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Chlorine in PDB 3vzd: Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp

Enzymatic activity of Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp

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

Protein crystallography data

The structure of Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp, PDB code: 3vzd 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 (°) 102.202, 106.573, 226.020, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 26.9

Other elements in 3vzd:

The structure of Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp (pdb code 3vzd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp, PDB code: 3vzd:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 3vzd

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Chlorine binding site 1 out of 10 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp


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 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:37.3
occ:1.00
 CL A:UUL401 0.0 37.3 1.0
C11 A:UUL401 1.7 33.4 1.0
C14 A:UUL401 2.7 33.7 1.0
C13 A:UUL401 2.7 32.0 1.0
CD1 A:PHE288 3.1 23.0 1.0
CE1 A:PHE288 3.4 26.4 1.0
CG A:PHE288 3.6 25.9 1.0
CD2 A:HIS311 3.8 30.5 1.0
NE2 A:HIS311 3.8 31.6 1.0
C8 A:UUL401 4.0 31.1 1.0
C9 A:UUL401 4.0 30.4 1.0
CZ A:PHE288 4.1 28.4 1.0
CD1 A:LEU319 4.1 25.1 1.0
CB A:PHE288 4.1 22.1 1.0
CD2 A:PHE288 4.2 25.0 1.0
O A:ALA274 4.3 22.6 1.0
CE2 A:PHE288 4.4 25.5 1.0
C7 A:UUL401 4.5 29.3 1.0
CD2 A:LEU319 4.7 29.1 1.0
CB A:ALA274 4.7 23.7 1.0
CD2 A:LEU261 4.9 21.8 1.0
CE1 A:HIS311 4.9 30.5 1.0
CG A:HIS311 5.0 32.2 1.0

Chlorine binding site 2 out of 10 in 3vzd

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Chlorine binding site 2 out of 10 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp


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 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:63.8
occ:1.00
 CL A:UUL402 0.0 63.8 1.0
C11 A:UUL402 1.7 54.9 1.0
C14 A:UUL402 2.6 53.9 1.0
C13 A:UUL402 2.8 52.5 1.0
CB A:ARG296 3.3 33.9 1.0
N A:ALA297 3.5 34.6 1.0
C A:ARG296 3.7 35.2 1.0
CA A:ALA297 3.8 34.5 1.0
C8 A:UUL402 3.9 52.7 1.0
C9 A:UUL402 4.0 51.5 1.0
CA A:ARG296 4.1 34.1 1.0
CD A:ARG296 4.2 44.6 1.0
O A:ARG296 4.2 35.1 1.0
CB A:ALA297 4.3 33.4 1.0
CG A:ARG296 4.4 37.2 1.0
C7 A:UUL402 4.4 52.2 1.0

Chlorine binding site 3 out of 10 in 3vzd

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Chlorine binding site 3 out of 10 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp


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 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:52.9
occ:1.00
 CL B:UUL401 0.0 52.9 1.0
C11 B:UUL401 1.7 58.0 1.0
C14 B:UUL401 2.7 59.1 1.0
C13 B:UUL401 2.7 57.9 1.0
CD1 B:PHE288 3.4 36.8 1.0
CG B:PHE288 3.5 36.7 1.0
NE2 B:HIS311 3.6 32.0 1.0
CE1 B:PHE288 3.7 35.4 1.0
O B:ALA274 3.8 29.7 1.0
CD2 B:HIS311 3.9 31.4 1.0
CD2 B:PHE288 3.9 34.8 1.0
C8 B:UUL401 4.0 61.1 1.0
CB B:PHE288 4.0 37.1 1.0
C9 B:UUL401 4.0 59.4 1.0
CZ B:PHE288 4.1 35.1 1.0
CE2 B:PHE288 4.2 32.7 1.0
CD1 B:LEU319 4.3 36.4 1.0
C7 B:UUL401 4.5 60.5 1.0
CB B:ALA274 4.6 28.6 1.0
C B:ALA274 4.7 29.4 1.0
CE1 B:HIS311 4.8 30.2 1.0
CD2 B:LEU261 4.8 32.3 1.0
CD2 B:LEU319 4.9 41.7 1.0
CA B:ALA274 5.0 28.6 1.0
SD B:MET306 5.0 42.0 1.0

Chlorine binding site 4 out of 10 in 3vzd

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Chlorine binding site 4 out of 10 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp


