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Calcium in PDB 6xrv: X-Ray Structure of the Monoclinic Crystal Form at 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 K

Enzymatic activity of X-Ray Structure of the Monoclinic Crystal Form at 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 K

All present enzymatic activity of X-Ray Structure of the Monoclinic Crystal Form at 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 K:
3.1.1.3;

Protein crystallography data

The structure of X-Ray Structure of the Monoclinic Crystal Form at 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 K, PDB code: 6xrv was solved by A.Mcpherson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.00 / 1.43
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.929, 89.937, 123.422, 90.00, 94.49, 90.00
R / Rfree (%) 15 / 18.7

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of the Monoclinic Crystal Form at 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 K (pdb code 6xrv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the X-Ray Structure of the Monoclinic Crystal Form at 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 K, PDB code: 6xrv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6xrv

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Calcium binding site 1 out of 6 in the X-Ray Structure of the Monoclinic Crystal Form at 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 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 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:20.5
occ:0.97
 O B:GLU45 2.4 20.0 1.0
O B:HOH512 2.5 19.3 1.0
O B:HOH609 2.5 24.4 1.0
O B:HOH536 2.5 26.8 1.0
O B:HOH590 2.5 31.4 1.0
O B:HOH484 2.5 21.6 1.0
O B:HOH541 2.5 34.3 1.0
O B:ALA47 2.5 19.9 1.0
C B:GLU45 3.5 21.0 1.0
HA B:GLU45 3.6 25.9 1.0
H B:ALA49 3.6 23.7 1.0
C B:ALA47 3.7 20.2 1.0
HA B:ASP48 3.8 26.8 1.0
HB3 B:ASN33 3.9 26.3 1.0
CA B:GLU45 4.1 21.6 1.0
O B:VAL44 4.3 20.8 1.0
C B:LYS46 4.3 21.2 1.0
O B:HOH655 4.4 48.1 1.0
O B:LYS46 4.4 22.2 1.0
N B:ALA47 4.4 20.1 1.0
N B:ALA49 4.4 19.8 1.0
N B:ASP48 4.5 21.3 1.0
CA B:ASP48 4.5 22.4 1.0
O B:ILE34 4.5 19.3 1.0
N B:LYS46 4.5 21.0 1.0
O B:HOH592 4.7 36.7 1.0
O B:HOH415 4.7 29.7 1.0
H B:ALA47 4.7 24.1 1.0
HB3 B:GLU45 4.7 27.9 1.0
CA B:ALA47 4.7 19.7 1.0
HA B:LYS46 4.8 26.4 1.0
O B:ALA49 4.8 20.2 1.0
CA B:LYS46 4.8 22.0 1.0
O B:HOH646 4.8 45.8 1.0
CB B:ASN33 4.8 21.9 1.0
HB3 B:ALA49 4.9 25.4 1.0

Calcium binding site 2 out of 6 in 6xrv

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Calcium binding site 2 out of 6 in the X-Ray Structure of the Monoclinic Crystal Form at 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 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 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:56.7
occ:1.00
 O B:HOH605 2.3 39.9 1.0
O B:HOH402 2.4 11.2 1.0
HH22 B:ARG81 2.5 22.1 1.0
HH12 B:ARG81 2.6 22.9 1.0
O B:HOH559 2.6 42.0 1.0
O B:HOH510 2.9 22.7 1.0
HB3 B:SER85 3.0 24.9 1.0
O B:HOH696 3.0 53.2 1.0
O B:HOH633 3.1 37.0 1.0
NH2 B:ARG81 3.3 18.4 1.0
NH1 B:ARG81 3.4 19.1 1.0
OD2 B:ASP62 3.4 20.3 1.0
O B:HOH658 3.5 35.4 1.0
CZ B:ARG81 3.8 17.8 1.0
O B:HOH691 3.8 35.4 1.0
O B:HOH522 3.9 23.6 1.0
HH21 B:ARG81 3.9 22.1 1.0
CB B:SER85 3.9 20.7 1.0
HH11 B:ARG81 4.1 22.9 1.0
HB2 B:SER85 4.2 24.9 1.0
HG B:SER85 4.2 23.7 1.0
CG B:ASP62 4.3 19.0 1.0
OD1 B:ASP57 4.4 29.8 1.0
O B:HOH642 4.4 39.5 1.0
OD1 B:ASP62 4.4 20.1 1.0
O B:HOH508 4.6 41.6 1.0
OG B:SER85 4.6 19.8 1.0
H B:SER85 4.6 25.1 1.0
HG2 B:ARG84 4.6 31.6 1.0
HA B:SER85 4.8 25.2 1.0
HB3 B:ARG84 4.8 28.9 1.0
CA B:SER85 4.8 21.0 1.0
N B:SER85 4.9 20.9 1.0
HG21 B:THR64 5.0 19.8 1.0

