Atomistry » Barium » PDB 4x1a-5wkx » 5ixc
Atomistry »
  Barium »
    PDB 4x1a-5wkx »
      5ixc »

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

Go back to Barium Binding Sites List in 5ixc
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

Go back to Barium Binding Sites List in 5ixc
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

Go back to Barium Binding Sites List in 5ixc
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

Go back to Barium Binding Sites List in 5ixc
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

Go back to Barium Binding Sites List in 5ixc
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

Go back to Barium Binding Sites List in 5ixc
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

Last articles

Ca in 7Z2N
Ca in 7Z3J
Ca in 7Z2U
Ca in 7Z1I
Ca in 7Z2I
Ca in 7Z25
Ca in 7Z01
Ca in 7YZX
Ca in 7YZ6
Ca in 7YZ5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy