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Calcium in PDB 6osz: High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products

Enzymatic activity of High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products

All present enzymatic activity of High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products:
3.1.1.3;

Protein crystallography data

The structure of High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products, PDB code: 6osz was solved by A.Mcpherson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.69 / 1.43
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.929, 89.937, 123.422, 90, 94.49, 90
R / Rfree (%) 14.9 / 18.5

Calcium Binding Sites:

The binding sites of Calcium atom in the High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products (pdb code 6osz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products, PDB code: 6osz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6osz

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Calcium binding site 1 out of 6 in the High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:20.3
occ:0.97
 O B:GLU45 2.3 20.0 1.0
O B:HOH593 2.5 31.1 1.0
O B:HOH618 2.5 24.5 1.0
O B:HOH522 2.5 21.9 1.0
O B:HOH589 2.5 26.0 1.0
O B:HOH500 2.5 19.4 1.0
O B:HOH542 2.5 35.1 1.0
O B:ALA47 2.5 19.9 1.0
C B:GLU45 3.4 20.8 1.0
HA B:GLU45 3.6 25.5 1.0
H B:ALA49 3.6 23.6 1.0
C B:ALA47 3.7 20.0 1.0
HA B:ASP48 3.8 26.4 1.0
HB3 B:ASN33 4.0 27.7 1.0
CA B:GLU45 4.1 21.3 1.0
O B:VAL44 4.3 20.6 1.0
C B:LYS46 4.3 21.2 1.0
HD21 B:ASN33 4.4 36.3 1.0
O B:LYS46 4.4 21.8 1.0
N B:ALA47 4.4 19.9 1.0
O B:HOH678 4.5 48.6 1.0
N B:ALA49 4.5 19.6 1.0
N B:ASP48 4.5 21.0 1.0
O B:ILE34 4.5 19.2 1.0
N B:LYS46 4.5 21.1 1.0
CA B:ASP48 4.5 22.0 1.0
ND2 B:ASN33 4.6 30.3 1.0
O B:HOH444 4.6 36.9 1.0
O B:HOH438 4.6 29.1 1.0
H B:ALA47 4.7 23.9 1.0
HB3 B:GLU45 4.7 27.6 1.0
CA B:ALA47 4.7 19.6 1.0
HA B:LYS46 4.7 26.4 1.0
O B:ALA49 4.8 20.1 1.0
O B:HOH663 4.8 45.3 1.0
CA B:LYS46 4.8 22.0 1.0
CG B:ASN33 4.8 27.9 1.0
HD22 B:ASN33 4.8 36.3 1.0
CB B:ASN33 4.9 23.1 1.0
HB3 B:ALA49 5.0 24.9 1.0
HO6 B:NAG305 5.0 43.9 1.0

Calcium binding site 2 out of 6 in 6osz

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Calcium binding site 2 out of 6 in the High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:52.1
occ:1.00
 O B:HOH601 2.1 37.7 1.0
HH22 B:ARG81 2.3 22.1 1.0
O B:HOH404 2.5 11.0 1.0
HH12 B:ARG81 2.5 22.5 1.0
O B:HOH587 2.7 41.9 1.0
HB3 B:SER85 2.8 24.9 1.0
O B:HOH513 2.9 22.7 1.0
O B:HOH650 3.1 36.7 1.0
O B:HOH715 3.1 53.8 1.0
NH2 B:ARG81 3.1 18.4 1.0
OD2 B:ASP62 3.3 20.1 1.0
NH1 B:ARG81 3.3 18.7 1.0
O B:HOH676 3.5 35.1 1.0
CZ B:ARG81 3.7 17.7 1.0
CB B:SER85 3.8 20.8 1.0
O B:HOH712 3.8 35.4 1.0
HH21 B:ARG81 3.8 22.1 1.0
O B:HOH536 4.0 23.7 1.0
HH11 B:ARG81 4.0 22.5 1.0
HB2 B:SER85 4.1 24.9 1.0
HG B:SER85 4.1 23.5 1.0
CG B:ASP62 4.2 19.1 1.0
OD1 B:ASP62 4.4 20.2 1.0
OG B:SER85 4.4 19.6 1.0
OD1 B:ASP57 4.5 29.4 1.0
H B:SER85 4.5 25.1 1.0
O B:HOH659 4.5 38.4 1.0
O B:HOH557 4.6 42.9 1.0
HB3 B:ARG84 4.6 28.6 1.0
HG2 B:ARG84 4.6 31.1 1.0
HA B:SER85 4.6 25.2 1.0
CA B:SER85 4.6 21.0 1.0
N B:SER85 4.7 20.9 1.0
NE B:ARG81 5.0 16.8 1.0
HG21 B:THR64 5.0 19.4 1.0

