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Calcium in PDB 6xs3: X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K

Enzymatic activity of X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K

All present enzymatic activity of X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K:
3.1.1.3;

Protein crystallography data

The structure of X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K, PDB code: 6xs3 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, 90.00, 94.70, 90.00
R / Rfree (%) 17.8 / 21.3

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K (pdb code 6xs3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K, PDB code: 6xs3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6xs3

Go back to Calcium Binding Sites List in 6xs3
Calcium binding site 1 out of 8 in the X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:59.4
occ:1.00
 O A:ALA47 2.6 39.4 1.0
O A:GLU45 2.6 32.2 1.0
H A:ALA49 3.4 63.2 1.0
HA A:ASP48 3.6 53.8 1.0
HA A:GLU45 3.6 41.5 1.0
C A:GLU45 3.6 34.8 1.0
C A:ALA47 3.8 35.7 1.0
HB3 A:ASN33 3.9 65.5 1.0
O6 A:NAG303 4.0 81.2 1.0
CA A:GLU45 4.2 34.6 1.0
O5 A:NAG303 4.2 0.2 1.0
N A:ALA49 4.2 52.7 1.0
HD21 A:ASN33 4.3 92.3 1.0
HO6 A:NAG303 4.3 97.4 1.0
CA A:ASP48 4.4 44.9 1.0
O A:VAL44 4.4 32.8 1.0
ND2 A:ASN33 4.4 76.9 1.0
N A:ASP48 4.5 39.9 1.0
O A:ALA49 4.5 40.3 1.0
C A:LYS46 4.5 39.2 1.0
O A:LYS46 4.6 46.0 1.0
N A:ALA47 4.6 37.4 1.0
CG A:ASN33 4.6 61.7 1.0
CB A:ASN33 4.7 54.6 1.0
HB3 A:GLU45 4.8 39.7 1.0
N A:LYS46 4.8 34.9 1.0
HB3 A:ALA49 4.8 41.8 1.0
CA A:ALA47 4.8 35.7 1.0
C A:ASP48 4.9 44.0 1.0
H A:ALA47 4.9 44.8 1.0
O A:ILE34 5.0 41.4 1.0
C1 A:NAG303 5.0 92.9 1.0
HA A:LYS46 5.0 44.7 1.0

Calcium binding site 2 out of 8 in 6xs3

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Calcium binding site 2 out of 8 in the X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:30.0
occ:1.00
 O B:HOH410 2.1 35.9 1.0
O B:HOH450 2.4 27.6 1.0
O B:GLU45 2.5 24.1 1.0
O B:HOH448 2.6 25.4 1.0
O B:HOH425 2.6 23.2 1.0
O B:ALA47 2.6 21.6 1.0
C B:GLU45 3.6 24.8 1.0
H B:ALA49 3.6 27.3 1.0
HA B:GLU45 3.6 30.1 1.0
HB3 B:ASN33 3.7 40.1 1.0
HA B:ASP48 3.7 33.4 1.0
C B:ALA47 3.8 23.0 1.0
CA B:GLU45 4.2 25.1 1.0
O B:VAL44 4.4 19.9 1.0
N B:ALA49 4.5 22.8 1.0
CA B:ASP48 4.5 27.9 1.0
C B:LYS46 4.6 23.8 1.0
N B:ASP48 4.6 23.6 1.0
CB B:ASN33 4.6 33.4 1.0
N B:ALA47 4.6 22.5 1.0
O B:LYS46 4.7 24.6 1.0
O B:ILE34 4.7 30.4 1.0
HB3 B:GLU45 4.7 30.9 1.0
O B:ALA49 4.7 19.9 1.0
N B:LYS46 4.7 24.1 1.0
CG B:ASN33 4.8 36.4 1.0
H B:ALA47 4.8 27.0 1.0
CA B:ALA47 4.9 23.1 1.0
H B:ILE34 4.9 30.3 1.0
O5 B:NAG305 5.0 58.4 1.0
HB3 B:ALA49 5.0 29.1 1.0

