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Potassium in PDB 3s28: The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose

Enzymatic activity of The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose

All present enzymatic activity of The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose:
2.4.1.13;

Protein crystallography data

The structure of The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose, PDB code: 3s28 was solved by Y.Zheng, R.M.Garavito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.98 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 276.750, 261.880, 160.190, 90.00, 108.70, 90.00
R / Rfree (%) 18.8 / 23.6

Potassium Binding Sites:

The binding sites of Potassium atom in the The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose (pdb code 3s28). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose, PDB code: 3s28:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 3s28

Go back to Potassium Binding Sites List in 3s28
Potassium binding site 1 out of 8 in the The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K931

b:61.3
occ:1.00
 O A:LEU194 2.4 41.9 1.0
O A:HIS187 2.5 43.4 1.0
O A:ARG185 2.6 54.2 1.0
O A:LEU196 2.7 53.7 1.0
O A:LEU184 2.8 48.1 1.0
OD1 A:ASN193 2.8 51.5 1.0
C A:ARG185 3.2 52.6 1.0
C A:HIS187 3.4 43.4 1.0
CG A:ASN193 3.5 50.6 1.0
N A:HIS187 3.5 45.5 1.0
C A:LEU194 3.6 42.5 1.0
N A:LEU194 3.6 44.9 1.0
CA A:ARG185 3.7 51.5 1.0
ND2 A:ASN193 3.7 50.7 1.0
C A:LEU196 3.8 49.2 1.0
C A:LEU184 3.8 49.4 1.0
CA A:HIS187 3.9 43.9 1.0
C A:LEU186 4.0 52.7 1.0
N A:LEU196 4.1 38.9 1.0
N A:LEU186 4.1 49.9 1.0
CA A:LEU194 4.2 43.5 1.0
CB A:HIS187 4.2 47.6 1.0
N A:ARG185 4.2 49.0 1.0
CA A:LEU196 4.5 41.7 1.0
O A:LEU186 4.5 52.5 1.0
CA A:LEU186 4.5 53.4 1.0
CB A:ASN193 4.6 48.2 1.0
N A:SER188 4.6 47.5 1.0
C A:ASN193 4.6 45.7 1.0
C A:MET195 4.7 40.1 1.0
N A:MET195 4.7 41.6 1.0
CA A:ASN193 4.7 45.6 1.0
CB A:LEU194 4.8 43.6 1.0
CB A:MET195 4.9 38.9 1.0
N A:SER197 4.9 47.0 1.0
CA A:MET195 4.9 41.6 1.0

Potassium binding site 2 out of 8 in 3s28

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Potassium binding site 2 out of 8 in the The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K931

b:83.8
occ:1.00
 O B:LEU196 2.4 66.3 1.0
O B:LEU194 2.5 59.3 1.0
O B:ARG185 2.6 65.1 1.0
O B:HIS187 2.7 65.3 1.0
O B:LEU184 2.8 61.4 1.0
OD1 B:ASN193 2.8 67.5 1.0
C B:ARG185 3.3 68.8 1.0
CG B:ASN193 3.5 69.7 1.0
C B:LEU196 3.6 64.2 1.0
C B:HIS187 3.6 67.4 1.0
C B:LEU194 3.7 60.7 1.0
N B:HIS187 3.7 68.7 1.0
ND2 B:ASN193 3.7 65.3 1.0
N B:LEU194 3.8 62.1 1.0
CA B:ARG185 3.8 68.6 1.0
C B:LEU184 3.8 62.0 1.0
C B:LEU186 4.0 69.7 1.0
N B:LEU196 4.0 54.2 1.0
N B:LEU186 4.1 63.9 1.0
CA B:HIS187 4.1 65.9 1.0
N B:ARG185 4.3 62.1 1.0
CA B:LEU194 4.3 60.0 1.0
CA B:LEU196 4.3 58.6 1.0
O B:LEU186 4.4 67.0 1.0
CA B:LEU186 4.5 68.2 1.0
CB B:HIS187 4.5 63.6 1.0
C B:MET195 4.6 54.4 1.0
CB B:ASN193 4.6 72.8 1.0
N B:SER197 4.6 64.5 1.0
N B:MET195 4.7 59.1 1.0
C B:ASN193 4.7 64.1 1.0
CB B:MET195 4.8 59.7 1.0
N B:SER188 4.8 74.7 1.0
CA B:SER197 4.8 70.1 1.0
CA B:ASN193 4.9 69.1 1.0
CB B:LEU196 4.9 57.3 1.0
CA B:MET195 4.9 55.9 1.0

