Atomistry » Potassium » PDB 3rs9-3spj » 3s28
Atomistry »
  Potassium »
    PDB 3rs9-3spj »
      3s28 »

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

Go back to Potassium Binding Sites List in 3s28
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

Go back to Potassium Binding Sites List in 3s28
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

Go back to Potassium Binding Sites List in 3s28
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

Go back to Potassium Binding Sites List in 3s28
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

Go back to Potassium Binding Sites List in 3s28
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy