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Potassium in PDB 1pwh: Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate

Enzymatic activity of Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate

All present enzymatic activity of Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate:
4.3.1.17;

Protein crystallography data

The structure of Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate, PDB code: 1pwh was solved by T.Yamada, J.Komoto, Y.Takata, H.Ogawa, F.Takusagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.01 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.241, 109.262, 98.940, 90.00, 91.66, 90.00
R / Rfree (%) 23 / 26

Potassium Binding Sites:

The binding sites of Potassium atom in the Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate (pdb code 1pwh). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate, PDB code: 1pwh:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 1pwh

Go back to Potassium Binding Sites List in 1pwh
Potassium binding site 1 out of 4 in the Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K332

b:8.4
occ:1.00
 O A:ALA198 2.9 13.1 1.0
OE2 A:GLU194 2.9 14.1 1.0
O A:VAL167 3.0 10.9 1.0
OG A:SER200 3.1 15.5 1.0
O A:LEU223 3.1 12.6 1.0
O A:GLY168 3.1 15.4 1.0
N A:SER200 3.8 14.0 1.0
C A:VAL167 3.8 11.5 1.0
CA A:GLY168 3.8 13.6 1.0
C A:GLY168 3.9 14.2 1.0
C A:ALA198 3.9 12.6 1.0
CD A:GLU194 4.1 16.8 1.0
N A:GLY168 4.1 13.5 1.0
C A:LEU223 4.2 12.5 1.0
CB A:SER200 4.3 15.5 1.0
O A:VAL225 4.3 16.7 1.0
N A:PHE201 4.3 15.3 1.0
CG1 A:VAL167 4.4 8.3 1.0
CA A:SER200 4.5 14.5 1.0
CB A:GLU194 4.5 14.8 1.0
CB A:LEU223 4.6 10.7 1.0
C A:HIS199 4.6 13.7 1.0
CA A:HIS199 4.6 13.0 1.0
N A:HIS199 4.7 13.0 1.0
N A:VAL225 4.7 14.3 1.0
CA A:LEU223 4.7 12.0 1.0
CB A:VAL167 4.7 9.2 1.0
OE1 A:GLU194 4.8 17.7 1.0
CG1 A:VAL228 4.9 18.5 1.0
C A:SER200 4.9 15.1 1.0
CG A:LEU223 4.9 10.6 1.0
CA A:VAL167 4.9 10.8 1.0
CG A:GLU194 4.9 15.8 1.0
CA A:ALA198 4.9 12.5 1.0
CB A:ALA198 4.9 13.4 1.0

Potassium binding site 2 out of 4 in 1pwh

Go back to Potassium Binding Sites List in 1pwh
Potassium binding site 2 out of 4 in the Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K333

b:18.8
occ:1.00
 O B:ALA198 2.8 11.8 1.0
OE2 B:GLU194 2.9 20.0 1.0
O B:GLY168 3.0 16.0 1.0
OG B:SER200 3.1 14.4 1.0
O B:VAL167 3.1 13.4 1.0
O B:LEU223 3.1 11.7 1.0
N B:SER200 3.7 14.6 1.0
C B:GLY168 3.8 16.4 1.0
CA B:GLY168 3.8 15.1 1.0
C B:VAL167 3.8 13.3 1.0
C B:ALA198 3.9 13.6 1.0
CD B:GLU194 4.1 21.0 1.0
CB B:SER200 4.2 14.5 1.0
N B:GLY168 4.2 14.3 1.0
O B:VAL225 4.2 15.5 1.0
C B:LEU223 4.2 13.3 1.0
N B:PHE201 4.3 15.2 1.0
CA B:SER200 4.4 14.7 1.0
CG1 B:VAL167 4.4 9.3 1.0
C B:HIS199 4.6 14.1 1.0
CB B:GLU194 4.6 15.5 1.0
CA B:HIS199 4.6 13.9 1.0
CB B:LEU223 4.7 12.0 1.0
N B:VAL225 4.7 14.5 1.0
N B:HIS199 4.7 14.0 1.0
CA B:LEU223 4.8 13.3 1.0
CG1 B:VAL228 4.8 15.6 1.0
CB B:VAL167 4.8 10.4 1.0
C B:SER200 4.8 15.4 1.0
OE1 B:GLU194 4.9 22.1 1.0
CA B:ALA198 4.9 14.0 1.0
CA B:VAL167 5.0 12.0 1.0
CG B:LEU223 5.0 12.4 1.0
CG B:GLU194 5.0 19.7 1.0
CB B:ALA198 5.0 14.1 1.0

