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Potassium in PDB 3eu8: Crystal Structure of Putative Glucoamylase (YP_210071.1) From Bacteroides Fragilis Nctc 9343 at 2.12 A Resolution

Protein crystallography data

The structure of Crystal Structure of Putative Glucoamylase (YP_210071.1) From Bacteroides Fragilis Nctc 9343 at 2.12 A Resolution, PDB code: 3eu8 was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.59 / 2.12
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.180, 71.760, 221.790, 90.00, 92.30, 90.00
R / Rfree (%) 15.8 / 21.3

Other elements in 3eu8:

The structure of Crystal Structure of Putative Glucoamylase (YP_210071.1) From Bacteroides Fragilis Nctc 9343 at 2.12 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Putative Glucoamylase (YP_210071.1) From Bacteroides Fragilis Nctc 9343 at 2.12 A Resolution (pdb code 3eu8). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Crystal Structure of Putative Glucoamylase (YP_210071.1) From Bacteroides Fragilis Nctc 9343 at 2.12 A Resolution, PDB code: 3eu8:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 3eu8

Go back to Potassium Binding Sites List in 3eu8
Potassium binding site 1 out of 5 in the Crystal Structure of Putative Glucoamylase (YP_210071.1) From Bacteroides Fragilis Nctc 9343 at 2.12 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Putative Glucoamylase (YP_210071.1) From Bacteroides Fragilis Nctc 9343 at 2.12 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1

b:36.5
occ:1.00
 O A:THR35 2.6 31.7 1.0
O2 A:EDO459 2.7 38.7 1.0
O A:SER32 2.8 20.6 1.0
O1 A:EDO459 2.9 38.0 1.0
O A:HOH534 3.0 19.4 1.0
O A:HOH584 3.0 20.8 1.0
OD1 B:ASP100 3.1 23.0 1.0
C A:THR35 3.4 31.3 1.0
OH B:TYR169 3.8 25.8 1.0
C1 A:EDO459 3.8 33.2 1.0
CB A:THR35 3.8 30.9 1.0
C2 A:EDO459 3.8 37.7 1.0
O A:SER36 3.9 27.1 1.0
C A:SER32 4.0 23.3 1.0
CA A:THR35 4.0 30.0 1.0
CG2 A:THR35 4.2 37.1 1.0
N A:THR35 4.2 28.3 1.0
C A:SER36 4.2 26.6 1.0
CG B:ASP100 4.2 24.4 1.0
N A:SER36 4.4 29.7 1.0
N A:SER32 4.6 26.4 1.0
O A:SER33 4.6 24.7 1.0
O B:ASP100 4.6 22.1 1.0
CZ B:TYR169 4.7 26.4 1.0
C A:SER33 4.7 23.3 1.0
CA A:SER33 4.7 21.8 1.0
N A:LEU37 4.7 26.7 1.0
CA A:SER36 4.8 28.8 1.0
N A:SER33 4.8 22.8 1.0
CA B:ASP100 4.8 22.3 1.0
CE1 B:TYR169 4.8 27.7 1.0
CA A:SER32 5.0 26.5 1.0
OD2 B:ASP100 5.0 21.3 1.0

Potassium binding site 2 out of 5 in 3eu8

Go back to Potassium Binding Sites List in 3eu8
Potassium binding site 2 out of 5 in the Crystal Structure of Putative Glucoamylase (YP_210071.1) From Bacteroides Fragilis Nctc 9343 at 2.12 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Putative Glucoamylase (YP_210071.1) From Bacteroides Fragilis Nctc 9343 at 2.12 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K4

b:36.6
occ:1.00
 O A:HOH681 2.6 25.0 1.0
O A:HOH667 2.8 25.0 1.0
O B:SER32 2.8 21.0 1.0
O2 B:EDO8 2.8 31.1 1.0
O B:THR35 2.8 33.0 1.0
OD1 A:ASP100 3.0 21.9 1.0
O1 B:EDO8 3.4 34.8 1.0
C B:THR35 3.5 31.8 1.0
CB B:THR35 3.6 31.0 1.0
OH A:TYR169 3.7 32.3 1.0
C2 B:EDO8 3.7 27.1 1.0
C1 B:EDO8 3.8 24.9 1.0
O B:SER36 3.8 27.9 1.0
CA B:THR35 3.9 29.6 1.0
C B:SER32 4.0 23.5 1.0
N B:THR35 4.1 28.8 1.0
CG A:ASP100 4.1 20.2 1.0
C B:SER36 4.2 27.9 1.0
N B:SER36 4.4 29.9 1.0
OG1 B:THR35 4.5 39.4 1.0
CG2 B:THR35 4.5 38.8 1.0
CZ A:TYR169 4.5 27.5 1.0
N B:SER32 4.5 25.6 1.0
CE1 A:TYR169 4.6 25.9 1.0
O B:SER33 4.6 23.6 1.0
C B:SER33 4.7 23.4 1.0
O A:ASP100 4.7 22.8 1.0
N B:LEU37 4.7 27.3 1.0
OD2 A:ASP100 4.8 19.1 1.0
CA B:SER36 4.8 29.2 1.0
N B:SER33 4.9 22.0 1.0
CA A:ASP100 4.9 22.0 1.0
CA B:SER33 4.9 20.8 1.0
CA B:SER32 4.9 26.1 1.0
O A:HOH961 4.9 38.2 1.0

