Atomistry » Rubidium » PDB 1dge-4z3p » 1dge
Atomistry »
  Rubidium »
    PDB 1dge-4z3p »
      1dge »

Rubidium in PDB 1dge: An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase

Enzymatic activity of An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase

All present enzymatic activity of An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase:
4.1.1.64;

Protein crystallography data

The structure of An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase, PDB code: 1dge was solved by E.Hohenester, J.N.Jansonius, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.80
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 153.500, 153.500, 86.600, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Rubidium Binding Sites:

The binding sites of Rubidium atom in the An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase (pdb code 1dge). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 2 binding sites of Rubidium where determined in the An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase, PDB code: 1dge:
Jump to Rubidium binding site number: 1; 2;

Rubidium binding site 1 out of 2 in 1dge

Go back to Rubidium Binding Sites List in 1dge
Rubidium binding site 1 out of 2 in the An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb435

b:24.3
occ:0.57
O A:PRO99 2.3 26.9 1.0
O A:LEU102 2.7 21.4 1.0
O A:ALA95 2.7 26.7 1.0
O A:THR98 2.9 24.6 1.0
C A:PRO99 3.1 24.0 1.0
O A:HOH576 3.1 45.0 1.0
OG1 A:THR98 3.4 17.9 1.0
N A:PRO100 3.6 23.7 1.0
C A:THR98 3.6 23.3 1.0
CA A:PRO100 3.7 21.9 1.0
C A:LEU102 3.8 20.3 1.0
C A:ALA95 3.9 23.1 1.0
N A:LEU102 3.9 24.9 1.0
N A:GLY101 4.1 21.6 1.0
CA A:PRO99 4.1 21.5 1.0
N A:PRO99 4.2 22.5 1.0
C A:PRO100 4.2 21.8 1.0
CA A:LEU102 4.3 21.3 1.0
CB A:LEU102 4.4 21.7 1.0
CB A:THR98 4.5 18.8 1.0
CA A:THR98 4.5 21.9 1.0
CA A:ALA95 4.6 18.0 1.0
N A:THR98 4.6 23.9 1.0
OD1 A:ASP103 4.7 33.5 1.0
CD A:PRO100 4.9 22.9 1.0
N A:ASP103 4.9 20.0 1.0
N A:ASN96 4.9 20.9 1.0
C A:GLY101 5.0 27.8 1.0

Rubidium binding site 2 out of 2 in 1dge

Go back to Rubidium Binding Sites List in 1dge
Rubidium binding site 2 out of 2 in the An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb436

b:25.1
occ:1.00
OD1 A:ASP307 2.5 21.5 1.0
OG A:SER80 2.6 16.8 1.0
O A:THR303 2.8 28.5 1.0
O A:VAL305 2.8 19.1 1.0
O A:LEU78 2.8 22.2 1.0
O A:HOH531 3.0 25.2 1.0
CG A:ASP307 3.4 23.7 1.0
CB A:SER80 3.7 19.8 1.0
C A:THR303 3.7 24.5 1.0
N A:SER80 3.8 23.6 1.0
CA A:SER80 3.8 23.6 1.0
C A:VAL305 3.9 19.7 1.0
OD2 A:ASP307 3.9 25.8 1.0
C A:LEU78 4.0 21.0 1.0
N A:VAL305 4.0 17.9 1.0
C A:HIS304 4.0 18.9 1.0
CA A:HIS304 4.1 21.5 1.0
O A:SER306 4.2 20.9 1.0
C A:PHE79 4.2 21.6 1.0
N A:HIS304 4.3 22.3 1.0
CG1 A:VAL305 4.3 20.4 1.0
C A:SER306 4.4 20.1 1.0
CE1 A:HIS77 4.4 17.3 1.0
O A:PHE79 4.5 20.3 1.0
CB A:ASP307 4.5 22.7 1.0
ND1 A:HIS77 4.5 17.0 1.0
O A:HIS304 4.6 18.8 1.0
CA A:VAL305 4.6 18.4 1.0
N A:LEU78 4.6 21.3 1.0
N A:ASP307 4.6 21.2 1.0
CA A:ASP307 4.7 21.8 1.0
O A:THR302 4.8 25.3 1.0
CA A:THR303 4.8 21.4 1.0
CA A:PHE79 4.8 21.4 1.0
CA A:LEU78 4.9 21.2 1.0
N A:PHE79 4.9 21.1 1.0
N A:SER306 4.9 20.0 1.0

Reference:

E.Hohenester, J.W.Keller, J.N.Jansonius. An Alkali Metal Ion Size-Dependent Switch in the Active Site Structure of Dialkylglycine Decarboxylase. Biochemistry V. 33 13561 1994.
ISSN: ISSN 0006-2960
PubMed: 7947767
DOI: 10.1021/BI00250A008
Page generated: Wed Dec 16 02:06:36 2020

Last articles

Zn in 7L0B
Zn in 7KZZ
Zn in 7KZL
Zn in 7L3O
Zn in 7L52
Zn in 7L6T
Zn in 7KZ7
Zn in 7L6R
Zn in 7KKM
Zn in 7KKQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy