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Potassium in PDB 3o0d: Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution

Enzymatic activity of Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution

All present enzymatic activity of Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution:
3.1.1.3;

Protein crystallography data

The structure of Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution, PDB code: 3o0d was solved by F.Bordes, S.Tranier, L.Mourey, A.Marty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 115.354, 132.141, 137.255, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.1

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution (pdb code 3o0d). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution, PDB code: 3o0d:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 3o0d

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Potassium binding site 1 out of 7 in the Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K308

b:21.6
occ:1.00
 ND1 A:HIS243 3.1 12.4 1.0
O A:HOH896 3.1 28.1 1.0
NE2 A:GLN189 3.2 11.8 1.0
N A:CYS244 3.4 14.9 1.0
CA A:HIS243 3.6 13.0 1.0
CD2 A:LEU169 3.8 14.6 1.0
SG A:CYS244 3.8 21.3 1.0
N A:VAL192 3.9 17.7 1.0
CG A:HIS243 4.0 11.6 1.0
CE1 A:HIS243 4.1 14.1 1.0
C A:HIS243 4.1 11.5 1.0
CB A:HIS243 4.1 12.7 1.0
CD A:ARG224 4.2 11.0 1.0
CB A:VAL192 4.3 21.2 1.0
CB A:CYS244 4.3 15.5 1.0
CD A:GLN189 4.4 14.0 1.0
NE A:ARG224 4.5 12.5 1.0
CA A:CYS244 4.5 15.9 1.0
O A:GLN242 4.5 14.9 1.0
CG2 A:VAL192 4.5 19.9 1.0
CA A:ILE191 4.5 13.7 1.0
O A:PRO190 4.6 12.8 1.0
CE2 A:PHE197 4.7 19.9 1.0
CA A:VAL192 4.7 18.8 1.0
N A:HIS243 4.8 13.9 1.0
C A:ILE191 4.8 16.8 1.0
OE1 A:GLN189 4.8 12.2 1.0
CG2 A:ILE191 4.9 12.4 1.0

Potassium binding site 2 out of 7 in 3o0d

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Potassium binding site 2 out of 7 in the Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K307

b:20.1
occ:1.00
 O B:HOH371 3.0 22.6 1.0
ND1 B:HIS243 3.1 14.1 1.0
NE2 B:GLN189 3.1 12.4 1.0
N B:CYS244 3.4 12.8 1.0
CA B:HIS243 3.6 13.1 1.0
CD2 B:LEU169 3.8 16.5 1.0
SG B:CYS244 3.9 17.7 1.0
N B:VAL192 3.9 16.3 1.0
CG B:HIS243 4.0 12.3 1.0
CE1 B:HIS243 4.0 12.5 1.0
C B:HIS243 4.1 14.1 1.0
CB B:HIS243 4.1 13.9 1.0
CD B:ARG224 4.2 10.6 1.0
CD B:GLN189 4.4 13.2 1.0
CB B:VAL192 4.5 20.0 1.0
CB B:CYS244 4.5 11.4 1.0
CA B:ILE191 4.5 12.9 0.5
CA B:ILE191 4.5 13.6 0.5
CA B:CYS244 4.5 13.3 1.0
O B:GLN242 4.5 14.8 1.0
NE B:ARG224 4.6 13.1 1.0
O B:PRO190 4.6 13.2 1.0
CG2 B:VAL192 4.7 13.4 1.0
CG2 B:ILE191 4.7 11.0 0.5
C B:ILE191 4.7 14.4 1.0
CE2 B:PHE197 4.7 24.1 1.0
CA B:VAL192 4.8 16.6 1.0
N B:HIS243 4.8 15.3 1.0
CG2 B:ILE191 4.8 12.5 0.5
OE1 B:GLN189 4.8 11.0 1.0

