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Terbium in PDB 5izr: Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride

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

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

Protein crystallography data

The structure of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride, PDB code: 5izr 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) 159.20 / 3.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 100.824, 112.667, 159.200, 90.00, 90.03, 90.00
R / Rfree (%) 23 / 26.7

Terbium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Terbium atom in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride (pdb code 5izr). This binding sites where shown within 5.0 Angstroms radius around Terbium atom.
In total 15 binding sites of Terbium where determined in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride, PDB code: 5izr:
Jump to Terbium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Terbium binding site 1 out of 15 in 5izr

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Terbium binding site 1 out of 15 in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 1 of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb902

b:94.6
occ:1.00
 O A:HOH1001 2.2 64.7 1.0
O A:HOH1003 2.4 45.5 1.0
OD1 A:ASP44 2.5 66.7 1.0
O A:HOH1002 2.6 36.9 1.0
OD1 A:ASP66 2.6 74.9 1.0
OD2 A:ASP44 2.8 66.7 1.0
CG A:ASP44 3.1 67.3 1.0
CG A:ASP66 3.6 77.8 1.0
OD2 A:ASP66 3.8 85.2 1.0
OG A:SER41 4.5 0.4 1.0
CB A:ASP44 4.6 66.7 1.0
O A:GLU42 4.7 75.0 1.0
CB A:ASP66 5.0 77.1 1.0

Terbium binding site 2 out of 15 in 5izr

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Terbium binding site 2 out of 15 in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 2 of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb903

b:0.5
occ:1.00
 OD2 A:ASP102 2.4 0.4 1.0
OD1 A:ASP102 2.6 93.6 1.0
CG A:ASP102 2.8 0.3 1.0
OD2 A:ASP96 3.6 0.4 1.0
CB A:ASP102 4.3 94.8 1.0
O A:GLU100 4.5 1.0 1.0
CG A:ASP96 4.8 1.0 1.0
CG2 A:THR99 4.9 0.8 1.0

Terbium binding site 3 out of 15 in 5izr

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Terbium binding site 3 out of 15 in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 3 of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb904

b:0.9
occ:1.00
 OD2 A:ASP101 2.2 0.1 1.0
OD1 A:ASP101 2.5 0.2 1.0
CG A:ASP101 2.7 0.2 1.0
CG A:GLU95 3.9 0.9 1.0
O A:ASP96 4.0 0.6 1.0
CB A:ASP101 4.2 1.0 1.0
O A:THR99 4.3 0.4 1.0
N A:ASP101 4.6 0.5 1.0
CD A:GLU95 4.7 0.6 1.0
N A:ASP96 4.7 0.8 1.0
CA A:ASP101 4.9 0.3 1.0
CA A:GLU95 4.9 91.3 1.0
OH A:TYR46 5.0 67.6 1.0

Terbium binding site 4 out of 15 in 5izr

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Terbium binding site 4 out of 15 in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 4 of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb905

b:0.1
occ:1.00
 OD2 A:ASP647 2.1 0.4 1.0
CG A:ASP647 3.2 92.2 1.0
CB A:ASP647 4.0 82.6 1.0
OD1 A:ASP647 4.1 95.8 1.0
CA A:ASP647 4.7 72.1 1.0

Terbium binding site 5 out of 15 in 5izr

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Terbium binding site 5 out of 15 in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 5 of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb902

b:81.0
occ:1.00
 OD2 B:ASP44 2.2 74.1 1.0
OD1 B:ASP44 2.3 82.2 1.0
OD2 B:ASP66 2.4 76.1 1.0
CG B:ASP44 2.6 80.2 1.0
CG B:ASP66 3.1 76.0 1.0
OD1 B:ASP66 3.1 78.7 1.0
CB B:ASP44 4.1 78.5 1.0
CG2 B:THR65 4.4 87.0 1.0
CB B:ASP66 4.5 76.7 1.0
N B:ASP66 4.5 81.0 1.0
O B:GLU42 4.5 83.7 1.0
CB B:THR65 4.7 86.5 1.0
CA B:ASP66 4.9 80.0 1.0
OG B:SER41 5.0 95.2 1.0
CA B:ASP44 5.0 73.3 1.0

