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Chlorine in PDB 3vzc: Crystal Structure of Sphingosine Kinase 1 with Inhibitor

Enzymatic activity of Crystal Structure of Sphingosine Kinase 1 with Inhibitor

All present enzymatic activity of Crystal Structure of Sphingosine Kinase 1 with Inhibitor:
2.7.1.91;

Protein crystallography data

The structure of Crystal Structure of Sphingosine Kinase 1 with Inhibitor, PDB code: 3vzc was solved by X.Min, N.P.Walker, Z.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 102.220, 106.610, 226.180, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 28.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor (pdb code 3vzc). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor, PDB code: 3vzc:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3vzc

Go back to Chlorine Binding Sites List in 3vzc
Chlorine binding site 1 out of 6 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Sphingosine Kinase 1 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1001

b:40.1
occ:1.00
 CL A:UUL1001 0.0 40.1 1.0
C11 A:UUL1001 1.7 38.7 1.0
C14 A:UUL1001 2.7 37.4 1.0
C13 A:UUL1001 2.7 38.5 1.0
CD1 A:PHE288 3.2 21.9 1.0
CE1 A:PHE288 3.6 23.1 1.0
CG A:PHE288 3.6 21.9 1.0
NE2 A:HIS311 3.7 31.4 1.0
CD2 A:HIS311 3.8 31.5 1.0
C8 A:UUL1001 4.0 37.4 1.0
C9 A:UUL1001 4.0 36.6 1.0
CB A:PHE288 4.1 21.9 1.0
O A:ALA274 4.1 25.7 1.0
CD1 A:LEU319 4.2 34.7 1.0
CZ A:PHE288 4.2 24.0 1.0
CD2 A:PHE288 4.2 22.6 1.0
CE2 A:PHE288 4.5 23.3 1.0
C7 A:UUL1001 4.5 35.3 1.0
CD2 A:LEU319 4.6 33.9 1.0
CB A:ALA274 4.7 26.3 1.0
CD2 A:LEU261 4.8 22.8 1.0
SD A:MET306 5.0 33.3 1.0
CE1 A:HIS311 5.0 31.7 1.0
CG A:LEU319 5.0 34.3 1.0

Chlorine binding site 2 out of 6 in 3vzc

Go back to Chlorine Binding Sites List in 3vzc
Chlorine binding site 2 out of 6 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Sphingosine Kinase 1 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1001

b:52.7
occ:1.00
 CL B:UUL1001 0.0 52.7 1.0
C11 B:UUL1001 1.7 55.0 1.0
C14 B:UUL1001 2.7 57.3 1.0
C13 B:UUL1001 2.7 53.9 1.0
CD1 B:PHE288 3.2 38.8 1.0
CG B:PHE288 3.3 40.0 1.0
CE1 B:PHE288 3.5 40.0 1.0
CD2 B:PHE288 3.8 38.3 1.0
NE2 B:HIS311 3.8 33.7 1.0
CB B:PHE288 3.9 38.4 1.0
O B:ALA274 4.0 31.2 1.0
C8 B:UUL1001 4.0 57.6 1.0
CZ B:PHE288 4.0 39.0 1.0
CD2 B:HIS311 4.0 31.4 1.0
C9 B:UUL1001 4.0 55.0 1.0
CE2 B:PHE288 4.1 37.5 1.0
CD1 B:LEU319 4.2 35.8 1.0
C7 B:UUL1001 4.5 58.5 1.0
CD2 B:LEU261 4.6 30.6 1.0
CB B:ALA274 4.8 31.5 1.0
C B:ALA274 4.9 31.6 1.0
CE1 B:HIS311 5.0 31.9 1.0

Chlorine binding site 3 out of 6 in 3vzc

Go back to Chlorine Binding Sites List in 3vzc
Chlorine binding site 3 out of 6 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Sphingosine Kinase 1 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1001

b:58.0
occ:1.00
 CL C:UUL1001 0.0 58.0 1.0
C11 C:UUL1001 1.7 67.1 1.0
C14 C:UUL1001 2.7 67.0 1.0
C13 C:UUL1001 2.7 66.3 1.0
CD1 C:PHE288 3.3 34.5 1.0
CE1 C:PHE288 3.5 33.1 1.0
NE2 C:HIS311 3.6 37.3 1.0
CG C:PHE288 3.6 34.0 1.0
CD2 C:HIS311 3.8 38.6 1.0
C8 C:UUL1001 4.0 67.7 1.0
CZ C:PHE288 4.0 31.6 1.0
C9 C:UUL1001 4.0 68.9 1.0
CD2 C:PHE288 4.1 32.4 1.0
O C:ALA274 4.1 33.1 1.0
CB C:PHE288 4.2 34.7 1.0
CE2 C:PHE288 4.2 30.1 1.0
CD1 C:LEU319 4.4 41.9 1.0
C7 C:UUL1001 4.5 70.7 1.0
CE1 C:HIS311 4.8 38.3 1.0
CB C:ALA274 4.8 31.4 1.0
CD2 C:LEU261 4.8 28.9 1.0
CD2 C:LEU319 4.9 40.0 1.0
SD C:MET306 4.9 59.6 1.0
C C:ALA274 5.0 32.7 1.0

