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Chlorine in PDB 6lx5: X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization

Protein crystallography data

The structure of X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization, PDB code: 6lx5 was solved by S.Kamata, K.Saito, A.Honda, R.Ishikawa, T.Oyama, I.Ishii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.41 / 1.87
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.585, 101.350, 61.745, 90.00, 100.73, 90.00
R / Rfree (%) 19.9 / 22.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization (pdb code 6lx5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization, PDB code: 6lx5:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6lx5

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Chlorine binding site 1 out of 8 in the X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:55.8
occ:1.00
 CL1 A:C5F502 0.0 55.8 1.0
C07 A:C5F502 1.8 51.8 1.0
C06 A:C5F502 2.8 44.0 1.0
C08 A:C5F502 2.8 47.7 1.0
H81 A:C5F502 2.8 57.2 1.0
CL2 A:C5F502 3.1 59.1 1.0
C09 A:C5F502 3.2 37.4 1.0
CG2 A:ILE447 3.4 42.1 1.0
O A:VAL444 3.4 44.6 1.0
H16 A:C5F502 3.6 52.9 1.0
CB A:ILE447 3.6 43.2 1.0
H82 A:C5F502 3.6 57.2 1.0
N A:LYS448 3.7 46.0 1.0
CG1 A:VAL444 3.8 37.4 1.0
C10 A:C5F502 3.9 34.5 1.0
C11 A:C5F502 3.9 37.6 1.0
H10 A:C5F502 4.0 41.4 1.0
H11 A:C5F502 4.0 45.2 1.0
CA A:VAL444 4.0 36.0 1.0
CA A:LYS448 4.1 48.6 1.0
C A:VAL444 4.2 45.4 1.0
C A:ILE447 4.2 48.8 1.0
CB A:LYS448 4.2 51.4 1.0
CB A:VAL444 4.4 36.7 1.0
CA A:ILE447 4.5 46.4 1.0
CG2 A:VAL444 4.7 37.7 1.0
CG1 A:ILE447 4.7 42.5 1.0
CD1 A:ILE447 4.8 43.1 1.0
O A:ILE447 4.9 48.3 1.0

Chlorine binding site 2 out of 8 in 6lx5

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Chlorine binding site 2 out of 8 in the X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:59.1
occ:1.00
 CL2 A:C5F502 0.0 59.1 1.0
C07 A:C5F502 1.8 51.8 1.0
H16 A:C5F502 2.7 52.9 1.0
C06 A:C5F502 2.8 44.0 1.0
C08 A:C5F502 2.8 47.7 1.0
H82 A:C5F502 2.8 57.2 1.0
CL1 A:C5F502 3.1 55.8 1.0
N A:LEU456 3.3 46.4 1.0
C A:ALA455 3.3 45.6 1.0
O A:ALA454 3.6 62.7 1.0
O A:ALA455 3.6 47.7 1.0
C A:ALA454 3.6 54.8 1.0
H81 A:C5F502 3.6 57.2 1.0
N A:ALA455 3.7 46.9 1.0
CA A:LEU456 3.7 41.6 1.0
CA A:ALA455 3.8 50.1 1.0
CB A:ALA454 3.9 52.2 1.0
CB A:LEU456 4.0 45.8 1.0
C09 A:C5F502 4.1 37.4 1.0
H11 A:C5F502 4.3 45.2 1.0
CA A:ALA454 4.4 52.6 1.0
CB A:LYS448 4.4 51.4 1.0
CA A:LYS448 4.4 48.6 1.0
CG A:LYS448 4.4 55.0 1.0
C11 A:C5F502 4.7 37.6 1.0
CD1 A:LEU456 4.7 37.6 1.0
NE2 A:GLN277 4.7 33.3 1.0
N A:LYS448 4.9 46.0 1.0
CG A:LEU456 5.0 41.8 1.0