Potassium binding site 3 out of 7 in 3o0d

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Potassium binding site 3 out of 7 in the Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K307

b:18.9
occ:1.00
 O C:HOH333 2.9 25.4 1.0
ND1 C:HIS243 3.0 16.6 1.0
NE2 C:GLN189 3.2 11.6 1.0
N C:CYS244 3.5 12.8 1.0
CA C:HIS243 3.6 12.9 1.0
SG C:CYS244 3.9 17.5 1.0
CD2 C:LEU169 3.9 13.6 1.0
N C:VAL192 3.9 14.4 1.0
CG C:HIS243 4.0 14.9 1.0
CE1 C:HIS243 4.0 13.6 1.0
CB C:HIS243 4.1 10.3 1.0
C C:HIS243 4.1 10.6 1.0
CD C:ARG224 4.3 12.8 1.0
CA C:ILE191 4.4 13.1 1.0
CB C:VAL192 4.4 17.3 1.0
CD C:GLN189 4.4 8.3 1.0
CB C:CYS244 4.4 11.3 1.0
O C:PRO190 4.5 13.7 1.0
CA C:CYS244 4.6 12.9 1.0
O C:GLN242 4.6 13.9 1.0
NE C:ARG224 4.6 14.8 1.0
CG2 C:VAL192 4.6 15.4 1.0
C C:ILE191 4.7 14.3 1.0
CG2 C:ILE191 4.7 11.2 1.0
N C:HIS243 4.8 15.1 1.0
CA C:VAL192 4.8 14.4 1.0
CE2 C:PHE197 4.8 21.1 1.0
OE1 C:GLN189 4.8 10.3 1.0

Potassium binding site 4 out of 7 in 3o0d

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Potassium binding site 4 out of 7 in the Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K307

b:25.1
occ:1.00
 O D:HOH444 3.0 24.7 1.0
ND1 D:HIS243 3.0 16.8 1.0
NE2 D:GLN189 3.1 13.2 1.0
N D:CYS244 3.4 15.7 1.0
CA D:HIS243 3.7 17.8 1.0
CD2 D:LEU169 3.8 18.5 1.0
SG D:CYS244 3.8 22.2 1.0
CG D:HIS243 3.9 15.2 1.0
CE1 D:HIS243 4.0 16.3 1.0
C D:HIS243 4.0 16.7 1.0
CB D:HIS243 4.1 16.9 1.0
CD D:ARG224 4.2 12.5 1.0
N D:VAL192 4.3 21.3 1.0
CD D:GLN189 4.4 13.7 1.0
NE D:ARG224 4.4 16.4 1.0
CB D:CYS244 4.4 19.3 1.0
O D:GLN242 4.5 19.4 1.0
CA D:CYS244 4.5 17.1 1.0
CB D:VAL192 4.7 23.1 1.0
CA D:ILE191 4.7 18.8 1.0
O D:PRO190 4.7 16.2 1.0
CE2 D:PHE197 4.7 24.7 1.0
OE1 D:GLN189 4.8 14.7 1.0
N D:HIS243 4.8 18.6 1.0
CG2 D:ILE191 4.9 18.1 1.0

Potassium binding site 5 out of 7 in 3o0d

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Potassium binding site 5 out of 7 in the Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K306

b:20.1
occ:1.00
 O E:HOH541 3.0 22.0 1.0
ND1 E:HIS243 3.1 15.6 1.0
NE2 E:GLN189 3.1 11.7 1.0
N E:CYS244 3.4 13.0 1.0
CA E:HIS243 3.6 14.1 1.0
SG E:CYS244 3.8 19.5 1.0
CD2 E:LEU169 3.8 13.7 1.0
CG E:HIS243 3.9 14.2 1.0
CB E:HIS243 4.0 13.5 1.0
C E:HIS243 4.0 15.1 1.0
CE1 E:HIS243 4.0 15.6 1.0
CD E:ARG224 4.1 10.8 1.0
N E:VAL192 4.2 14.4 1.0
CD E:GLN189 4.4 13.2 1.0
NE E:ARG224 4.4 11.6 1.0
CB E:VAL192 4.4 17.1 1.0
CB E:CYS244 4.4 16.3 1.0
CA E:CYS244 4.5 14.0 1.0
O E:GLN242 4.5 13.9 1.0
CG2 E:VAL192 4.6 15.8 1.0
O E:PRO190 4.7 13.7 1.0
CA E:ILE191 4.7 14.2 1.0
CE2 E:PHE197 4.7 22.6 1.0
N E:HIS243 4.8 15.0 1.0
OE1 E:GLN189 4.8 15.0 1.0
CG2 E:ILE191 4.9 15.0 1.0
CA E:VAL192 4.9 15.8 1.0
C E:ILE191 5.0 14.6 1.0