Chlorine binding site 4 out of 6 in 3vzc

Go back to Chlorine Binding Sites List in 3vzc
Chlorine binding site 4 out of 6 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Sphingosine Kinase 1 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1001

b:43.9
occ:1.00
 CL D:UUL1001 0.0 43.9 1.0
C11 D:UUL1001 1.7 46.2 1.0
C13 D:UUL1001 2.7 44.3 1.0
C14 D:UUL1001 2.7 45.0 1.0
CD1 D:PHE288 3.3 27.5 1.0
CE1 D:PHE288 3.5 29.4 1.0
NE2 D:HIS311 3.5 41.4 1.0
CD2 D:HIS311 3.5 42.2 1.0
CG D:PHE288 3.6 28.2 1.0
O D:ALA274 4.0 31.8 1.0
CZ D:PHE288 4.0 29.7 1.0
C9 D:UUL1001 4.0 43.6 1.0
C8 D:UUL1001 4.0 45.6 1.0
CD2 D:PHE288 4.1 29.3 1.0
CD1 D:LEU319 4.1 40.3 1.0
CB D:PHE288 4.2 28.7 1.0
CE2 D:PHE288 4.3 30.9 1.0
C7 D:UUL1001 4.5 43.0 1.0
CD2 D:LEU319 4.8 40.9 1.0
CE1 D:HIS311 4.8 42.1 1.0
C D:ALA274 4.9 30.0 1.0
CG D:HIS311 4.9 43.8 1.0
CB D:ALA274 4.9 31.9 1.0

Chlorine binding site 5 out of 6 in 3vzc

Go back to Chlorine Binding Sites List in 3vzc
Chlorine binding site 5 out of 6 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Sphingosine Kinase 1 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1001

b:41.9
occ:1.00
 CL E:UUL1001 0.0 41.9 1.0
C11 E:UUL1001 1.7 42.9 1.0
C14 E:UUL1001 2.7 41.6 1.0
C13 E:UUL1001 2.7 42.8 1.0
CD1 E:PHE288 3.2 39.3 1.0
CG E:PHE288 3.3 38.6 1.0
CE1 E:PHE288 3.5 39.7 1.0
CD2 E:PHE288 3.8 40.0 1.0
CB E:PHE288 3.9 37.3 1.0
NE2 E:HIS311 3.9 36.4 1.0
O E:ALA274 3.9 37.0 1.0
CZ E:PHE288 3.9 39.4 1.0
CD2 E:HIS311 4.0 34.6 1.0
C8 E:UUL1001 4.0 41.1 1.0
CE2 E:PHE288 4.0 39.7 1.0
C9 E:UUL1001 4.0 42.9 1.0
C7 E:UUL1001 4.6 43.7 1.0
CB E:ALA274 4.6 34.4 1.0
CD1 E:LEU319 4.6 36.4 1.0
C E:ALA274 4.8 35.1 1.0
CD2 E:LEU261 4.9 34.4 1.0
CA E:ALA274 4.9 34.8 1.0
CD2 E:LEU319 5.0 33.8 1.0

Chlorine binding site 6 out of 6 in 3vzc

Go back to Chlorine Binding Sites List in 3vzc
Chlorine binding site 6 out of 6 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Sphingosine Kinase 1 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl1001

b:77.5
occ:1.00
 CL F:UUL1001 0.0 77.5 1.0
C11 F:UUL1001 1.7 75.5 1.0
C14 F:UUL1001 2.7 76.3 1.0
C13 F:UUL1001 2.7 73.2 1.0
CD1 F:PHE288 3.3 46.7 1.0
NE2 F:HIS311 3.4 46.4 1.0
CE1 F:PHE288 3.5 46.8 1.0
CD2 F:HIS311 3.7 47.5 1.0
O F:ALA274 3.7 40.3 1.0
CG F:PHE288 3.7 46.4 1.0
C8 F:UUL1001 4.0 77.7 1.0
C9 F:UUL1001 4.0 74.9 1.0
CD1 F:LEU319 4.1 60.3 1.0
CZ F:PHE288 4.2 48.2 1.0
CB F:PHE288 4.3 45.7 1.0
CD2 F:PHE288 4.3 49.3 1.0
CB F:ALA274 4.4 42.9 1.0
CE2 F:PHE288 4.5 49.6 1.0
C7 F:UUL1001 4.5 76.1 1.0
CE1 F:HIS311 4.5 46.9 1.0
CD2 F:LEU319 4.5 61.1 1.0
C F:ALA274 4.7 42.5 1.0
CA F:ALA274 4.7 41.2 1.0
SD F:MET306 4.8 55.8 1.0
CD2 F:LEU261 4.9 38.7 1.0
CG F:LEU319 4.9 60.4 1.0
CG F:HIS311 4.9 49.1 1.0

Reference:

Z.Wang, X.Min, S.H.Xiao, S.Johnstone, W.Romanow, D.Meininger, H.Xu, J.Liu, J.Dai, S.An, S.Thibault, N.Walker. Molecular Basis of Sphingosine Kinase 1 Substrate Recognition and Catalysis. Structure V. 21 798 2013.
ISSN: ISSN 0969-2126
PubMed: 23602659
DOI: 10.1016/J.STR.2013.02.025
Page generated: Sat Dec 12 10:18:38 2020

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