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Potassium in PDB 2rkb: Serine Dehydratase Like-1 From Human Cancer Cells

Protein crystallography data

The structure of Serine Dehydratase Like-1 From Human Cancer Cells, PDB code: 2rkb was solved by T.Yamada, J.Komoto, T.Kasuya, H.Mori, H.Ogawa, F.Takusagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 97.210, 154.740, 306.370, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 23

Potassium Binding Sites:

The binding sites of Potassium atom in the Serine Dehydratase Like-1 From Human Cancer Cells (pdb code 2rkb). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Serine Dehydratase Like-1 From Human Cancer Cells, PDB code: 2rkb:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 2rkb

Go back to Potassium Binding Sites List in 2rkb
Potassium binding site 1 out of 5 in the Serine Dehydratase Like-1 From Human Cancer Cells


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Serine Dehydratase Like-1 From Human Cancer Cells within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K401

b:21.1
occ:1.00
 O A:VAL173 2.6 17.2 1.0
O A:ALA204 2.7 21.3 1.0
OE1 A:GLU200 2.7 23.3 1.0
O A:GLY174 2.9 18.7 1.0
O A:LEU229 2.9 22.9 1.0
SG A:CYS206 3.3 20.0 1.0
CD A:GLU200 3.6 23.9 1.0
C A:VAL173 3.6 17.6 1.0
C A:ALA204 3.6 21.8 1.0
C A:GLY174 3.7 18.7 1.0
CG A:GLU200 3.7 22.7 1.0
N A:CYS206 3.7 21.6 1.0
CA A:GLY174 3.7 19.0 1.0
C A:LEU229 4.0 21.5 1.0
N A:GLY174 4.1 18.2 1.0
CA A:HIS205 4.3 21.4 1.0
CB A:LEU229 4.3 20.1 1.0
N A:HIS205 4.3 21.1 1.0
CB A:CYS206 4.4 21.4 1.0
C A:HIS205 4.4 21.0 1.0
N A:PHE207 4.4 22.1 1.0
CA A:LEU229 4.5 20.8 1.0
CG1 A:VAL173 4.5 16.7 1.0
CA A:CYS206 4.5 22.0 1.0
O A:ALA231 4.5 22.4 1.0
CA A:ALA204 4.7 21.9 1.0
CB A:VAL173 4.7 17.3 1.0
CB A:ALA204 4.8 20.5 1.0
CA A:VAL173 4.8 17.7 1.0
OE2 A:GLU200 4.8 23.1 1.0
CB A:GLU200 4.8 21.6 1.0
N A:ALA231 4.9 21.7 1.0
N A:GLY175 4.9 17.8 1.0

Potassium binding site 2 out of 5 in 2rkb

Go back to Potassium Binding Sites List in 2rkb
Potassium binding site 2 out of 5 in the Serine Dehydratase Like-1 From Human Cancer Cells


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Serine Dehydratase Like-1 From Human Cancer Cells within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K401

b:26.1
occ:1.00
 O B:VAL173 2.6 21.2 1.0
O B:ALA204 2.7 23.5 1.0
OE1 B:GLU200 2.7 22.9 1.0
O B:GLY174 2.8 20.2 1.0
O B:LEU229 2.9 25.6 1.0
SG B:CYS206 3.3 24.8 1.0
C B:VAL173 3.5 19.8 1.0
CD B:GLU200 3.6 24.1 1.0
C B:GLY174 3.6 20.2 1.0
C B:ALA204 3.7 23.3 1.0
CG B:GLU200 3.7 22.5 1.0
CA B:GLY174 3.7 20.2 1.0
N B:CYS206 3.8 24.3 1.0
C B:LEU229 4.0 24.0 1.0
N B:GLY174 4.0 19.8 1.0
CB B:LEU229 4.2 20.6 1.0
CA B:HIS205 4.3 22.7 1.0
N B:HIS205 4.3 23.0 1.0
CB B:CYS206 4.4 23.1 1.0
N B:PHE207 4.4 25.4 1.0
C B:HIS205 4.4 23.0 1.0
CA B:LEU229 4.4 21.4 1.0
CG1 B:VAL173 4.5 17.6 1.0
O B:ALA231 4.6 25.4 1.0
CA B:CYS206 4.6 24.1 1.0
CA B:ALA204 4.7 23.6 1.0
CB B:VAL173 4.7 18.7 1.0
CA B:VAL173 4.7 18.7 1.0
CB B:ALA204 4.8 21.1 1.0
OE2 B:GLU200 4.8 24.7 1.0
CB B:GLU200 4.8 20.8 1.0
N B:GLY175 4.9 19.1 1.0
N B:ALA231 4.9 23.2 1.0

Potassium binding site 3 out of 5 in 2rkb

Go back to Potassium Binding Sites List in 2rkb
Potassium binding site 3 out of 5 in the Serine Dehydratase Like-1 From Human Cancer Cells