Calcium binding site 3 out of 6 in 6osz

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Calcium binding site 3 out of 6 in the High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:37.1
occ:0.79
 O C:HOH590 2.2 49.8 1.0
O C:HOH597 2.3 36.8 1.0
O C:GLU45 2.3 24.5 1.0
O C:HOH542 2.4 31.1 1.0
O C:ALA47 2.4 26.0 1.0
O C:HOH458 2.5 33.6 1.0
HA C:GLU45 3.3 29.0 1.0
C C:GLU45 3.4 24.9 1.0
H C:ALA49 3.4 30.2 1.0
C C:ALA47 3.6 26.6 1.0
HA C:ASP48 3.8 35.2 1.0
CA C:GLU45 3.9 24.2 1.0
O C:VAL44 4.0 21.8 1.0
HB3 C:ASN33 4.0 36.2 1.0
HO6 C:NAG303 4.3 62.8 1.0
N C:ALA49 4.3 25.2 1.0
C C:LYS46 4.3 26.7 1.0
N C:ALA47 4.3 26.2 1.0
N C:ASP48 4.5 27.9 1.0
N C:LYS46 4.5 25.2 1.0
CA C:ASP48 4.5 29.3 1.0
O C:HOH401 4.5 44.7 1.0
O C:HOH404 4.5 41.7 1.0
H C:ALA47 4.5 31.5 1.0
O C:LYS46 4.6 27.2 1.0
O C:ILE34 4.6 21.8 1.0
O C:ALA49 4.6 21.8 1.0
O5 C:NAG303 4.6 50.0 1.0
HB3 C:ALA49 4.6 29.8 1.0
HB3 C:GLU45 4.6 29.5 1.0
CG C:ASN33 4.6 38.4 1.0
CA C:ALA47 4.6 27.4 1.0
OD1 C:ASN33 4.6 40.7 1.0
O6 C:NAG303 4.8 52.4 1.0
H61 C:NAG303 4.8 62.5 1.0
CB C:ASN33 4.8 30.1 1.0
HA C:LYS46 4.8 33.4 1.0
CA C:LYS46 4.8 27.8 1.0
CB C:GLU45 4.9 24.6 1.0
C C:VAL44 4.9 21.9 1.0
N C:GLU45 4.9 22.4 1.0
C C:ASP48 5.0 28.2 1.0
H C:ILE34 5.0 25.1 1.0

Calcium binding site 4 out of 6 in 6osz

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Calcium binding site 4 out of 6 in the High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca302

b:50.0
occ:1.00
 O E:HOH405 2.3 55.3 1.0
O E:HOH495 2.4 41.6 1.0
O E:GLU45 2.4 39.8 1.0
O E:ALA47 2.5 39.8 1.0
O E:HOH481 2.5 46.9 1.0
O E:HOH564 2.5 44.1 1.0
HO6 E:NAG303 3.4 71.7 1.0
HA E:GLU45 3.4 46.6 1.0
C E:GLU45 3.5 40.3 1.0
H E:ALA49 3.5 46.3 1.0
C E:ALA47 3.7 40.2 1.0
HA E:ASP48 3.8 49.1 1.0
CA E:GLU45 4.0 38.9 1.0
HB3 E:ASN33 4.1 52.8 1.0
O6 E:NAG303 4.2 59.8 1.0
O E:VAL44 4.2 35.7 1.0
N E:ALA49 4.3 38.6 1.0
C E:LYS46 4.3 42.2 1.0
N E:ALA47 4.4 41.3 1.0
O E:LYS46 4.4 42.1 1.0
O5 E:NAG303 4.5 57.5 1.0
O E:ILE34 4.5 35.9 1.0
N E:LYS46 4.5 42.1 1.0
CA E:ASP48 4.5 40.9 1.0
N E:ASP48 4.5 40.7 1.0
H E:ALA47 4.6 49.6 1.0
HB3 E:ALA49 4.6 44.3 1.0
O E:ALA49 4.6 36.1 1.0
HB3 E:GLU45 4.7 48.0 1.0
CG E:ASN33 4.7 48.5 1.0
CA E:ALA47 4.7 40.5 1.0
ND2 E:ASN33 4.7 52.3 1.0
HA E:LYS46 4.8 51.8 1.0
H E:ILE34 4.8 44.4 1.0
CA E:LYS46 4.8 43.2 1.0
HD21 E:ASN33 4.8 62.7 1.0
HD22 E:ASN33 4.8 62.7 1.0
CB E:ASN33 4.9 44.0 1.0
O E:HOH408 4.9 46.8 1.0
OD1 E:ASN33 5.0 48.2 1.0
CB E:GLU45 5.0 40.0 1.0
C E:ASP48 5.0 39.8 1.0