Calcium binding site 3 out of 6 in 6xrv

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Calcium binding site 3 out of 6 in the X-Ray Structure of the Monoclinic Crystal Form at 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 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 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 K within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:37.4
occ:0.73
 O C:HOH572 2.3 50.8 1.0
O C:GLU45 2.4 25.0 1.0
O C:HOH591 2.4 37.3 1.0
O C:HOH534 2.4 31.6 1.0
O C:ALA47 2.4 26.0 1.0
O C:HOH485 2.5 33.3 1.0
HA C:GLU45 3.3 29.1 1.0
C C:GLU45 3.4 25.1 1.0
H C:ALA49 3.4 31.2 1.0
C C:ALA47 3.6 26.8 1.0
HA C:ASP48 3.8 35.8 1.0
CA C:GLU45 3.9 24.2 1.0
HB3 C:ASN33 3.9 31.8 1.0
O C:VAL44 4.0 22.0 1.0
N C:ALA49 4.3 26.0 1.0
C C:LYS46 4.3 27.3 1.0
HO6 C:NAG303 4.3 62.8 1.0
N C:ALA47 4.4 26.6 1.0
O C:HOH470 4.4 44.5 1.0
O C:HOH428 4.5 41.9 1.0
N C:ASP48 4.5 28.4 1.0
CA C:ASP48 4.5 29.9 1.0
N C:LYS46 4.5 25.4 1.0
O C:LYS46 4.5 27.8 1.0
O5 C:NAG303 4.5 48.7 1.0
HD21 C:ASN33 4.5 47.1 1.0
H C:ALA47 4.6 31.9 1.0
O C:ALA49 4.6 22.0 1.0
O C:ILE34 4.6 21.6 1.0
HB3 C:GLU45 4.6 29.6 1.0
HB3 C:ALA49 4.6 30.4 1.0
CA C:ALA47 4.6 27.6 1.0
ND2 C:ASN33 4.7 39.2 1.0
O6 C:NAG303 4.7 52.3 1.0
CB C:ASN33 4.7 26.5 1.0
CG C:ASN33 4.8 32.7 1.0
HA C:LYS46 4.8 34.0 1.0
CA C:LYS46 4.8 28.4 1.0
CB C:GLU45 4.9 24.7 1.0
C C:VAL44 4.9 21.9 1.0
H61 C:NAG303 4.9 62.3 1.0
N C:GLU45 4.9 22.5 1.0
H C:ILE34 5.0 24.9 1.0
C C:ASP48 5.0 28.9 1.0

Calcium binding site 4 out of 6 in 6xrv

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Calcium binding site 4 out of 6 in the X-Ray Structure of the Monoclinic Crystal Form at 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 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 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 K within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca302

b:50.4
occ:1.00
 O E:HOH485 2.4 55.1 1.0
O E:HOH477 2.5 41.6 1.0
O E:GLU45 2.5 39.9 1.0
O E:ALA47 2.5 39.8 1.0
O E:HOH469 2.5 47.1 1.0
O E:HOH547 2.5 43.4 1.0
HA E:GLU45 3.4 46.8 1.0
H E:ALA49 3.5 46.6 1.0
C E:GLU45 3.5 40.3 1.0
C E:ALA47 3.7 40.3 1.0
HA E:ASP48 3.8 49.3 1.0
HO6 E:NAG303 3.9 71.9 1.0
CA E:GLU45 4.0 39.0 1.0
HB3 E:ASN33 4.0 50.4 1.0
O E:VAL44 4.2 36.1 1.0
N E:ALA49 4.3 38.8 1.0
C E:LYS46 4.3 42.4 1.0
N E:ALA47 4.4 41.5 1.0
O E:LYS46 4.4 42.2 1.0
O E:ILE34 4.5 35.6 1.0
N E:LYS46 4.5 42.2 1.0
CA E:ASP48 4.5 41.1 1.0
N E:ASP48 4.6 40.6 1.0
O6 E:NAG303 4.6 59.9 1.0
H E:ALA47 4.6 49.8 1.0
HB3 E:ALA49 4.6 45.1 1.0
O5 E:NAG303 4.6 57.1 1.0
O E:ALA49 4.6 36.4 1.0
HB3 E:GLU45 4.6 48.0 1.0
HD21 E:ASN33 4.7 60.5 1.0
CA E:ALA47 4.7 40.7 1.0
ND2 E:ASN33 4.8 50.4 1.0
HA E:LYS46 4.8 52.0 1.0
H E:ILE34 4.8 44.0 1.0
CA E:LYS46 4.8 43.3 1.0
O E:HOH544 4.8 49.0 1.0
CB E:ASN33 4.8 42.0 1.0
CG E:ASN33 4.9 46.3 1.0
CB E:GLU45 4.9 40.0 1.0

