Potassium in PDB 9cen: Structure of the Thiocysteine Lyase (Sh) Domain From Guangnanmycin A Biosynthetic Pathway

Protein crystallography data

The structure of Structure of the Thiocysteine Lyase (Sh) Domain From Guangnanmycin A Biosynthetic Pathway, PDB code: 9cen was solved by G.Li, C.Chang, B.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.77 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.963, 89.555, 70.012, 90, 108.15, 90
R / Rfree (%) 14.7 / 18.1

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of the Thiocysteine Lyase (Sh) Domain From Guangnanmycin A Biosynthetic Pathway (pdb code 9cen). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Structure of the Thiocysteine Lyase (Sh) Domain From Guangnanmycin A Biosynthetic Pathway, PDB code: 9cen:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 9cen

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Potassium binding site 1 out of 6 in the Structure of the Thiocysteine Lyase (Sh) Domain From Guangnanmycin A Biosynthetic Pathway


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of the Thiocysteine Lyase (Sh) Domain From Guangnanmycin A Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K501

b:33.8
occ:0.45
 O A:HOH885 2.6 35.6 1.0
OE1 A:GLN279 2.8 34.6 1.0
O A:LEU277 2.8 24.7 1.0
CD A:GLN279 3.6 28.0 1.0
C A:LEU277 3.7 26.3 1.0
CD A:PRO68 3.8 31.8 1.0
CG A:GLN279 3.8 24.2 1.0
CA A:LEU277 3.8 22.2 1.0
CD2 A:LEU277 4.1 25.8 1.0
CG A:PRO68 4.3 38.1 1.0
O A:LEU276 4.3 22.1 1.0
O A:HOH611 4.5 46.5 1.0
CD2 A:LEU67 4.5 25.3 1.0
CB A:LEU277 4.5 20.2 1.0
O A:HOH782 4.7 43.7 1.0
CB A:GLN279 4.7 20.1 1.0
N A:GLN279 4.8 17.3 1.0
NE2 A:GLN279 4.9 24.7 1.0
CG A:LEU277 4.9 20.7 1.0
N A:HIS278 5.0 20.4 1.0
N A:LEU277 5.0 18.0 1.0

Potassium binding site 2 out of 6 in 9cen

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Potassium binding site 2 out of 6 in the Structure of the Thiocysteine Lyase (Sh) Domain From Guangnanmycin A Biosynthetic Pathway


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of the Thiocysteine Lyase (Sh) Domain From Guangnanmycin A Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:87.5
occ:0.92
 O A:HOH881 2.7 36.4 1.0
O A:VAL26 2.9 19.9 1.0
O A:GLU27 2.9 22.8 0.4
O A:GLU27 3.0 22.3 0.6
O A:HOH708 3.3 27.8 1.0
C A:GLU27 3.6 21.9 0.4
C A:GLU27 3.6 22.4 0.6
CA A:GLU27 3.8 19.2 0.6
CA A:GLU27 3.8 19.7 0.4
C A:VAL26 3.9 19.6 1.0
N A:GLU27 4.3 19.6 0.6
N A:GLU27 4.3 19.4 0.4
O A:HOH718 4.5 26.6 1.0
N A:LEU28 4.7 17.7 1.0
O A:HOH753 4.8 31.9 1.0
O A:VAL24 4.9 19.5 1.0
O A:HOH727 5.0 43.4 1.0

Potassium binding site 3 out of 6 in 9cen

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Potassium binding site 3 out of 6 in the Structure of the Thiocysteine Lyase (Sh) Domain From Guangnanmycin A Biosynthetic Pathway


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of the Thiocysteine Lyase (Sh) Domain From Guangnanmycin A Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:20.0
occ:0.28
 OG1 A:THR47 2.6 29.6 1.0
OD1 A:ASP237 2.6 22.0 1.0
O A:GLN43 2.7 21.5 1.0
O A:HOH761 2.7 21.2 1.0
CG A:ASP237 3.3 25.2 1.0
CZ3 A:TRP35 3.4 13.8 1.0
C A:GLN43 3.5 18.0 1.0
OD2 A:ASP237 3.5 24.9 1.0
CA A:GLN43 3.7 16.7 1.0
CE3 A:TRP35 3.7 12.4 1.0
N A:THR47 3.7 14.8 1.0
CB A:GLN43 3.7 16.6 1.0
CB A:THR47 3.8 22.0 1.0
O A:HOH639 3.8 28.2 1.0
O A:HOH739 3.9 23.2 1.0
CG A:ARG46 4.1 21.9 1.0
CB A:ARG46 4.1 17.8 1.0
CA A:THR47 4.1 14.4 1.0
O A:GLY235 4.2 15.4 1.0
N A:ASP237 4.3 14.8 1.0
O A:HOH712 4.3 35.4 1.0
CB A:ASP237 4.5 19.7 1.0
C A:ARG46 4.5 16.4 1.0
CG A:GLN43 4.5 14.7 1.0
CA A:VAL236 4.5 14.5 1.0
C A:VAL236 4.6 15.7 1.0
CH2 A:TRP35 4.6 17.4 1.0
N A:ARG44 4.6 19.5 1.0
CA A:ASP237 4.8 17.2 1.0
NE2 A:GLN43 4.8 13.8 1.0
CA A:ARG46 4.8 18.6 1.0
C A:GLY235 4.8 16.4 1.0
CG2 A:THR47 4.9 26.5 1.0