Calcium binding site 5 out of 6 in 6osz

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Calcium binding site 5 out of 6 in the High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:28.3
occ:0.74
 O D:HOH591 2.3 33.0 1.0
O D:HOH596 2.3 47.2 1.0
O D:GLU45 2.3 26.4 1.0
O D:ALA47 2.4 25.4 1.0
O D:HOH493 2.4 27.1 1.0
O D:HOH548 2.5 26.9 1.0
C D:GLU45 3.3 25.7 1.0
HA D:GLU45 3.4 29.6 1.0
H D:ALA49 3.5 28.8 1.0
C D:ALA47 3.6 25.1 1.0
HA D:ASP48 3.8 31.2 1.0
CA D:GLU45 3.9 24.6 1.0
HB3 D:ASN33 4.0 30.0 1.0
O D:VAL44 4.1 23.8 1.0
HO6 D:NAG303 4.2 60.8 1.0
N D:ALA49 4.3 24.0 1.0
N D:ALA47 4.3 26.1 1.0
O D:HOH440 4.4 44.1 1.0
C D:LYS46 4.4 27.2 1.0
HD21 D:ASN33 4.4 39.3 1.0
N D:LYS46 4.4 27.5 1.0
O D:ILE34 4.4 23.9 1.0
O D:HOH515 4.4 44.1 1.0
N D:ASP48 4.5 25.4 1.0
CA D:ASP48 4.5 26.0 1.0
ND2 D:ASN33 4.5 32.7 1.0
H D:ALA47 4.5 31.3 1.0
O D:ALA49 4.6 21.6 1.0
CA D:ALA47 4.6 25.2 1.0
O D:LYS46 4.6 27.9 1.0
HB3 D:GLU45 4.6 30.8 1.0
HA D:LYS46 4.7 35.3 1.0
CG D:ASN33 4.7 29.0 1.0
HB3 D:ALA49 4.7 27.5 1.0
HD22 D:ASN33 4.8 39.3 1.0
CA D:LYS46 4.8 29.4 1.0
CB D:ASN33 4.8 25.0 1.0
H D:ILE34 4.9 25.4 1.0
CB D:GLU45 4.9 25.7 1.0
N D:GLU45 4.9 22.7 1.0
O6 D:NAG303 4.9 50.7 1.0
C D:VAL44 4.9 22.3 1.0
C D:ASP48 5.0 24.9 1.0

Calcium binding site 6 out of 6 in 6osz

Go back to Calcium Binding Sites List in 6osz
Calcium binding site 6 out of 6 in the High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of High Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca302

b:39.4
occ:0.76
 O F:GLU45 2.3 29.9 1.0
O F:HOH412 2.4 54.4 1.0
O F:HOH550 2.4 31.4 1.0
O F:HOH612 2.4 49.0 1.0
O F:HOH495 2.4 29.4 1.0
O F:ALA47 2.6 28.2 1.0
C F:GLU45 3.4 28.8 1.0
HA F:GLU45 3.4 34.0 1.0
HO6 F:NAG303 3.5 55.1 1.0
H F:ALA49 3.6 29.1 1.0
C F:ALA47 3.7 27.7 1.0
CA F:GLU45 3.9 28.3 1.0
HA F:ASP48 3.9 32.5 1.0
ND2 F:ASN33 3.9 35.3 1.0
O6 F:NAG303 4.0 45.9 1.0
HD22 F:ASN33 4.0 42.4 1.0
HD21 F:ASN33 4.0 42.4 1.0
O F:VAL44 4.0 26.1 1.0
HB3 F:ASN33 4.1 34.0 1.0
H61 F:NAG303 4.1 54.5 1.0
CG F:ASN33 4.2 32.2 1.0
C F:LYS46 4.4 30.8 1.0
O5 F:NAG303 4.4 44.4 1.0
N F:ALA49 4.4 24.2 1.0
O F:HOH656 4.4 49.6 1.0
N F:ALA47 4.4 28.9 1.0
O F:HOH445 4.4 34.6 1.0
N F:LYS46 4.4 29.1 1.0
C6 F:NAG303 4.6 45.4 1.0
N F:ASP48 4.6 27.7 1.0
O F:HOH414 4.6 42.2 1.0
O F:ILE34 4.6 25.4 1.0
O F:LYS46 4.6 31.8 1.0
CA F:ASP48 4.6 27.1 1.0
HA F:LYS46 4.6 37.8 1.0
HB3 F:GLU45 4.6 34.2 1.0
H F:ALA47 4.6 34.7 1.0
O F:ALA49 4.7 22.8 1.0
OD1 F:ASN33 4.7 32.0 1.0
HB3 F:ALA49 4.7 29.1 1.0
CB F:ASN33 4.7 28.3 1.0
CA F:ALA47 4.7 28.3 1.0
CA F:LYS46 4.8 31.5 1.0
CB F:GLU45 4.9 28.5 1.0
HG22 F:THR35 4.9 32.2 1.0
C F:VAL44 4.9 25.3 1.0
N F:GLU45 4.9 26.4 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 12:36:39 2024

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