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 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:42.1
occ:1.00
 NH2 C:ARG56 3.1 53.0 1.0
CG2 B:THR50 3.3 20.8 1.0
C B:PHE49 3.5 22.3 1.0
OG B:SER48 3.6 30.1 1.0
CB B:ARG16 3.6 30.7 1.0
O B:PHE49 3.7 22.3 1.0
N B:PHE49 3.7 22.6 1.0
CD B:ARG16 3.8 44.3 1.0
CZ3 B:TRP72 3.9 22.3 1.0
CA B:PHE49 3.9 22.3 1.0
N B:THR50 3.9 22.2 1.0
C B:SER48 3.9 24.1 1.0
NE2 C:HIS59 4.0 33.4 1.0
O B:SER48 4.0 25.8 1.0
CB B:SER48 4.3 26.3 1.0
CG B:ARG16 4.3 34.9 1.0
CB B:THR50 4.4 21.6 1.0
CZ C:ARG56 4.4 54.0 1.0
O B:VAL17 4.5 20.6 1.0
CD2 C:HIS59 4.5 31.4 1.0
CH2 B:TRP72 4.6 24.2 1.0
CA B:THR50 4.7 21.4 1.0
CA B:ARG16 4.7 28.5 1.0
N B:VAL17 4.7 24.0 1.0
CA B:SER48 4.7 25.3 1.0
CE1 C:HIS59 4.8 32.1 1.0
CE3 B:TRP72 4.8 18.7 1.0

Chlorine binding site 5 out of 10 in 3vzd

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Chlorine binding site 5 out of 10 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp


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 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:50.7
occ:1.00
 CL C:UUL401 0.0 50.7 1.0
C11 C:UUL401 1.7 51.4 1.0
C14 C:UUL401 2.7 49.7 1.0
C13 C:UUL401 2.7 50.9 1.0
CD1 C:PHE288 3.1 27.9 1.0
CE1 C:PHE288 3.4 25.6 1.0
CG C:PHE288 3.4 27.9 1.0
NE2 C:HIS311 3.8 30.1 1.0
CZ C:PHE288 3.8 26.1 1.0
CD2 C:PHE288 3.9 25.8 1.0
CD2 C:HIS311 3.9 30.5 1.0
C8 C:UUL401 4.0 47.9 1.0
C9 C:UUL401 4.0 51.7 1.0
CB C:PHE288 4.0 28.9 1.0
CE2 C:PHE288 4.1 25.6 1.0
O C:ALA274 4.3 27.4 1.0
C7 C:UUL401 4.5 50.0 1.0
CD1 C:LEU319 4.5 34.6 1.0
CB C:ALA274 4.7 26.3 1.0
CD2 C:LEU319 4.8 33.2 1.0
CD2 C:LEU261 4.9 22.9 1.0
SD C:MET306 5.0 45.4 1.0

Chlorine binding site 6 out of 10 in 3vzd

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Chlorine binding site 6 out of 10 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp


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 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:58.6
occ:1.00
 CG2 C:THR50 3.1 26.2 1.0
C C:PHE49 3.5 27.9 1.0
O C:PHE49 3.6 26.5 1.0
NH2 B:ARG56 3.6 56.2 1.0
O B:HOH538 3.6 44.7 1.0
CZ3 C:TRP72 3.7 26.7 1.0
N C:THR50 3.8 27.5 1.0
CD C:ARG16 3.8 47.8 1.0
CB C:ARG16 3.8 34.0 1.0
CA C:PHE49 3.9 26.8 1.0
N C:PHE49 4.0 28.2 1.0
C C:SER48 4.1 28.7 1.0
O C:SER48 4.1 28.8 1.0
CH2 C:TRP72 4.3 24.3 1.0
NE2 B:HIS59 4.3 36.3 1.0
CB C:THR50 4.3 28.0 1.0
OG C:SER48 4.4 32.1 1.0
NH1 C:ARG16 4.5 60.6 1.0
CG C:ARG16 4.5 40.3 1.0
CA C:THR50 4.6 27.7 1.0
CB C:SER48 4.6 29.0 1.0
CD2 B:HIS59 4.7 35.2 1.0
O C:VAL17 4.7 26.9 1.0
CE3 C:TRP72 4.7 26.1 1.0
N C:VAL17 4.8 28.2 1.0
CZ B:ARG56 4.9 59.4 1.0
NE C:ARG16 4.9 56.2 1.0
CA C:SER48 5.0 28.7 1.0
CA C:ARG16 5.0 32.3 1.0

Chlorine binding site 7 out of 10 in 3vzd

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Chlorine binding site 7 out of 10 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl500

b:49.8
occ:1.00
 CL D:UUL500 0.0 49.8 1.0
C11 D:UUL500 1.7 49.7 1.0
C14 D:UUL500 2.7 47.6 1.0
C13 D:UUL500 2.7 48.0 1.0
CD1 D:PHE288 3.2 32.4 1.0
CE1 D:PHE288 3.4 32.0 1.0
CG D:PHE288 3.6 30.9 1.0
NE2 D:HIS311 3.6 47.0 1.0
CD2 D:HIS311 3.7 47.5 1.0
C8 D:UUL500 4.0 49.6 1.0
CZ D:PHE288 4.0 37.8 1.0
C9 D:UUL500 4.0 47.9 1.0
O D:ALA274 4.1 32.7 1.0
CD2 D:PHE288 4.1 34.5 1.0
CB D:PHE288 4.2 30.9 1.0
CE2 D:PHE288 4.3 37.6 1.0
CD1 D:LEU319 4.4 43.0 1.0
C7 D:UUL500 4.6 47.3 1.0
CB D:ALA274 4.6 31.1 1.0
SD D:MET306 4.8 44.6 1.0
CD2 D:LEU319 4.9 47.0 1.0
C D:ALA274 4.9 31.0 1.0
CE1 D:HIS311 4.9 47.1 1.0
CA D:ALA274 5.0 31.3 1.0
CD2 D:LEU261 5.0 26.9 1.0