Potassium binding site 3 out of 8 in 3s28

Go back to Potassium Binding Sites List in 3s28
Potassium binding site 3 out of 8 in the The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K931

b:81.2
occ:1.00
 O C:ARG185 2.5 62.1 1.0
O C:LEU196 2.5 57.4 1.0
O C:LEU194 2.6 53.3 1.0
O C:HIS187 2.7 59.2 1.0
OD1 C:ASN193 2.8 68.4 1.0
O C:LEU184 2.9 53.8 1.0
C C:ARG185 3.1 58.2 1.0
CG C:ASN193 3.5 65.5 1.0
CA C:ARG185 3.7 58.1 1.0
C C:LEU196 3.7 57.8 1.0
N C:HIS187 3.7 57.5 1.0
C C:HIS187 3.8 57.0 1.0
C C:LEU194 3.8 52.6 1.0
N C:LEU194 3.8 50.8 1.0
ND2 C:ASN193 3.8 64.5 1.0
C C:LEU186 3.9 57.9 1.0
C C:LEU184 3.9 51.9 1.0
N C:LEU186 3.9 52.7 1.0
N C:LEU196 4.1 50.5 1.0
CA C:HIS187 4.2 55.7 1.0
N C:ARG185 4.2 54.8 1.0
CA C:LEU186 4.3 56.6 1.0
O C:LEU186 4.3 62.5 1.0
CA C:LEU194 4.4 56.4 1.0
CA C:LEU196 4.4 53.1 1.0
CB C:HIS187 4.5 53.7 1.0
N C:SER197 4.7 59.4 1.0
CB C:ASN193 4.7 56.3 1.0
C C:MET195 4.7 49.8 1.0
C C:ASN193 4.7 56.6 1.0
CB C:MET195 4.8 49.5 1.0
N C:MET195 4.8 48.7 1.0
CA C:ASN193 4.9 60.1 1.0
CA C:SER197 4.9 60.2 1.0
N C:SER188 4.9 62.0 1.0
CB C:LEU196 5.0 50.7 1.0

Potassium binding site 4 out of 8 in 3s28

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Potassium binding site 4 out of 8 in the The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K931

b:72.8
occ:1.00
 O D:ARG185 2.5 55.8 1.0
O D:LEU194 2.6 46.1 1.0
O D:HIS187 2.6 55.1 1.0
O D:LEU196 2.6 53.9 1.0
O D:LEU184 2.8 49.7 1.0
OD1 D:ASN193 2.8 61.6 1.0
C D:ARG185 3.1 50.8 1.0
CG D:ASN193 3.6 56.5 1.0
N D:HIS187 3.6 52.0 1.0
C D:HIS187 3.6 51.0 1.0
CA D:ARG185 3.7 49.6 1.0
C D:LEU194 3.8 48.1 1.0
C D:LEU184 3.8 51.3 1.0
C D:LEU196 3.8 50.2 1.0
C D:LEU186 3.8 56.6 1.0
N D:LEU194 3.9 47.4 1.0
N D:LEU186 4.0 53.1 1.0
ND2 D:ASN193 4.1 54.3 1.0
CA D:HIS187 4.1 50.4 1.0
N D:LEU196 4.2 47.2 1.0
N D:ARG185 4.2 49.0 1.0
O D:LEU186 4.2 62.9 1.0
CA D:LEU186 4.3 52.5 1.0
CB D:HIS187 4.4 48.1 1.0
CA D:LEU194 4.4 48.1 1.0
CA D:LEU196 4.5 47.6 1.0
C D:MET195 4.7 48.2 1.0
CB D:ASN193 4.8 55.0 1.0
C D:ASN193 4.8 49.8 1.0
N D:SER188 4.8 52.2 1.0
N D:MET195 4.8 47.4 1.0
N D:SER197 4.8 49.4 1.0
CB D:MET195 4.8 48.1 1.0
CA D:ASN193 4.9 51.7 1.0

