.00
 O D:ALA47 2.6 32.4 1.0
O D:HOH423 2.8 32.9 1.0
O D:GLU45 2.8 25.4 1.0
HO6 D:NAG303 3.0 115.0 1.0
H D:ALA49 3.5 40.3 1.0
HA D:ASP48 3.5 42.1 1.0
C D:ALA47 3.8 28.4 1.0
O6 D:NAG303 3.8 95.8 1.0
HA D:GLU45 3.8 35.4 1.0
C D:GLU45 3.9 28.1 1.0
OD1 D:ASN33 4.2 73.7 1.0
HB3 D:ASN33 4.2 53.6 1.0
CG D:ASN33 4.2 57.4 1.0
N D:ALA49 4.3 33.6 1.0
CA D:ASP48 4.3 35.0 1.0
CA D:GLU45 4.4 29.4 1.0
N D:ASP48 4.5 30.4 1.0
ND2 D:ASN33 4.5 45.0 1.0
HD22 D:ASN33 4.6 54.0 1.0
O D:VAL44 4.6 25.9 1.0
O D:ALA49 4.6 30.9 1.0
O5 D:NAG303 4.7 86.0 1.0
H61 D:NAG303 4.7 129.5 1.0
O D:HOH432 4.7 45.4 1.0
N D:ALA47 4.7 28.2 1.0
CB D:ASN33 4.7 44.7 1.0
C D:LYS46 4.8 33.4 1.0
C6 D:NAG303 4.8 107.9 1.0
HD21 D:ASN33 4.9 54.0 1.0
C D:ASP48 4.9 32.5 1.0
H D:ILE34 4.9 41.0 1.0
CA D:ALA47 4.9 25.8 1.0
O D:ILE34 4.9 25.5 1.0
O D:LYS46 4.9 32.3 1.0
H D:ALA47 4.9 33.9 1.0
HB3 D:ALA49 4.9 34.3 1.0
HB3 D:GLU45 5.0 29.3 1.0
N D:LYS46 5.0 29.4 1.0
HA D:ASN33 5.0 39.2 1.0

Calcium binding site 8 out of 8 in 6o9f

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Calcium binding site 8 out of 8 in the The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Structure of Thermomyces Lanuginosa Lipase in Complex with 1,3 Diacylglycerol in A Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca302

b:56.6
occ:1.00
 O F:GLU45 2.5 49.6 1.0
O F:HOH415 2.5 49.9 1.0
O F:ALA47 2.6 57.9 1.0
HO6 F:NAG303 3.4 104.3 1.0
H F:ALA49 3.5 66.6 1.0
C F:GLU45 3.6 50.9 1.0
HA F:GLU45 3.6 58.2 1.0
HA F:ASP48 3.7 79.2 1.0
C F:ALA47 3.8 55.9 1.0
HB3 F:ASN33 3.8 69.3 1.0
O6 F:NAG303 4.0 86.9 1.0
O5 F:NAG303 4.1 113.4 1.0
CA F:GLU45 4.1 48.5 1.0
O F:VAL44 4.3 40.6 1.0
N F:ALA49 4.3 55.5 1.0
C F:LYS46 4.4 51.1 1.0
ND2 F:ASN33 4.4 84.7 1.0
CG F:ASN33 4.4 72.1 1.0
O F:LYS46 4.4 50.0 1.0
HD22 F:ASN33 4.5 101.6 1.0
CA F:ASP48 4.5 66.0 1.0
N F:ASP48 4.5 59.3 1.0
N F:ALA47 4.5 49.4 1.0
CB F:ASN33 4.6 57.8 1.0
O F:ALA49 4.6 42.3 1.0
N F:LYS46 4.7 53.4 1.0
HD21 F:ASN33 4.7 101.6 1.0
HB3 F:GLU45 4.7 55.9 1.0
C1 F:NAG303 4.8 102.8 1.0
O F:ILE34 4.8 48.3 1.0
H F:ILE34 4.8 52.3 1.0
CA F:ALA47 4.8 53.0 1.0
HB3 F:ALA49 4.8 53.9 1.0
H F:ALA47 4.8 59.3 1.0
OD1 F:ASN33 4.8 64.7 1.0
HA F:LYS46 4.9 66.1 1.0
CA F:LYS46 4.9 55.0 1.0
C F:ASP48 5.0 59.0 1.0
HA F:ASN33 5.0 54.8 1.0

Reference:

A.Mcpherson, B.S.Larson, A.Kalasky. The Crystal Structures of Thermomyces (Humicola) Lanuginosa Lipase in Complex with Enzymatic Reactants Curr Enzym Inhib V. 16 199 2020.
ISSN: ESSN 1875-6662
DOI: HTTP://DX.DOI.ORG/10.2174/1573408016999200511090910
Page generated: Tue Jul 16 12:22:42 2024

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