Calcium binding site 5 out of 6 in 6xrv

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Calcium binding site 5 out of 6 in the X-Ray Structure of the Monoclinic Crystal Form at 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 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 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 K within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:26.6
occ:0.65
 O D:HOH586 2.3 33.9 1.0
O D:GLU45 2.3 26.8 1.0
O D:HOH590 2.4 47.0 1.0
O D:HOH485 2.4 27.6 1.0
O D:ALA47 2.4 26.2 1.0
O D:HOH544 2.5 26.6 1.0
C D:GLU45 3.4 26.0 1.0
HA D:GLU45 3.4 30.0 1.0
H D:ALA49 3.5 29.3 1.0
C D:ALA47 3.6 25.9 1.0
HA D:ASP48 3.8 32.0 1.0
HB3 D:ASN33 3.9 30.6 1.0
CA D:GLU45 3.9 25.0 1.0
O D:VAL44 4.1 23.9 1.0
HO6 D:NAG303 4.2 62.2 1.0
N D:ALA49 4.3 24.4 1.0
N D:ALA47 4.3 26.4 1.0
C D:LYS46 4.4 27.8 1.0
O D:HOH440 4.4 43.6 1.0
O D:HOH587 4.4 44.1 1.0
N D:LYS46 4.4 28.1 1.0
O D:ILE34 4.4 23.9 1.0
N D:ASP48 4.5 26.1 1.0
CA D:ASP48 4.5 26.6 1.0
H D:ALA47 4.5 31.7 1.0
O D:ALA49 4.6 21.5 1.0
O D:LYS46 4.6 28.8 1.0
CA D:ALA47 4.6 25.7 1.0
HB3 D:GLU45 4.6 31.6 1.0
HA D:LYS46 4.7 36.1 1.0
HB3 D:ALA49 4.7 28.0 1.0
CB D:ASN33 4.7 25.5 1.0
HD21 D:ASN33 4.7 45.4 1.0
CA D:LYS46 4.8 30.1 1.0
H D:ILE34 4.8 25.4 1.0
O6 D:NAG303 4.8 51.9 1.0
O5 D:NAG303 4.8 49.0 1.0
ND2 D:ASN33 4.9 37.8 1.0
CG D:ASN33 4.9 31.0 1.0
CB D:GLU45 4.9 26.3 1.0
C D:VAL44 4.9 22.3 1.0
N D:GLU45 4.9 22.9 1.0
C D:ASP48 5.0 25.4 1.0

Calcium binding site 6 out of 6 in 6xrv

Go back to Calcium Binding Sites List in 6xrv
Calcium binding site 6 out of 6 in the X-Ray Structure of the Monoclinic Crystal Form at 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 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 1.43 A Resolution of Lipase From Thermomyces (Humicola) Lanuginosa at 173 K within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca302

b:40.2
occ:0.75
 O F:GLU45 2.4 30.2 1.0
O F:HOH532 2.4 31.8 1.0
O F:HOH485 2.4 29.7 1.0
O F:HOH496 2.4 54.0 1.0
O F:ALA47 2.6 28.4 1.0
HA F:GLU45 3.4 34.3 1.0
C F:GLU45 3.4 29.1 1.0
H F:ALA49 3.6 29.1 1.0
C F:ALA47 3.8 28.1 1.0
HB3 F:ASN33 3.9 33.1 1.0
CA F:GLU45 3.9 28.6 1.0
HA F:ASP48 3.9 32.9 1.0
O F:VAL44 4.1 26.4 1.0
O5 F:NAG303 4.1 41.3 1.0
HO6 F:NAG303 4.2 54.2 1.0
H61 F:NAG303 4.3 53.4 1.0
O6 F:NAG303 4.4 45.2 1.0
C F:LYS46 4.4 30.9 1.0
ND2 F:ASN33 4.4 35.4 1.0
O F:HOH640 4.4 48.9 1.0
HD21 F:ASN33 4.4 42.5 1.0
N F:LYS46 4.5 29.2 1.0
N F:ALA49 4.5 24.3 1.0
O F:HOH421 4.5 34.4 1.0
CG F:ASN33 4.5 31.5 1.0
N F:ALA47 4.5 29.2 1.0
O F:HOH585 4.5 42.4 1.0
O F:LYS46 4.6 32.3 1.0
HB3 F:GLU45 4.6 34.2 1.0
O F:ILE34 4.6 25.5 1.0
N F:ASP48 4.6 28.0 1.0
CB F:ASN33 4.6 27.6 1.0
HA F:LYS46 4.6 38.0 1.0
CA F:ASP48 4.6 27.4 1.0
O F:ALA49 4.7 23.1 1.0
H F:ALA47 4.7 35.0 1.0
HB3 F:ALA49 4.7 29.4 1.0
C6 F:NAG303 4.8 44.5 1.0
CA F:LYS46 4.8 31.6 1.0
CA F:ALA47 4.8 28.4 1.0
CB F:GLU45 4.9 28.5 1.0
OD1 F:ASN33 4.9 31.6 1.0
C1 F:NAG303 4.9 39.8 1.0
HG22 F:THR35 4.9 32.9 1.0
N F:GLU45 5.0 26.5 1.0
C F:VAL44 5.0 25.4 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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