Calcium binding site 3 out of 8 in 6xs3

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Calcium binding site 3 out of 8 in the X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:55.5
occ:1.00
 O B:HOH403 2.2 23.7 1.0
O B:HOH467 2.3 23.1 1.0
O B:HOH406 2.3 27.0 1.0
O B:HOH404 2.4 40.4 1.0
HH22 B:ARG81 2.7 27.2 1.0
OD2 B:ASP62 3.0 19.5 1.0
HB3 B:SER85 3.1 28.1 1.0
HH12 B:ARG81 3.1 27.1 1.0
O B:HOH466 3.4 29.6 1.0
O B:HOH463 3.4 35.0 1.0
NH2 B:ARG81 3.5 22.7 1.0
OD1 B:ASP57 3.7 30.6 1.0
NH1 B:ARG81 3.8 22.6 1.0
CG B:ASP62 3.9 20.9 1.0
OD1 B:ASP62 3.9 23.0 1.0
CB B:SER85 4.0 23.5 1.0
HG B:SER85 4.1 25.6 1.0
HH21 B:ARG81 4.1 27.2 1.0
CZ B:ARG81 4.1 21.8 1.0
HB2 B:SER85 4.2 28.1 1.0
OG B:SER85 4.5 21.3 1.0
HH11 B:ARG81 4.5 27.1 1.0
HB2 B:GLU56 4.8 29.6 1.0
CG B:ASP57 4.9 31.8 1.0
H B:ASP57 4.9 27.3 1.0
H B:SER85 4.9 28.5 1.0
OG1 B:THR64 5.0 20.2 1.0

Calcium binding site 4 out of 8 in 6xs3

Go back to Calcium Binding Sites List in 6xs3
Calcium binding site 4 out of 8 in the X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:48.0
occ:1.00
 O C:HOH473 2.4 37.1 1.0
O C:HOH452 2.5 34.0 1.0
O C:GLU45 2.6 24.8 1.0
O C:ALA47 2.7 28.9 1.0
O C:HOH433 2.7 40.4 1.0
O C:HOH409 3.2 49.9 1.0
HA C:GLU45 3.6 33.2 1.0
C C:GLU45 3.7 26.8 1.0
H C:ALA49 3.7 33.9 1.0
HA C:ASP48 3.8 45.6 1.0
C C:ALA47 3.8 29.7 1.0
HB3 C:ASN33 3.9 36.3 1.0
CA C:GLU45 4.2 27.6 1.0
O5 C:NAG304 4.3 93.5 1.0
O C:HOH402 4.3 57.4 1.0
O C:LYS46 4.3 28.5 1.0
C C:LYS46 4.4 28.0 1.0
HO6 C:NAG304 4.4 0.6 1.0
O C:VAL44 4.5 23.8 1.0
OD1 C:ASN33 4.5 52.0 1.0
N C:ALA49 4.5 28.2 1.0
CG C:ASN33 4.6 41.6 1.0
CA C:ASP48 4.6 38.0 1.0
N C:ASP48 4.6 32.5 1.0
N C:ALA47 4.6 27.0 1.0
CB C:ASN33 4.7 30.2 1.0
HB3 C:GLU45 4.7 34.8 1.0
N C:LYS46 4.8 28.7 1.0
C1 C:NAG304 4.8 78.1 1.0
O C:ALA49 4.9 26.4 1.0
O C:ILE34 4.9 25.9 1.0
CA C:ALA47 4.9 29.5 1.0
H C:ALA47 5.0 32.3 1.0
O6 C:NAG304 5.0 0.5 1.0