Potassium binding site 3 out of 4 in 1pwh

Go back to Potassium Binding Sites List in 1pwh
Potassium binding site 3 out of 4 in the Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K334

b:17.8
occ:1.00
 O C:ALA198 2.8 16.4 1.0
OE2 C:GLU194 2.9 21.6 1.0
OG C:SER200 3.0 16.6 1.0
O C:VAL167 3.1 15.7 1.0
O C:GLY168 3.2 17.1 1.0
O C:LEU223 3.3 15.4 1.0
N C:SER200 3.6 17.1 1.0
C C:VAL167 3.8 14.6 1.0
CA C:GLY168 3.9 16.1 1.0
C C:ALA198 3.9 16.4 1.0
C C:GLY168 3.9 16.6 1.0
CD C:GLU194 4.0 21.8 1.0
CB C:SER200 4.1 17.4 1.0
N C:PHE201 4.1 17.1 1.0
N C:GLY168 4.2 15.8 1.0
CA C:SER200 4.3 16.7 1.0
O C:VAL225 4.4 14.9 1.0
C C:LEU223 4.4 14.8 1.0
CG1 C:VAL167 4.5 10.6 1.0
CB C:GLU194 4.5 17.4 1.0
C C:HIS199 4.5 16.7 1.0
CA C:HIS199 4.5 16.2 1.0
N C:HIS199 4.6 16.2 1.0
OE1 C:GLU194 4.7 23.3 1.0
C C:SER200 4.7 17.2 1.0
CB C:LEU223 4.7 13.1 1.0
CG1 C:VAL228 4.8 19.3 1.0
CB C:VAL167 4.8 13.1 1.0
CG C:GLU194 4.8 20.3 1.0
N C:VAL225 4.8 16.3 1.0
CA C:ALA198 4.9 16.9 1.0
CA C:LEU223 4.9 14.5 1.0
CA C:VAL167 5.0 13.5 1.0
CB C:ALA198 5.0 18.0 1.0
CB C:PHE201 5.0 15.8 1.0

Potassium binding site 4 out of 4 in 1pwh

Go back to Potassium Binding Sites List in 1pwh
Potassium binding site 4 out of 4 in the Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K335

b:18.1
occ:1.00
 O D:ALA198 2.9 15.3 1.0
OE2 D:GLU194 2.9 16.1 1.0
O D:VAL167 3.0 13.2 1.0
OG D:SER200 3.1 14.0 1.0
O D:GLY168 3.1 17.2 1.0
O D:LEU223 3.1 13.1 1.0
N D:SER200 3.8 14.7 1.0
C D:VAL167 3.8 13.8 1.0
CA D:GLY168 3.8 15.6 1.0
C D:GLY168 3.8 16.2 1.0
C D:ALA198 3.9 15.4 1.0
CD D:GLU194 4.1 18.9 1.0
N D:GLY168 4.1 14.8 1.0
CB D:SER200 4.2 14.5 1.0
C D:LEU223 4.2 13.4 1.0
O D:VAL225 4.3 16.5 1.0
N D:PHE201 4.3 14.7 1.0
CG1 D:VAL167 4.4 7.9 1.0
CA D:SER200 4.4 14.5 1.0
CB D:GLU194 4.5 14.8 1.0
C D:HIS199 4.6 15.2 1.0
CA D:HIS199 4.6 15.1 1.0
CB D:LEU223 4.6 12.2 1.0
N D:HIS199 4.7 15.4 1.0
N D:VAL225 4.7 14.7 1.0
CB D:VAL167 4.8 11.0 1.0
CG1 D:VAL228 4.8 17.8 1.0
CA D:LEU223 4.8 13.0 1.0
OE1 D:GLU194 4.9 20.8 1.0
C D:SER200 4.9 14.5 1.0
CA D:VAL167 4.9 12.1 1.0
CG D:GLU194 4.9 18.2 1.0
CA D:ALA198 4.9 14.6 1.0
CG D:LEU223 5.0 13.2 1.0
CB D:ALA198 5.0 13.2 1.0

Reference:

T.Yamada, J.Komoto, Y.Takata, H.Ogawa, H.C.Pitot, F.Takusagawa. Crystal Structure of Serine Dehydratase From Rat Liver. Biochemistry V. 42 12854 2003.
ISSN: ISSN 0006-2960
PubMed: 14596599
DOI: 10.1021/BI035324P
Page generated: Mon Aug 12 05:13:42 2024

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