Chlorine binding site 3 out of 8 in 6lx5

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Chlorine binding site 3 out of 8 in the X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:58.8
occ:1.00
 CL1 A:C5F503 0.0 58.8 1.0
C07 A:C5F503 1.8 47.4 1.0
H16 A:C5F503 2.8 46.3 1.0
C08 A:C5F503 2.8 39.5 1.0
H82 A:C5F503 2.8 47.5 1.0
C06 A:C5F503 2.8 38.5 1.0
CL2 A:C5F503 3.1 49.5 1.0
CD1 A:ILE339 3.3 29.5 1.0
H81 A:C5F503 3.6 47.5 1.0
CD1 A:ILE241 3.6 38.7 1.0
CB A:ILE339 3.7 31.9 1.0
CG1 A:ILE339 3.9 26.7 1.0
CG2 A:VAL332 4.2 28.0 1.0
C09 A:C5F503 4.2 38.6 1.0
CG2 A:ILE339 4.2 28.4 1.0
CG1 A:VAL332 4.4 27.8 1.0
CG2 A:ILE241 4.6 27.8 1.0
CB A:ILE241 4.6 25.7 1.0
CG2 A:ILE272 4.6 31.2 1.0
CG1 A:ILE241 4.7 28.6 1.0
CB A:VAL332 4.7 30.8 1.0
CA A:ILE339 4.9 26.2 1.0
CD1 A:LEU247 4.9 29.0 1.0
H10 A:C5F503 4.9 44.5 1.0
H11 A:C5F503 5.0 49.5 1.0

Chlorine binding site 4 out of 8 in 6lx5

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Chlorine binding site 4 out of 8 in the X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:49.5
occ:1.00
 CL2 A:C5F503 0.0 49.5 1.0
C07 A:C5F503 1.8 47.4 1.0
C06 A:C5F503 2.8 38.5 1.0
C08 A:C5F503 2.8 39.5 1.0
H11 A:C5F503 2.8 49.5 1.0
H81 A:C5F503 2.8 47.5 1.0
CL1 A:C5F503 3.1 58.8 1.0
CD1 A:ILE241 3.1 38.7 1.0
C11 A:C5F503 3.2 41.2 1.0
C09 A:C5F503 3.2 38.6 1.0
H16 A:C5F503 3.6 46.3 1.0
H82 A:C5F503 3.6 47.5 1.0
CG2 A:VAL332 4.0 28.0 1.0
CD1 A:LEU254 4.3 29.7 1.0
CB A:ALA250 4.3 30.6 1.0
C13 A:C5F503 4.4 43.0 1.0
C10 A:C5F503 4.5 37.1 1.0
CG1 A:ILE241 4.5 28.6 1.0
H31 A:C5F503 4.8 51.6 1.0
CB A:VAL332 4.9 30.8 1.0
H10 A:C5F503 4.9 44.5 1.0

Chlorine binding site 5 out of 8 in 6lx5

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Chlorine binding site 5 out of 8 in the X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:45.5
occ:1.00
 CL1 B:C5F501 0.0 45.5 1.0
C07 B:C5F501 1.8 41.8 1.0
H16 B:C5F501 2.7 40.4 1.0
C06 B:C5F501 2.8 33.6 1.0
C08 B:C5F501 2.8 42.1 1.0
H82 B:C5F501 2.8 50.6 1.0
CL2 B:C5F501 3.1 43.4 1.0
C B:ALA455 3.2 37.0 1.0
N B:LEU456 3.3 39.6 1.0
O B:ALA455 3.3 36.6 1.0
H81 B:C5F501 3.6 50.6 1.0
N B:ALA455 3.7 36.5 1.0
CA B:LEU456 3.8 40.8 1.0
C B:ALA454 3.8 44.8 1.0
CB B:ALA454 3.8 36.3 1.0
CA B:ALA455 3.8 33.5 1.0
CB B:LEU456 3.9 39.4 1.0
O B:ALA454 4.0 45.2 1.0
C09 B:C5F501 4.1 35.4 1.0
H11 B:C5F501 4.2 37.4 1.0
CA B:LYS448 4.4 39.1 1.0
CB B:LYS448 4.4 38.9 1.0
CA B:ALA454 4.4 40.2 1.0
NE2 B:GLN277 4.5 33.3 1.0
CG B:LYS448 4.6 38.3 1.0
O B:HOH602 4.6 43.8 1.0
C11 B:C5F501 4.6 31.2 1.0
CD1 B:LEU456 4.8 39.0 1.0
N B:LYS448 4.9 32.6 1.0
O B:HOH723 4.9 32.8 1.0
CG B:LEU456 5.0 41.8 1.0

