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Barium in PDB 5ixc: Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate

Enzymatic activity of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate

All present enzymatic activity of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate:
3.1.1.4;

Protein crystallography data

The structure of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate, PDB code: 5ixc was solved by H.Wang, M.G.Klein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 90.97 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.567, 111.379, 157.645, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 25.1

Barium Binding Sites:

The binding sites of Barium atom in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate (pdb code 5ixc). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 6 binding sites of Barium where determined in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate, PDB code: 5ixc:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6;

Barium binding site 1 out of 6 in 5ixc

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Barium binding site 1 out of 6 in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba902

b:0.7
occ:0.50
 OD2 A:ASP165 3.1 96.9 1.0
NE2 A:HIS167 3.5 98.0 1.0
CG A:ASP165 3.6 83.8 1.0
OD1 A:ASP165 3.8 96.7 1.0
CE1 A:HIS167 4.0 0.4 1.0
CD2 A:HIS167 4.3 0.5 1.0
CB A:ASP165 4.8 74.2 1.0

Barium binding site 2 out of 6 in 5ixc

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Barium binding site 2 out of 6 in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba903

b:80.8
occ:1.00
 O A:GLU42 2.7 54.5 1.0
OD1 A:ASP44 2.9 68.6 1.0
OG A:SER41 3.0 75.5 1.0
OD2 A:ASP44 3.1 60.5 1.0
CG A:ASP44 3.4 59.7 1.0
OD1 A:ASP66 3.4 70.8 1.0
C A:GLU42 3.8 53.1 1.0
CG A:ASP66 4.0 62.2 1.0
OD2 A:ASP66 4.2 67.8 1.0
O A:HOH1003 4.2 55.1 1.0
N A:GLU42 4.2 54.9 1.0
CB A:SER41 4.3 69.0 1.0
C A:SER41 4.5 59.6 1.0
CA A:GLU42 4.6 56.2 1.0
C A:ALA43 4.6 50.5 1.0
CA A:SER41 4.7 63.0 1.0
N A:ASP44 4.7 53.9 1.0
CB A:ASP44 4.8 55.5 1.0
O A:ALA43 4.8 49.9 1.0
N A:ALA43 4.9 51.2 1.0
N A:ASP66 4.9 58.8 1.0
CA A:ASP66 5.0 59.6 1.0
CA A:ALA43 5.0 50.0 1.0

Barium binding site 3 out of 6 in 5ixc

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Barium binding site 3 out of 6 in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba904

b:0.4
occ:1.00
 O A:THR99 2.7 95.1 1.0
O A:ASP96 3.2 71.8 1.0
OD2 A:ASP101 3.3 57.1 1.0
C A:THR99 3.7 90.7 1.0
CG A:ASP101 3.9 60.0 1.0
CA A:GLU100 3.9 86.7 1.0
OD1 A:ASP101 4.1 55.2 1.0
N A:ASP101 4.1 66.5 1.0
N A:GLU100 4.2 87.2 1.0
C A:GLU100 4.3 78.2 1.0
C A:ASP96 4.4 78.3 1.0
N A:ASP96 4.8 68.1 1.0
CB A:ASP101 4.9 62.0 1.0
CA A:THR99 4.9 91.2 1.0
CA A:ASP101 5.0 63.4 1.0
N A:THR99 5.0 89.2 1.0

Barium binding site 4 out of 6 in 5ixc

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Barium binding site 4 out of 6 in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba902

b:0.3
occ:0.50
 OD2 B:ASP165 2.8 81.1 1.0
NE2 B:HIS167 3.2 82.9 1.0
CG B:ASP165 3.4 71.5 1.0
OD1 B:ASP165 3.7 80.7 1.0
CE1 B:HIS167 3.9 85.4 1.0
CD2 B:HIS167 4.0 84.7 1.0
CB B:ASP165 4.6 63.1 1.0
ND1 B:HIS167 4.8 87.3 1.0
CG B:HIS167 4.9 80.1 1.0
CB B:ALA206 5.0 59.0 1.0

Barium binding site 5 out of 6 in 5ixc

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Barium binding site 5 out of 6 in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba903

b:85.9
occ:1.00
 O B:HOH1032 2.7 57.5 1.0
O B:GLU42 2.7 55.8 1.0
OG B:SER41 3.0 66.0 1.0
OD1 B:ASP44 3.1 61.7 1.0
OD2 B:ASP44 3.2 58.3 1.0
OD1 B:ASP66 3.5 70.0 1.0
CG B:ASP44 3.5 60.2 1.0
C B:GLU42 3.8 54.1 1.0
CG B:ASP66 4.0 63.6 1.0
OD2 B:ASP66 4.1 68.1 1.0
N B:GLU42 4.2 53.2 1.0
CB B:SER41 4.3 64.1 1.0
O B:HOH1003 4.3 40.0 1.0
C B:SER41 4.5 57.2 1.0
CA B:GLU42 4.5 53.7 1.0
CA B:SER41 4.6 60.7 1.0
C B:ALA43 4.7 53.0 1.0
N B:ASP44 4.8 54.2 1.0
O B:ALA43 4.9 51.8 1.0
N B:ALA43 4.9 52.8 1.0
CB B:ASP44 4.9 57.3 1.0
N B:ASP66 4.9 57.2 1.0
CA B:ASP66 5.0 57.7 1.0

Barium binding site 6 out of 6 in 5ixc

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Barium binding site 6 out of 6 in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba904

b:0.2
occ:1.00
 O B:THR99 2.7 85.3 1.0
O B:ASP96 2.8 81.6 1.0
OD2 B:ASP101 3.2 64.0 1.0
C B:THR99 3.8 84.0 1.0
CG B:ASP101 3.9 60.9 1.0
C B:ASP96 4.0 81.3 1.0
OD1 B:ASP101 4.1 54.7 1.0
CA B:GLU100 4.2 81.5 1.0
N B:ASP101 4.3 64.1 1.0
N B:GLU100 4.4 81.7 1.0
C B:GLU100 4.5 73.8 1.0
N B:ASP96 4.6 70.3 1.0
CA B:ASP96 4.7 76.9 1.0
N B:THR99 4.9 87.5 1.0
CB B:ASP96 4.9 82.5 1.0
C B:SER97 5.0 88.1 1.0
CA B:THR99 5.0 88.5 1.0

Reference:

H.Wang, M.G.Klein, G.Snell, W.Lane, H.Zou, I.Levin, K.Li, B.C.Sang. Structure of Human Givd Cytosolic Phospholipase A2 Reveals Insights Into Substrate Recognition. J.Mol.Biol. V. 428 2769 2016.
ISSN: ESSN 1089-8638
PubMed: 27220631
DOI: 10.1016/J.JMB.2016.05.012
Page generated: Wed Jul 10 15:50:52 2024

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