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Rubidium in PDB 1ud5: Crystal Structure of AMYK38 with Rubidium Ion

Enzymatic activity of Crystal Structure of AMYK38 with Rubidium Ion

All present enzymatic activity of Crystal Structure of AMYK38 with Rubidium Ion:
3.2.1.1;

Protein crystallography data

The structure of Crystal Structure of AMYK38 with Rubidium Ion, PDB code: 1ud5 was solved by T.Nonaka, M.Fujihashi, A.Kita, H.Hagihara, K.Ozaki, S.Ito, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.30 / 2.70
Space group P 2 3
Cell size a, b, c (Å), α, β, γ (°) 132.605, 132.605, 132.605, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 26.9

Other elements in 1ud5:

The structure of Crystal Structure of AMYK38 with Rubidium Ion also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Rubidium Binding Sites:

The binding sites of Rubidium atom in the Crystal Structure of AMYK38 with Rubidium Ion (pdb code 1ud5). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 6 binding sites of Rubidium where determined in the Crystal Structure of AMYK38 with Rubidium Ion, PDB code: 1ud5:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5; 6;

Rubidium binding site 1 out of 6 in 1ud5

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Rubidium binding site 1 out of 6 in the Crystal Structure of AMYK38 with Rubidium Ion


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of Crystal Structure of AMYK38 with Rubidium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1003

b:35.3
occ:0.78
 OD1 A:ASP325 2.6 25.3 1.0
O A:SER337 2.6 27.2 1.0
OD1 A:ASN289 2.8 30.0 1.0
O A:VAL324 2.8 16.2 1.0
CG A:ASN289 3.2 29.5 1.0
ND2 A:ASN289 3.2 29.4 1.0
O A:ASN289 3.4 24.1 1.0
CG A:ASP325 3.4 21.3 1.0
CG2 A:VAL339 3.7 16.2 1.0
C A:SER337 3.8 36.2 1.0
OG A:SER337 3.8 45.5 1.0
C A:VAL324 3.9 16.6 1.0
OD2 A:ASP325 4.0 24.6 1.0
C A:ASN289 4.1 25.7 1.0
CG2 A:THR329 4.2 27.2 1.0
CB A:THR329 4.3 28.1 1.0
CA A:ASP325 4.3 20.9 1.0
OG1 A:THR329 4.3 33.3 1.0
CB A:SER337 4.3 40.1 1.0
CB A:TYR293 4.4 26.0 1.0
CB A:ASN289 4.4 28.7 1.0
CB A:ASP325 4.5 17.8 1.0
N A:VAL339 4.5 20.3 1.0
CA A:ASN289 4.5 21.8 1.0
N A:ASP325 4.6 17.8 1.0
N A:TRP338 4.7 29.1 1.0
CA A:SER337 4.7 40.3 1.0
CA A:TRP338 4.8 25.3 1.0
N A:TYR293 4.9 23.6 1.0
CB A:VAL339 4.9 21.4 1.0
C A:TRP338 4.9 25.2 1.0
CA A:TYR293 5.0 20.5 1.0

Rubidium binding site 2 out of 6 in 1ud5

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Rubidium binding site 2 out of 6 in the Crystal Structure of AMYK38 with Rubidium Ion


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of Crystal Structure of AMYK38 with Rubidium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1004

b:43.2
occ:1.00
 O A:ASN68 3.0 15.8 1.0
O A:SER144 3.1 10.2 1.0
CA A:GLN69 3.8 21.8 1.0
C A:ASN68 4.0 17.1 1.0
C A:SER144 4.0 17.4 1.0
O A:HOH2060 4.1 14.6 1.0
N A:GLN69 4.4 21.6 1.0
CB A:GLN69 4.4 22.7 1.0
CG A:GLN69 4.5 29.0 1.0
CB A:SER144 4.6 15.3 1.0
CA A:GLY145 4.6 17.2 1.0
OD1 A:ASN68 4.7 22.5 1.0
N A:GLY145 4.7 22.6 1.0
N A:LYS70 4.8 29.2 1.0
C A:GLN69 4.8 26.9 1.0
CA A:SER144 5.0 15.3 1.0

Rubidium binding site 3 out of 6 in 1ud5

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Rubidium binding site 3 out of 6 in the Crystal Structure of AMYK38 with Rubidium Ion