Potassium binding site 5 out of 8 in 3s28

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Potassium binding site 5 out of 8 in the The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K931

b:74.0
occ:1.00
 O E:LEU184 2.4 52.6 1.0
O E:LEU196 2.4 58.3 1.0
O E:ARG185 2.5 62.0 1.0
O E:LEU194 2.5 47.0 1.0
C E:ARG185 2.9 52.5 1.0
O E:HIS187 3.2 51.3 1.0
CA E:ARG185 3.2 48.8 1.0
C E:LEU184 3.4 51.4 1.0
OD1 E:ASN193 3.4 53.4 1.0
C E:LEU196 3.6 55.5 1.0
C E:LEU194 3.7 48.0 1.0
N E:ARG185 3.7 48.4 1.0
N E:HIS187 3.7 51.9 1.0
N E:LEU196 3.8 48.7 1.0
N E:LEU186 3.8 50.6 1.0
C E:LEU186 4.1 54.6 1.0
C E:HIS187 4.1 51.6 1.0
CG E:ASN193 4.1 62.1 1.0
CA E:LEU196 4.1 52.8 1.0
N E:LEU194 4.2 52.2 1.0
CA E:HIS187 4.3 51.4 1.0
CA E:LEU186 4.4 51.1 1.0
CB E:MET195 4.4 46.9 1.0
ND2 E:ASN193 4.4 61.3 1.0
C E:MET195 4.5 47.2 1.0
CA E:LEU194 4.5 50.1 1.0
CB E:HIS187 4.5 49.5 1.0
CB E:LEU196 4.6 54.1 1.0
CB E:ARG185 4.6 57.6 1.0
N E:MET195 4.7 46.8 1.0
N E:SER197 4.7 59.2 1.0
CA E:LEU184 4.7 45.9 1.0
CA E:MET195 4.7 47.4 1.0
O E:LEU186 4.7 60.3 1.0
CA E:SER197 5.0 62.7 1.0

Potassium binding site 6 out of 8 in 3s28

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Potassium binding site 6 out of 8 in the The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K931

b:82.9
occ:1.00
 O F:LEU194 2.4 52.7 1.0
O F:LEU196 2.6 62.5 1.0
O F:ARG185 2.7 64.7 1.0
O F:HIS187 2.7 64.3 1.0
O F:LEU184 2.7 57.4 1.0
C F:ARG185 3.3 63.3 1.0
C F:LEU194 3.5 57.2 1.0
C F:HIS187 3.6 67.4 1.0
N F:LEU194 3.7 64.7 1.0
N F:HIS187 3.7 65.9 1.0
OD1 F:ASN193 3.7 78.3 1.0
C F:LEU184 3.8 57.8 1.0
C F:LEU196 3.8 62.0 1.0
ND2 F:ASN193 3.8 77.0 1.0
CA F:ARG185 3.8 59.9 1.0
CG F:ASN193 3.8 79.5 1.0
N F:LEU196 4.0 55.4 1.0
C F:LEU186 4.0 65.6 1.0
CA F:HIS187 4.1 62.3 1.0
CA F:LEU194 4.2 60.0 1.0
N F:LEU186 4.2 61.1 1.0
N F:ARG185 4.2 55.5 1.0
CB F:HIS187 4.3 57.6 1.0
CA F:LEU196 4.4 55.4 1.0
O F:LEU186 4.5 68.4 1.0
CB F:MET195 4.5 55.4 1.0
CA F:LEU186 4.6 62.9 1.0
C F:MET195 4.6 56.9 1.0
N F:MET195 4.6 54.4 1.0
C F:ASN193 4.6 63.0 1.0
CB F:ASN193 4.7 76.9 1.0
CB F:LEU194 4.8 59.0 1.0
CA F:ASN193 4.8 68.4 1.0
CA F:MET195 4.8 56.4 1.0
N F:SER188 4.8 72.2 1.0
N F:SER197 4.9 66.1 1.0
CB F:LEU196 5.0 55.7 1.0