Chlorine binding site 8 out of 10 in 3vzd

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Chlorine binding site 8 out of 10 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl401

b:39.2
occ:1.00
 CL E:UUL401 0.0 39.2 1.0
C11 E:UUL401 1.7 36.8 1.0
C14 E:UUL401 2.7 35.1 1.0
C13 E:UUL401 2.8 36.2 1.0
CD1 E:PHE288 3.3 27.1 1.0
CG E:PHE288 3.5 26.2 1.0
CE1 E:PHE288 3.6 27.1 1.0
NE2 E:HIS311 3.7 25.2 1.0
CD2 E:HIS311 3.7 23.4 1.0
O E:ALA274 4.0 26.7 1.0
C8 E:UUL401 4.0 35.9 1.0
CD2 E:PHE288 4.0 26.0 1.0
CB E:PHE288 4.0 28.1 1.0
C9 E:UUL401 4.1 37.0 1.0
CZ E:PHE288 4.1 24.6 1.0
CD1 E:LEU319 4.3 29.1 1.0
CE2 E:PHE288 4.3 26.3 1.0
C7 E:UUL401 4.6 35.4 1.0
CB E:ALA274 4.7 23.9 1.0
CD2 E:LEU319 4.8 29.3 1.0
CE1 E:HIS311 4.9 22.6 1.0
CD2 E:LEU261 4.9 23.7 1.0
C E:ALA274 4.9 26.2 1.0
SD E:MET306 4.9 37.3 1.0
CG E:HIS311 5.0 24.0 1.0

Chlorine binding site 9 out of 10 in 3vzd

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Chlorine binding site 9 out of 10 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl404

b:54.0
occ:1.00
 CG2 E:THR50 3.2 21.5 1.0
C E:PHE49 3.5 25.5 1.0
O E:PHE49 3.6 24.5 1.0
CB E:SER48 3.7 29.8 1.0
CB E:ARG16 3.7 33.1 1.0
NH1 F:ARG56 3.8 61.5 1.0
N E:THR50 3.8 25.0 1.0
N E:PHE49 3.8 25.9 1.0
CZ3 E:TRP72 3.8 27.2 1.0
NE2 F:HIS59 3.9 48.4 1.0
C E:SER48 3.9 27.1 1.0
CA E:PHE49 4.0 25.3 1.0
O E:SER48 4.1 27.3 1.0
CD E:ARG16 4.1 49.0 1.0
O E:VAL17 4.4 25.3 1.0
CB E:THR50 4.4 25.7 1.0
CD2 F:HIS59 4.4 45.5 1.0
CG E:ARG16 4.4 40.8 1.0
CH2 E:TRP72 4.5 27.6 1.0
CA E:SER48 4.5 29.2 1.0
N E:VAL17 4.6 27.9 1.0
CA E:THR50 4.6 24.5 1.0
OG E:SER48 4.7 32.0 1.0
CA E:ARG16 4.7 32.2 1.0
CE1 F:HIS59 4.7 46.7 1.0
CZ F:ARG56 4.8 64.8 1.0
CE3 E:TRP72 4.8 25.3 1.0
C E:ARG16 5.0 30.0 1.0

Chlorine binding site 10 out of 10 in 3vzd

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Chlorine binding site 10 out of 10 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl500

b:48.5
occ:1.00
 CL F:UUL500 0.0 48.5 1.0
C11 F:UUL500 1.7 49.7 1.0
C14 F:UUL500 2.7 47.9 1.0
C13 F:UUL500 2.7 48.8 1.0
CD1 F:PHE288 3.3 34.7 1.0
CE1 F:PHE288 3.4 36.1 1.0
NE2 F:HIS311 3.5 35.2 1.0
CD2 F:HIS311 3.7 38.2 1.0
CG F:PHE288 3.7 37.7 1.0
O F:ALA274 3.8 32.8 1.0
CZ F:PHE288 3.9 34.8 1.0
C8 F:UUL500 4.0 49.9 1.0
C9 F:UUL500 4.0 50.4 1.0
CD2 F:PHE288 4.1 36.4 1.0
CE2 F:PHE288 4.2 37.1 1.0
CD1 F:LEU319 4.3 38.6 1.0
CB F:PHE288 4.4 39.0 1.0
C7 F:UUL500 4.5 49.8 1.0
CB F:ALA274 4.5 31.2 1.0
CD2 F:LEU319 4.6 41.2 1.0
CE1 F:HIS311 4.7 38.7 1.0
C F:ALA274 4.8 32.6 1.0
CD2 F:LEU261 4.9 28.6 1.0
CA F:ALA274 4.9 32.0 1.0
CG F:HIS311 5.0 40.7 1.0
SD F:MET306 5.0 44.5 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 10:18:39 2020

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