Calcium binding site 5 out of 8 in 6xs3

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Calcium binding site 5 out of 8 in the X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:84.2
occ:1.00
 O C:HOH479 2.6 46.8 1.0
O C:HOH475 2.6 35.9 1.0
HH12 C:ARG81 2.6 22.9 1.0
O C:HOH405 2.8 20.5 1.0
O C:HOH466 3.1 50.6 1.0
HH22 C:ARG81 3.2 26.3 1.0
HB3 C:SER85 3.3 30.4 1.0
NH1 C:ARG81 3.5 19.1 1.0
O C:HOH458 3.5 20.6 0.6
O C:HOH458 3.5 21.3 0.4
NH2 C:ARG81 3.9 21.9 1.0
HH11 C:ARG81 4.1 22.9 1.0
OD2 C:ASP62 4.2 26.6 1.0
CZ C:ARG81 4.2 20.2 1.0
O C:HOH468 4.2 29.5 1.0
HG2 C:ARG84 4.2 32.1 1.0
CB C:SER85 4.3 25.3 1.0
O C:HOH403 4.3 37.9 1.0
HB2 C:SER85 4.5 30.4 1.0
HD2 C:ARG84 4.6 31.6 1.0
O B:HOH452 4.6 36.7 1.0
HH21 C:ARG81 4.6 26.3 1.0
HB3 C:ARG84 4.7 28.7 1.0
HA C:SER85 4.8 30.9 1.0
HG C:SER85 4.8 28.0 1.0
OD1 C:ASP57 5.0 53.7 1.0
CA C:SER85 5.0 25.8 1.0

Calcium binding site 6 out of 8 in 6xs3

Go back to Calcium Binding Sites List in 6xs3
Calcium binding site 6 out of 8 in the X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca302

b:66.8
occ:1.00
 O E:GLU45 2.8 48.7 1.0
O E:ALA47 3.0 49.0 1.0
OD1 E:ASN33 3.1 88.7 1.0
HO6 E:NAG303 3.2 0.4 1.0
HA E:GLU45 3.5 67.4 1.0
H E:ALA49 3.6 61.3 1.0
HB3 E:ASN33 3.6 78.8 1.0
C E:GLU45 3.8 55.2 1.0
O6 E:NAG303 3.9 92.0 1.0
CG E:ASN33 4.0 81.3 1.0
HA E:ASP48 4.1 68.0 1.0
CA E:GLU45 4.2 56.1 1.0
C E:ALA47 4.2 48.8 1.0
O E:ILE34 4.3 54.5 1.0
CB E:ASN33 4.3 65.7 1.0
O E:ALA49 4.3 52.3 1.0
N E:ALA49 4.4 51.1 1.0
H E:ILE34 4.4 75.6 1.0
O E:VAL44 4.5 46.5 1.0
O5 E:NAG303 4.5 0.5 1.0
HB3 E:ALA49 4.6 64.5 1.0
HB3 E:GLU45 4.7 70.8 1.0
HG22 E:THR35 4.8 68.7 1.0
CA E:ASP48 4.8 56.7 1.0
C E:LYS46 4.9 51.1 1.0
O E:LYS46 4.9 51.3 1.0
N E:ALA47 5.0 51.9 1.0
N E:ILE34 5.0 63.0 1.0
N E:LYS46 5.0 53.4 1.0
N E:ASP48 5.0 50.2 1.0
HB2 E:ASN33 5.0 78.8 1.0