Potassium binding site 4 out of 6 in 9cen

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Potassium binding site 4 out of 6 in the Structure of the Thiocysteine Lyase (Sh) Domain From Guangnanmycin A Biosynthetic Pathway


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of the Thiocysteine Lyase (Sh) Domain From Guangnanmycin A Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:24.7
occ:0.31
 O B:HOH977 2.5 28.1 1.0
OG1 B:THR47 2.8 24.3 1.0
OD2 B:ASP237 2.8 20.4 1.0
O B:HOH957 2.9 38.4 1.0
O B:HOH758 3.0 15.6 1.0
CG2 B:THR47 3.1 31.7 1.0
CB B:THR47 3.5 21.2 1.0
CG B:ASP237 3.6 23.5 1.0
O B:HOH814 3.7 26.2 1.0
O B:HOH973 3.7 28.5 1.0
O A:HOH873 3.8 46.3 1.0
CB B:ASP237 4.0 13.5 1.0
O B:HOH661 4.1 21.3 1.0
O B:HOH904 4.3 29.8 1.0
O B:HOH647 4.3 24.8 1.0
O B:HOH828 4.4 18.2 1.0
OD1 B:ASP237 4.4 19.5 1.0
O B:HOH869 4.5 22.9 1.0
O A:HOH844 4.6 27.9 1.0
CA B:THR47 4.7 12.5 1.0
N B:ASP237 4.9 11.2 1.0

Potassium binding site 5 out of 6 in 9cen

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Potassium binding site 5 out of 6 in the Structure of the Thiocysteine Lyase (Sh) Domain From Guangnanmycin A Biosynthetic Pathway


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of the Thiocysteine Lyase (Sh) Domain From Guangnanmycin A Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K504

b:56.5
occ:0.60
 OD2 B:ASP37 2.6 30.4 1.0
OG1 B:THR32 2.7 14.2 1.0
O B:HOH879 2.9 43.0 1.0
CB B:THR32 3.3 10.6 1.0
O B:HOH912 3.5 47.9 1.0
CG2 B:THR32 3.7 11.7 1.0
CG B:ASP37 3.8 23.9 1.0
CB B:SER34 3.9 14.3 1.0
O B:HOH621 4.0 30.5 1.0
O B:HOH949 4.0 50.6 1.0
CB B:ASP37 4.4 12.3 1.0
OG B:SER34 4.7 16.5 1.0
CA B:THR32 4.7 10.3 1.0
OD1 B:ASP37 4.7 25.0 1.0
NH2 B:ARG371 4.8 22.8 1.0

Potassium binding site 6 out of 6 in 9cen

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Potassium binding site 6 out of 6 in the Structure of the Thiocysteine Lyase (Sh) Domain From Guangnanmycin A Biosynthetic Pathway


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of the Thiocysteine Lyase (Sh) Domain From Guangnanmycin A Biosynthetic Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K505

b:72.8
occ:0.69
 O B:HOH878 2.8 40.4 1.0
OP3 B:LLP232 3.1 24.3 1.0
O B:HOH622 3.2 36.5 1.0
OP1 B:LLP232 3.3 17.2 1.0
P B:LLP232 3.4 20.8 1.0
O B:HOH623 3.5 34.8 1.0
OP2 B:LLP232 3.5 19.7 1.0
CB B:SER80 3.6 17.8 1.0
O B:HOH621 3.7 30.5 1.0
CB B:ALA36 3.7 16.0 1.0
NE B:ARG82 4.4 29.5 1.0
O A:HOH713 4.4 36.7 1.0
NH2 B:ARG82 4.5 27.8 1.0
OG B:SER80 4.5 13.2 1.0
CA B:SER80 4.7 16.5 1.0
CZ B:ARG82 4.7 32.6 1.0
OP4 B:LLP232 4.9 22.2 1.0

Reference:

A.D.Steele, S.Meng, G.Li, E.Kalkreuter, C.Chang, B.Shen. Structural Insights Into the Mechanism of A Polyketide Synthase Thiocysteine Lyase Domain To Be Published.
Page generated: Thu Oct 31 21:36:28 2024

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