Chlorine binding site 6 out of 8 in 6lx5

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Chlorine binding site 6 out of 8 in the X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:43.4
occ:1.00
 CL2 B:C5F501 0.0 43.4 1.0
C07 B:C5F501 1.8 41.8 1.0
C06 B:C5F501 2.8 33.6 1.0
C08 B:C5F501 2.8 42.1 1.0
H81 B:C5F501 2.9 50.6 1.0
CL1 B:C5F501 3.1 45.5 1.0
C09 B:C5F501 3.2 35.4 1.0
O B:VAL444 3.3 32.9 1.0
H16 B:C5F501 3.5 40.4 1.0
H82 B:C5F501 3.7 50.6 1.0
N B:LYS448 3.7 32.6 1.0
C11 B:C5F501 3.7 31.2 1.0
CG1 B:VAL444 3.7 31.4 1.0
CG2 B:ILE447 3.7 33.4 1.0
CB B:ILE447 3.8 35.4 1.0
H11 B:C5F501 3.8 37.4 1.0
C10 B:C5F501 3.9 31.1 1.0
CA B:VAL444 4.0 30.5 1.0
C B:VAL444 4.0 35.7 1.0
H10 B:C5F501 4.0 37.4 1.0
CA B:LYS448 4.2 39.1 1.0
CB B:LYS448 4.2 38.9 1.0
C B:ILE447 4.3 31.8 1.0
CB B:VAL444 4.3 32.0 1.0
CA B:ILE447 4.6 34.7 1.0
CG2 B:VAL444 4.6 30.2 1.0
C13 B:C5F501 4.8 28.4 1.0
CG1 B:ILE447 4.9 33.2 1.0
C12 B:C5F501 4.9 29.4 1.0
CD1 B:ILE447 5.0 35.9 1.0

Chlorine binding site 7 out of 8 in 6lx5

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Chlorine binding site 7 out of 8 in the X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:64.1
occ:1.00
 CL1 B:C5F502 0.0 64.1 1.0
C07 B:C5F502 1.8 46.4 1.0
H16 B:C5F502 2.7 50.6 1.0
C08 B:C5F502 2.8 40.3 1.0
H82 B:C5F502 2.8 48.4 1.0
C06 B:C5F502 2.8 42.1 1.0
CL2 B:C5F502 3.1 47.0 1.0
CD1 B:ILE339 3.6 27.1 1.0
H81 B:C5F502 3.6 48.4 1.0
CD1 B:ILE241 4.1 34.0 1.0
C09 B:C5F502 4.2 43.3 1.0
CG2 B:VAL332 4.2 23.8 1.0
CG1 B:VAL332 4.3 23.3 1.0
CB B:ILE339 4.3 21.9 1.0
H11 B:C5F502 4.5 47.0 1.0
CG2 B:ILE272 4.5 23.4 1.0
CG1 B:ILE339 4.5 22.6 1.0
CB B:VAL332 4.6 26.8 1.0
CG2 B:ILE339 4.6 24.1 1.0
C11 B:C5F502 4.8 39.2 1.0

Chlorine binding site 8 out of 8 in 6lx5

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Chlorine binding site 8 out of 8 in the X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of X-Ray Structure of Human Pparalpha Ligand Binding Domain-Ciprofibrate Co-Crystals Obtained By Delipidation and Co-Crystallization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:47.0
occ:1.00
 CL2 B:C5F502 0.0 47.0 1.0
C07 B:C5F502 1.8 46.4 1.0
C06 B:C5F502 2.8 42.1 1.0
C08 B:C5F502 2.8 40.3 1.0
H81 B:C5F502 2.8 48.4 1.0
CL1 B:C5F502 3.1 64.1 1.0
C09 B:C5F502 3.2 43.3 1.0
CD1 B:ILE241 3.4 34.0 1.0
H16 B:C5F502 3.6 50.6 1.0
H10 B:C5F502 3.6 50.6 1.0
H82 B:C5F502 3.6 48.4 1.0
C10 B:C5F502 3.7 42.2 1.0
CG2 B:VAL332 3.8 23.8 1.0
CD1 B:LEU254 3.9 28.1 1.0
CZ A:PHE421 4.0 24.9 1.0
C11 B:C5F502 4.1 39.2 1.0
H11 B:C5F502 4.4 47.0 1.0
CE2 A:PHE421 4.6 25.4 1.0
CB B:VAL332 4.6 26.8 1.0
CB B:ALA250 4.8 24.3 1.0
C12 B:C5F502 4.8 49.0 1.0
CE1 A:PHE421 4.8 26.2 1.0
CG1 B:ILE241 4.9 25.8 1.0

Reference:

S.Kamata, T.Oyama, K.Saito, A.Honda, Y.Yamamoto, K.Suda, R.Ishikawa, T.Itoh, Y.Watanabe, T.Shibata, K.Uchida, M.Suematsu, I.Ishii. Ppar Alpha Ligand-Binding Domain Structures with Endogenous Fatty Acids and Fibrates. Iscience V. 23 01727 2020.
ISSN: ESSN 2589-0042
PubMed: 33205029
DOI: 10.1016/J.ISCI.2020.101727
Page generated: Sun Jul 28 02:57:56 2024

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