Terbium binding site 6 out of 15 in 5izr

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Terbium binding site 6 out of 15 in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 6 of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb903

b:0.9
occ:1.00
 OD1 B:ASP102 2.3 83.9 1.0
OD2 B:ASP102 2.3 79.8 1.0
CG B:ASP102 2.7 81.1 1.0
OD2 B:ASP96 4.0 0.9 1.0
CB B:ASP102 4.2 76.5 1.0
O B:GLU100 4.3 0.5 1.0
CG2 B:THR99 4.9 0.1 1.0
CA B:ASP102 5.0 78.4 1.0
N B:ASP102 5.0 81.5 1.0
CB B:THR99 5.0 0.2 1.0

Terbium binding site 7 out of 15 in 5izr

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Terbium binding site 7 out of 15 in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 7 of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb904

b:0.2
occ:1.00
 OD2 B:ASP101 2.3 99.9 1.0
OD1 B:ASP101 2.7 92.9 1.0
CG B:ASP101 2.8 94.6 1.0
O B:ASP96 3.8 0.2 1.0
CG B:GLU95 4.1 90.7 1.0
O B:THR99 4.2 0.4 1.0
CB B:ASP101 4.3 91.8 1.0
N B:ASP101 4.6 0.4 1.0
N B:ASP96 4.6 0.3 1.0
C B:ASP96 4.6 0.3 1.0
CD B:GLU95 4.9 92.6 1.0
CA B:ASP101 4.9 91.4 1.0

Terbium binding site 8 out of 15 in 5izr

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Terbium binding site 8 out of 15 in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 8 of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb905

b:0.4
occ:1.00
 OD1 B:ASP647 2.0 0.3 1.0
CG B:ASP647 3.2 90.7 1.0
CB B:ASP647 4.1 82.2 1.0
OD2 B:ASP647 4.1 94.5 1.0
CA B:ASP647 5.0 75.1 1.0

Terbium binding site 9 out of 15 in 5izr

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Terbium binding site 9 out of 15 in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 9 of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tb902

b:95.5
occ:1.00
 OD1 C:ASP44 2.5 94.5 1.0
O C:HOH1002 2.5 43.0 1.0
OD2 C:ASP66 2.5 92.6 1.0
OD2 C:ASP44 2.6 89.2 1.0
CG C:ASP44 2.9 93.9 1.0
OD1 C:ASP66 3.2 77.3 1.0
CG C:ASP66 3.2 85.0 1.0
CG2 C:THR65 4.0 92.3 1.0
CB C:ASP44 4.4 93.4 1.0
O C:GLU42 4.7 0.3 1.0
CB C:ASP66 4.7 85.2 1.0
N C:ASP66 4.8 85.4 1.0
OG C:SER41 4.8 0.8 1.0

Terbium binding site 10 out of 15 in 5izr

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Terbium binding site 10 out of 15 in the Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 10 of Human Givd Cytosolic Phospholipase A2 in Complex with Methyl Gamma- Linolenyl Fluorophosphonate Inhibitor and Terbium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tb903

b:0.1
occ:1.00
 OD1 C:ASP102 2.4 91.0 1.0
OD2 C:ASP102 2.5 90.8 1.0
CG C:ASP102 2.8 92.1 1.0
OD2 C:ASP96 3.6 0.6 1.0
CB C:ASP102 4.3 89.9 1.0
O C:GLU100 4.5 0.4 1.0
CG C:ASP96 4.6 0.9 1.0
OD1 C:ASP96 4.7 0.3 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: Fri Oct 11 08:16:24 2024

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