Potassium binding site 6 out of 7 in 3o0d

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Potassium binding site 6 out of 7 in the Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K306

b:25.1
occ:1.00
 O F:HOH470 3.0 31.2 1.0
ND1 F:HIS243 3.0 19.4 1.0
NE2 F:GLN189 3.0 16.5 1.0
N F:CYS244 3.5 17.6 1.0
CA F:HIS243 3.6 18.1 1.0
CD2 F:LEU169 3.8 16.5 1.0
SG F:CYS244 3.8 22.3 1.0
CE1 F:HIS243 3.9 19.0 1.0
CG F:HIS243 3.9 16.2 1.0
N F:VAL192 4.0 19.7 1.0
CB F:HIS243 4.1 17.8 1.0
C F:HIS243 4.1 17.8 1.0
CD F:ARG224 4.2 16.0 1.0
CD F:GLN189 4.3 18.2 1.0
CB F:CYS244 4.4 19.9 1.0
NE F:ARG224 4.4 17.6 1.0
CB F:VAL192 4.5 21.9 1.0
CA F:ILE191 4.5 17.1 1.0
O F:GLN242 4.5 21.0 1.0
CG2 F:VAL192 4.5 20.9 1.0
CA F:CYS244 4.5 19.9 1.0
O F:PRO190 4.7 17.1 1.0
OE1 F:GLN189 4.7 14.7 1.0
N F:HIS243 4.7 20.1 1.0
C F:ILE191 4.8 20.5 1.0
CE2 F:PHE197 4.8 26.9 1.0
CG2 F:ILE191 4.8 19.3 1.0
CA F:VAL192 4.9 21.7 1.0

Potassium binding site 7 out of 7 in 3o0d

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Potassium binding site 7 out of 7 in the Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of LIP2 Lipase From Yarrowia Lipolytica at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K304

b:42.9
occ:1.00
 O G:HOH1277 2.8 35.0 1.0
NE2 G:GLN189 3.2 29.0 1.0
ND1 G:HIS243 3.2 33.4 1.0
N G:CYS244 3.3 31.4 1.0
SG G:CYS244 3.7 36.1 1.0
CA G:HIS243 3.8 32.1 1.0
CD2 G:LEU169 3.8 33.9 1.0
C G:HIS243 4.0 31.5 1.0
CD G:ARG224 4.1 43.4 1.0
CE1 G:HIS243 4.1 32.4 1.0
CG G:HIS243 4.2 34.9 1.0
CB G:HIS243 4.3 32.1 1.0
CB G:CYS244 4.3 31.5 1.0
N G:VAL192 4.3 31.7 1.0
CD G:GLN189 4.3 31.0 1.0
CA G:CYS244 4.4 31.9 1.0
NE G:ARG224 4.5 40.7 1.0
CB G:VAL192 4.6 32.0 1.0
O G:GLN242 4.6 34.2 1.0
OE1 G:GLN189 4.7 28.5 1.0
CE2 G:PHE197 4.8 44.8 1.0
O G:PRO190 4.8 28.3 1.0
CA G:ILE191 4.9 31.1 1.0
CG2 G:VAL192 4.9 32.0 1.0
N G:HIS243 4.9 31.9 1.0

Reference:

F.Bordes, S.Barbe, P.Escalier, L.Mourey, I.Andre, A.Marty, S.Tranier. Exploring the Conformational States and Rearrangements of Yarrowia Lipolytica Lipase. Biophys.J. V. 99 2225 2010.
ISSN: ISSN 0006-3495
PubMed: 20923657
DOI: 10.1016/J.BPJ.2010.07.040
Page generated: Mon Aug 12 08:51:32 2024

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