Potassium binding site 7 out of 8 in 3s28

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Potassium binding site 7 out of 8 in the The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K931

b:74.7
occ:1.00
 O G:LEU194 2.3 50.5 1.0
O G:LEU196 2.5 57.9 1.0
O G:ARG185 2.5 56.9 1.0
O G:HIS187 2.6 57.9 1.0
O G:LEU184 2.6 54.8 1.0
C G:ARG185 3.2 55.0 1.0
OD1 G:ASN193 3.5 58.1 1.0
C G:LEU194 3.5 50.0 1.0
C G:HIS187 3.6 55.8 1.0
C G:LEU196 3.7 60.5 1.0
N G:HIS187 3.7 54.8 1.0
N G:LEU194 3.7 57.0 1.0
CA G:ARG185 3.7 51.5 1.0
C G:LEU184 3.7 50.6 1.0
CG G:ASN193 3.9 61.6 1.0
N G:LEU196 3.9 50.4 1.0
C G:LEU186 3.9 55.8 1.0
CA G:HIS187 4.0 52.5 1.0
ND2 G:ASN193 4.1 65.8 1.0
N G:LEU186 4.1 54.6 1.0
N G:ARG185 4.2 49.3 1.0
CA G:LEU194 4.2 53.1 1.0
CA G:LEU196 4.3 50.0 1.0
O G:LEU186 4.3 61.4 1.0
CB G:HIS187 4.3 53.0 1.0
C G:MET195 4.5 50.4 1.0
CB G:MET195 4.5 49.9 1.0
N G:MET195 4.5 52.1 1.0
CA G:LEU186 4.5 54.3 1.0
C G:ASN193 4.7 53.7 1.0
CA G:MET195 4.7 48.6 1.0
CB G:ASN193 4.8 60.1 1.0
N G:SER197 4.8 63.1 1.0
N G:SER188 4.8 59.1 1.0
CA G:ASN193 4.8 55.5 1.0
CB G:LEU196 4.8 47.8 1.0
CB G:LEU194 4.9 49.7 1.0
CA G:LEU184 5.0 47.1 1.0

Potassium binding site 8 out of 8 in 3s28

Go back to Potassium Binding Sites List in 3s28
Potassium binding site 8 out of 8 in the The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of The Crystal Structure of Sucrose Synthase-1 in Complex with A Breakdown Product of the Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K931

b:69.5
occ:1.00
 O H:ARG185 2.4 59.6 1.0
O H:LEU196 2.6 52.2 1.0
O H:HIS187 2.7 56.1 1.0
O H:LEU194 2.7 43.6 1.0
OD1 H:ASN193 2.8 59.8 1.0
CG H:ASN193 3.3 52.6 1.0
C H:ARG185 3.3 59.4 1.0
O H:LEU184 3.3 54.1 1.0
ND2 H:ASN193 3.5 53.2 1.0
C H:HIS187 3.7 57.8 1.0
N H:LEU194 3.7 49.8 1.0
C H:LEU196 3.8 53.1 1.0
N H:HIS187 3.8 53.9 1.0
C H:LEU194 3.8 46.5 1.0
C H:LEU186 3.9 58.1 1.0
CA H:ARG185 4.0 57.6 1.0
O H:LEU186 4.1 63.1 1.0
N H:LEU186 4.2 57.6 1.0
CA H:HIS187 4.2 56.0 1.0
C H:LEU184 4.3 55.9 1.0
N H:LEU196 4.3 48.2 1.0
CA H:LEU194 4.4 49.8 1.0
CB H:ASN193 4.4 53.8 1.0
CA H:LEU186 4.4 57.0 1.0
N H:ARG185 4.6 59.1 1.0
C H:ASN193 4.6 46.3 1.0
CA H:ASN193 4.6 47.9 1.0
CA H:LEU196 4.6 49.1 1.0
CB H:HIS187 4.7 53.5 1.0
N H:SER197 4.7 53.8 1.0
N H:SER188 4.8 59.0 1.0
CA H:SER197 4.8 54.4 1.0
C H:MET195 4.9 46.5 1.0
N H:MET195 4.9 47.5 1.0

Reference:

Y.Zheng, S.Anderson, Y.Zhang, R.M.Garavito. The Structure of Sucrose Synthase-1 From Arabidopsis Thaliana and Its Functional Implications. J.Biol.Chem. V. 286 36108 2011.
ISSN: ISSN 0021-9258
PubMed: 21865170
DOI: 10.1074/JBC.M111.275974
Page generated: Mon Aug 12 09:24:31 2024

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