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of Crystal Structure of AMYK38 with Rubidium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1005

b:65.2
occ:0.90
 O A:ALA252 2.8 34.5 1.0
O A:ARG249 2.9 35.4 1.0
O A:ASN250 3.2 39.2 1.0
C A:ALA252 3.7 35.8 1.0
C A:ASN250 3.7 35.7 1.0
C A:ARG249 4.0 34.7 1.0
CA A:ASN250 4.1 36.8 1.0
N A:ALA252 4.3 36.0 1.0
CA A:ASP253 4.3 39.7 1.0
N A:ASP253 4.4 36.2 1.0
N A:GLU251 4.5 34.0 1.0
C A:GLU251 4.6 38.3 1.0
N A:ASN250 4.6 36.6 1.0
CA A:ALA252 4.6 38.8 1.0
OD1 A:ASP253 4.8 58.4 1.0
O A:ASP253 4.8 41.7 1.0
O A:GLU251 4.9 38.0 1.0
CA A:GLU251 5.0 37.0 1.0
C A:ASP253 5.0 39.4 1.0

Rubidium binding site 4 out of 6 in 1ud5

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Rubidium binding site 4 out of 6 in the Crystal Structure of AMYK38 with Rubidium Ion


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 4 of Crystal Structure of AMYK38 with Rubidium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1006

b:61.1
occ:0.74
 O A:GLN480 2.7 44.0 1.0
OD1 A:ASN479 3.0 40.0 1.0
O A:THR445 3.1 28.4 1.0
C A:GLN480 3.8 38.1 1.0
CG A:ASN479 4.1 36.5 1.0
C A:THR445 4.2 27.6 1.0
N A:GLN480 4.3 34.7 1.0
C A:ASN479 4.4 33.1 1.0
OXT A:GLN480 4.5 41.9 1.0
CB A:THR445 4.6 35.6 1.0
CA A:ASN479 4.6 32.3 1.0
N A:THR445 4.7 31.3 1.0
CA A:GLN480 4.7 37.4 1.0
CA A:THR445 4.8 31.1 1.0
O A:ASN479 4.8 33.7 1.0
ND2 A:ASN479 4.9 35.3 1.0
CB A:ASN479 5.0 35.0 1.0

Rubidium binding site 5 out of 6 in 1ud5

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Rubidium binding site 5 out of 6 in the Crystal Structure of AMYK38 with Rubidium Ion


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 5 of Crystal Structure of AMYK38 with Rubidium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1007

b:76.8
occ:0.76
 O A:HOH2112 2.7 31.0 0.6
O A:HOH2111 2.9 28.6 0.6
OD1 A:ASN441 3.0 34.0 1.0
O A:SER419 3.0 28.7 1.0
O A:GLU411 3.9 40.9 1.0
CG A:ASN441 4.0 37.1 1.0
C A:SER419 4.1 24.5 1.0
N A:SER419 4.2 35.2 1.0
C A:ASN418 4.3 38.9 1.0
N A:ASN418 4.3 46.7 1.0
OG A:SER419 4.4 38.7 1.0
ND2 A:ASN441 4.4 35.9 1.0
CA A:GLY412 4.4 39.5 1.0
CA A:ASN418 4.4 43.4 1.0
NE2 A:GLN444 4.6 28.2 1.0
CA A:SER419 4.8 33.7 1.0
C A:GLY412 4.8 42.9 1.0
O A:ASN418 4.8 32.9 1.0
C A:GLU411 4.9 37.0 1.0
N A:SER413 4.9 45.3 1.0

Rubidium binding site 6 out of 6 in 1ud5

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Rubidium binding site 6 out of 6 in the Crystal Structure of AMYK38 with Rubidium Ion


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 6 of Crystal Structure of AMYK38 with Rubidium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1008

b:45.4
occ:0.46
 O A:THR450 2.9 32.4 1.0
OE2 A:GLU383 3.6 31.0 1.0
O A:HOH2098 3.6 25.1 1.0
C A:THR450 3.8 23.2 1.0
CA A:GLY451 4.1 20.0 1.0
N A:GLY451 4.3 26.7 1.0
CD A:GLU383 4.5 24.2 1.0
C A:GLY451 4.5 25.3 1.0
OE1 A:GLU383 4.6 24.7 1.0
O A:GLY451 4.6 29.9 1.0
CA A:THR450 4.8 22.3 1.0

Reference:

T.Nonaka, M.Fujihashi, A.Kita, H.Hagihara, K.Ozaki, S.Ito, K.Miki. Crystal Structure of Calcium-Free Alpha-Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38) and Its Sodium Ion Binding Sites J.Biol.Chem. V. 278 24818 2003.
ISSN: ISSN 0021-9258
PubMed: 12719434
DOI: 10.1074/JBC.M212763200
Page generated: Thu Oct 10 11:57:10 2024

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