Potassium binding site 3 out of 5 in 3eu8

Go back to Potassium Binding Sites List in 3eu8
Potassium binding site 3 out of 5 in the Crystal Structure of Putative Glucoamylase (YP_210071.1) From Bacteroides Fragilis Nctc 9343 at 2.12 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Putative Glucoamylase (YP_210071.1) From Bacteroides Fragilis Nctc 9343 at 2.12 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K3

b:41.5
occ:1.00
 O1 C:EDO459 2.5 31.6 1.0
O C:SER32 2.7 21.5 1.0
O C:THR35 2.8 32.5 1.0
O A:HOH702 3.1 27.6 1.0
O2 C:EDO459 3.2 47.3 1.0
C C:THR35 3.6 30.9 1.0
C1 C:EDO459 3.7 46.5 1.0
CB C:THR35 3.8 29.1 1.0
C C:SER32 3.9 23.4 1.0
O C:SER36 4.0 27.8 1.0
CG2 C:THR35 4.0 35.8 1.0
CA C:THR35 4.1 30.4 1.0
C2 C:EDO459 4.1 37.3 1.0
N C:THR35 4.2 28.9 1.0
C C:SER36 4.4 27.2 1.0
N C:SER32 4.5 26.6 1.0
N C:SER36 4.6 29.4 1.0
O C:SER33 4.7 23.5 1.0
C C:SER33 4.7 23.9 1.0
CA C:SER33 4.7 21.7 1.0
N C:SER33 4.8 22.5 1.0
CA C:SER32 4.9 26.0 1.0
N C:LEU37 4.9 26.2 1.0
CA C:SER36 5.0 28.9 1.0

Potassium binding site 4 out of 5 in 3eu8

Go back to Potassium Binding Sites List in 3eu8
Potassium binding site 4 out of 5 in the Crystal Structure of Putative Glucoamylase (YP_210071.1) From Bacteroides Fragilis Nctc 9343 at 2.12 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Putative Glucoamylase (YP_210071.1) From Bacteroides Fragilis Nctc 9343 at 2.12 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K5

b:60.5
occ:1.00
 OH C:TYR169 3.6 27.4 1.0
O C:ILE99 3.8 19.2 1.0
O C:ASP100 4.3 20.9 1.0
CA C:ASP100 4.3 22.4 1.0
O A:HOH579 4.3 21.0 1.0
C C:ILE99 4.6 22.0 1.0
C C:ASP100 4.6 21.9 1.0
CG C:ARG106 4.7 31.2 1.0
OD1 C:ASP100 4.7 22.8 1.0
CG2 C:ILE99 4.8 18.6 1.0
CZ C:TYR169 4.9 27.2 1.0
N C:ASP100 4.9 23.3 1.0
CD C:ARG106 5.0 32.9 1.0

Potassium binding site 5 out of 5 in 3eu8

Go back to Potassium Binding Sites List in 3eu8
Potassium binding site 5 out of 5 in the Crystal Structure of Putative Glucoamylase (YP_210071.1) From Bacteroides Fragilis Nctc 9343 at 2.12 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Putative Glucoamylase (YP_210071.1) From Bacteroides Fragilis Nctc 9343 at 2.12 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K2

b:40.8
occ:1.00
 O D:SER32 2.7 22.2 1.0
O D:THR35 2.9 31.9 1.0
O A:HOH676 3.0 24.9 1.0
C D:THR35 3.7 31.2 1.0
CB D:THR35 3.8 30.2 1.0
C D:SER32 3.9 24.7 1.0
O D:SER36 4.1 28.1 1.0
CA D:THR35 4.1 30.8 1.0
N D:THR35 4.3 28.8 1.0
CG2 D:THR35 4.4 37.1 1.0
N D:SER32 4.5 27.6 1.0
C D:SER36 4.5 27.3 1.0
CA D:SER33 4.7 22.4 1.0
N D:SER33 4.7 22.9 1.0
C D:SER33 4.7 23.6 1.0
N D:SER36 4.8 29.7 1.0
OG1 D:THR35 4.8 40.5 1.0
O D:SER33 4.8 24.7 1.0
CA D:SER32 4.8 26.8 1.0
N D:LEU37 5.0 27.7 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Mon Aug 12 08:08:43 2024

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