Calcium binding site 7 out of 8 in 6xs3

Go back to Calcium Binding Sites List in 6xs3
Calcium binding site 7 out of 8 in the X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:51.0
occ:1.00
 O D:ALA47 2.6 31.0 1.0
O D:HOH426 2.8 32.8 1.0
O D:GLU45 2.9 26.0 1.0
HO6 D:NAG303 3.0 0.0 1.0
H D:ALA49 3.4 39.1 1.0
HA D:ASP48 3.5 41.5 1.0
HB3 D:ASN33 3.6 56.7 1.0
O6 D:NAG303 3.7 0.3 1.0
C D:ALA47 3.8 28.9 1.0
HA D:GLU45 3.9 33.9 1.0
C D:GLU45 3.9 28.1 1.0
O5 D:NAG303 4.1 90.0 1.0
N D:ALA49 4.3 32.6 1.0
CG D:ASN33 4.3 55.8 1.0
CA D:ASP48 4.3 34.6 1.0
OD1 D:ASN33 4.4 0.1 1.0
CB D:ASN33 4.4 47.3 1.0
CA D:GLU45 4.5 28.2 1.0
N D:ASP48 4.5 30.9 1.0
O D:ALA49 4.5 29.6 1.0
O D:VAL44 4.6 25.4 1.0
ND2 D:ASN33 4.7 61.0 1.0
O D:HOH451 4.7 45.9 1.0
O D:ILE34 4.7 26.2 1.0
H61 D:NAG303 4.7 0.6 1.0
C6 D:NAG303 4.7 0.7 1.0
N D:ALA47 4.8 28.9 1.0
H D:ILE34 4.8 39.6 1.0
C D:LYS46 4.8 32.1 1.0
C D:ASP48 4.9 32.0 1.0
HB3 D:ALA49 4.9 34.2 1.0
HD21 D:ASN33 4.9 73.2 1.0
C1 D:NAG303 4.9 91.3 1.0
HD22 D:ASN33 4.9 73.2 1.0
HA D:ASN33 4.9 40.7 1.0
CA D:ALA47 5.0 27.1 1.0
O D:LYS46 5.0 32.2 1.0

Calcium binding site 8 out of 8 in 6xs3

Go back to Calcium Binding Sites List in 6xs3
Calcium binding site 8 out of 8 in the X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of X-Ray Structure of the Monoclinic Crystal Form at 2.48 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca302

b:57.7
occ:1.00
 O F:GLU45 2.3 48.0 1.0
O F:HOH417 2.5 49.3 1.0
O F:ALA47 2.7 57.5 1.0
C F:GLU45 3.4 49.5 1.0
HA F:GLU45 3.4 57.1 1.0
HO6 F:NAG303 3.6 0.2 1.0
H F:ALA49 3.7 66.8 1.0
HB3 F:ASN33 3.8 72.1 1.0
C F:ALA47 3.9 56.5 1.0
HA F:ASP48 3.9 89.3 1.0
CA F:GLU45 4.0 47.6 1.0
O6 F:NAG303 4.1 92.7 1.0
O5 F:NAG303 4.2 0.9 1.0
O F:VAL44 4.3 39.4 1.0
C F:LYS46 4.4 49.5 1.0
HD21 F:ASN33 4.4 0.4 1.0
O F:LYS46 4.4 48.4 1.0
ND2 F:ASN33 4.4 87.8 1.0
CG F:ASN33 4.5 74.0 1.0
N F:ALA49 4.5 55.6 1.0
HB3 F:GLU45 4.5 55.4 1.0
N F:LYS46 4.5 52.8 1.0
N F:ALA47 4.5 48.6 1.0
CB F:ASN33 4.6 60.1 1.0
CA F:ASP48 4.7 74.4 1.0
O F:ILE34 4.7 47.1 1.0
N F:ASP48 4.7 62.4 1.0
HA F:LYS46 4.7 67.3 1.0
O F:ALA49 4.8 42.8 1.0
H F:ALA47 4.8 58.3 1.0
CA F:LYS46 4.8 56.1 1.0
CA F:ALA47 4.9 51.9 1.0
C1 F:NAG303 4.9 0.3 1.0
CB F:GLU45 4.9 46.2 1.0
OD1 F:ASN33 4.9 67.3 1.0
HB3 F:ALA49 4.9 52.1 1.0
HG22 F:THR35 4.9 57.0 1.0
H F:ILE34 5.0 51.0 1.0

Reference:

A.Mcpherson, S.B.Larson, A.Kalasky. The Crystal Structures of Thermomyces (Humicola) Lanuginosa Lipase in Complex with Enzymatic Reactants Current Enzyme Inhibition V. 16 2020.
DOI: 10.2174/1573408016999200511090910
Page generated: Tue Jul 16 18:11:24 2024

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