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Serine Dehydratase Like-1 From Human Cancer Cells within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K401

b:29.1
occ:1.00
 O C:VAL173 2.6 22.9 1.0
O C:ALA204 2.7 26.6 1.0
OE1 C:GLU200 2.7 29.3 1.0
O C:GLY174 2.8 26.4 1.0
O C:LEU229 3.0 24.1 1.0
SG C:CYS206 3.3 28.9 1.0
C C:VAL173 3.6 22.6 1.0
CD C:GLU200 3.6 29.8 1.0
C C:GLY174 3.6 25.2 1.0
C C:ALA204 3.7 25.1 1.0
CG C:GLU200 3.7 27.8 1.0
CA C:GLY174 3.7 23.8 1.0
N C:CYS206 3.7 26.5 1.0
C C:LEU229 4.0 23.9 1.0
N C:GLY174 4.1 22.5 1.0
CB C:LEU229 4.2 22.8 1.0
CA C:HIS205 4.3 26.4 1.0
N C:HIS205 4.3 25.2 1.0
CB C:CYS206 4.4 25.8 1.0
N C:PHE207 4.4 26.2 1.0
C C:HIS205 4.4 26.4 1.0
CA C:LEU229 4.4 23.5 1.0
CG1 C:VAL173 4.4 19.7 1.0
O C:ALA231 4.5 28.7 1.0
CA C:CYS206 4.6 26.1 1.0
CA C:ALA204 4.7 25.2 1.0
CB C:VAL173 4.7 19.8 1.0
CA C:VAL173 4.7 21.3 1.0
CB C:ALA204 4.8 23.6 1.0
OE2 C:GLU200 4.8 30.7 1.0
CB C:GLU200 4.8 26.1 1.0
N C:ALA231 4.9 26.8 1.0
N C:GLY175 4.9 25.1 1.0

Potassium binding site 4 out of 5 in 2rkb

Go back to Potassium Binding Sites List in 2rkb
Potassium binding site 4 out of 5 in the Serine Dehydratase Like-1 From Human Cancer Cells


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Serine Dehydratase Like-1 From Human Cancer Cells within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K401

b:24.5
occ:1.00
 O D:VAL173 2.6 21.6 1.0
O D:ALA204 2.7 24.6 1.0
OE1 D:GLU200 2.7 26.9 1.0
O D:GLY174 2.8 24.9 1.0
O D:LEU229 3.0 25.1 1.0
SG D:CYS206 3.3 30.6 1.0
C D:VAL173 3.5 21.5 1.0
CD D:GLU200 3.6 27.1 1.0
C D:GLY174 3.6 23.2 1.0
C D:ALA204 3.7 24.3 1.0
CG D:GLU200 3.7 25.9 1.0
CA D:GLY174 3.7 21.9 1.0
N D:CYS206 3.7 24.5 1.0
C D:LEU229 4.0 23.8 1.0
N D:GLY174 4.1 21.8 1.0
CB D:LEU229 4.2 21.8 1.0
CA D:HIS205 4.3 23.7 1.0
N D:HIS205 4.3 24.1 1.0
N D:PHE207 4.4 25.5 1.0
CB D:CYS206 4.4 26.3 1.0
C D:HIS205 4.4 23.9 1.0
CG1 D:VAL173 4.4 19.0 1.0
CA D:LEU229 4.5 23.3 1.0
CA D:CYS206 4.5 26.0 1.0
O D:ALA231 4.6 28.1 1.0
CB D:VAL173 4.7 18.7 1.0
CA D:ALA204 4.7 24.4 1.0
CA D:VAL173 4.7 20.4 1.0
OE2 D:GLU200 4.8 30.0 1.0
CB D:ALA204 4.8 24.5 1.0
CB D:GLU200 4.8 25.0 1.0
N D:GLY175 4.9 21.2 1.0
N D:ALA231 4.9 24.6 1.0

Potassium binding site 5 out of 5 in 2rkb

Go back to Potassium Binding Sites List in 2rkb
Potassium binding site 5 out of 5 in the Serine Dehydratase Like-1 From Human Cancer Cells


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Serine Dehydratase Like-1 From Human Cancer Cells within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K401

b:22.4
occ:1.00
 O E:VAL173 2.6 17.5 1.0
O E:ALA204 2.7 23.8 1.0
OE1 E:GLU200 2.8 20.9 1.0
O E:GLY174 2.8 20.8 1.0
O E:LEU229 2.9 21.1 1.0
SG E:CYS206 3.4 16.4 1.0
C E:VAL173 3.5 17.9 1.0
C E:GLY174 3.6 19.4 1.0
CD E:GLU200 3.6 22.6 1.0
CA E:GLY174 3.7 18.9 1.0
C E:ALA204 3.7 22.9 1.0
CG E:GLU200 3.7 22.4 1.0
N E:CYS206 3.8 20.6 1.0
C E:LEU229 4.0 20.3 1.0
N E:GLY174 4.0 17.8 1.0
CB E:LEU229 4.2 19.3 1.0
CA E:HIS205 4.3 21.1 1.0
N E:HIS205 4.4 21.6 1.0
CA E:LEU229 4.4 19.9 1.0
CB E:CYS206 4.4 19.4 1.0
N E:PHE207 4.4 20.8 1.0
C E:HIS205 4.4 20.5 1.0
CG1 E:VAL173 4.5 17.4 1.0
O E:ALA231 4.6 24.5 1.0
CA E:CYS206 4.6 19.6 1.0
CA E:ALA204 4.7 23.1 1.0
CB E:VAL173 4.7 17.9 1.0
CA E:VAL173 4.7 17.9 1.0
CB E:ALA204 4.8 20.8 1.0
OE2 E:GLU200 4.8 22.0 1.0
CB E:GLU200 4.9 22.1 1.0
N E:ALA231 4.9 23.3 1.0
N E:GLY175 4.9 18.5 1.0

Reference:

T.Yamada, J.Komoto, T.Kasuya, Y.Takata, H.Ogawa, H.Mori, F.Takusagawa. A Catalytic Mechanism That Explains A Low Catalytic Activity of Serine Dehydratase Like-1 From Human Cancer Cells: Crystal Structure and Site-Directed Mutagenesis Studies. Biochim.Biophys.Acta V.1780 809 2008.
ISSN: ISSN 0006-3002
PubMed: 18342636
DOI: 10.1016/J.BBAGEN.2008.01.020
Page generated: Mon Aug 12 06:56:59 2024

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