Atomistry » Calcium » PDB 6o1t-6ojd » 6o9f
Atomistry »
  Calcium »
    PDB 6o1t-6ojd »
      6o9f »

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

Go back to Calcium Binding Sites List in 6o9f
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

Go back to Calcium Binding Sites List in 6o9f
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

Go back to Calcium Binding Sites List in 6o9f
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

Go back to Calcium Binding Sites List in 6o9f
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

Go back to Calcium Binding Sites List in 6o9f
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

Go back to Calcium Binding Sites List in 6o9f
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

Go back to Calcium Binding Sites List in 6o9f
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy