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Potassium in PDB 4r1l: Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.42 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.42 A Resolution, PDB code: 4r1l 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) 48.78 / 2.42
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 127.701, 211.141, 71.861, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 21.3

Other elements in 4r1l:

The structure of Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.42 A Resolution also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.42 A Resolution (pdb code 4r1l). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.42 A Resolution, PDB code: 4r1l:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 4r1l

Go back to Potassium Binding Sites List in 4r1l
Potassium binding site 1 out of 6 in the Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.42 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 A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.42 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K505

b:40.6
occ:1.00
 O3B A:ADP502 2.5 45.4 0.5
OD1 A:ASN339 2.5 40.8 1.0
O5' A:AMP503 2.9 23.4 0.5
O4' A:AMP503 2.9 23.4 0.5
O A:ALA214 2.9 42.8 1.0
O A:GLY337 3.0 45.5 1.0
O5' A:ADP502 3.0 50.3 0.5
O3A A:ADP502 3.0 47.8 0.5
O4' A:ADP502 3.1 53.5 0.5
PB A:ADP502 3.3 44.5 0.5
CG A:ASN339 3.5 57.5 1.0
O2P A:AMP503 3.6 25.4 0.5
C4' A:AMP503 3.7 20.8 0.5
C5' A:AMP503 3.7 21.9 0.5
PA A:ADP502 3.8 48.9 0.5
P A:AMP503 3.8 21.7 0.5
C5' A:ADP502 3.8 51.0 0.5
C4' A:ADP502 3.9 51.8 0.5
C A:GLY337 3.9 47.1 1.0
C A:ALA214 3.9 39.9 1.0
ND2 A:ASN339 3.9 56.0 1.0
O2B A:ADP502 3.9 46.1 0.5
CG2 A:ILE334 4.0 46.5 1.0
C1' A:AMP503 4.1 24.2 0.5
CA A:ALA214 4.1 33.7 1.0
CB A:ALA214 4.2 34.4 1.0
C1' A:ADP502 4.2 54.9 0.5
O A:HOH709 4.4 35.9 1.0
N A:ASN339 4.4 43.1 1.0
O1P A:AMP503 4.5 20.6 0.5
CD1 A:ILE334 4.5 54.1 1.0
N9 A:AMP503 4.6 21.6 0.5
O2A A:ADP502 4.6 47.7 0.5
O1B A:ADP502 4.6 38.5 0.5
N A:VAL338 4.6 43.7 1.0
CA A:GLY337 4.7 44.2 1.0
N9 A:ADP502 4.7 55.0 0.5
CB A:ASN339 4.7 40.9 1.0
C8 A:AMP503 4.7 20.4 0.5
CG1 A:ILE334 4.7 46.9 1.0
C8 A:ADP502 4.7 54.8 0.5
C A:VAL338 4.8 41.3 1.0
CA A:VAL338 4.8 41.5 1.0
O1A A:ADP502 4.9 50.3 0.5
CA A:ASN339 5.0 42.3 1.0
CB A:ILE334 5.0 47.4 1.0

Potassium binding site 2 out of 6 in 4r1l

Go back to Potassium Binding Sites List in 4r1l
Potassium binding site 2 out of 6 in the Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.42 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 A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.42 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K506

b:32.5
occ:1.00
 O A:HOH768 2.3 27.3 1.0
O B:LYS128 2.5 37.9 1.0
O A:GLY87 2.6 31.5 1.0
O B:GLY155 2.7 32.4 1.0
O A:LYS84 2.8 42.5 1.0
O A:MSE83 3.4 43.3 1.0
O B:HOH601 3.4 33.1 1.0
N B:LEU157 3.5 32.4 1.0
C A:LYS84 3.5 41.8 1.0
C B:LYS128 3.6 40.3 1.0
C A:GLY87 3.7 31.6 1.0
C B:CYS156 3.8 34.0 1.0
C B:GLY155 3.8 34.2 1.0
N A:GLY87 3.9 26.0 1.0
O A:ARG85 4.0 40.1 1.0
CA B:CYS156 4.1 31.8 1.0
C A:ARG85 4.1 40.4 1.0
CB B:LEU157 4.2 31.7 1.0
CA B:LEU157 4.2 31.6 1.0
CA A:GLY87 4.3 24.0 1.0
N A:ARG85 4.3 38.1 1.0
CA A:LYS84 4.3 39.0 1.0
O B:CYS156 4.4 31.9 1.0
N B:CYS156 4.4 31.0 1.0
C A:MSE83 4.4 40.9 1.0
N A:ASP86 4.5 34.9 1.0
CA A:ARG85 4.5 38.1 0.5
CA A:ARG85 4.5 38.1 0.5
CA B:LYS128 4.5 37.1 1.0
C A:ASP86 4.5 30.7 1.0
N B:THR129 4.5 38.4 1.0
O B:ASP130 4.7 38.8 1.0
CB B:LYS128 4.7 40.0 1.0
CA B:THR129 4.7 38.1 1.0
N A:VAL88 4.9 29.6 1.0
N A:LYS84 4.9 39.3 1.0
CA A:ASP86 4.9 32.5 1.0

Potassium binding site 3 out of 6 in 4r1l

Go back to Potassium Binding Sites List in 4r1l
Potassium binding site 3 out of 6 in the Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.42 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 A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.42 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K507

b:43.5
occ:1.00
 O B:GLY87 2.5 39.3 1.0
O A:LYS128 2.6 47.3 1.0
O B:LYS84 2.8 48.2 1.0
O A:GLY155 2.9 44.6 1.0
O B:MSE83 3.3 43.2 1.0
N A:LEU157 3.4 38.8 1.0
C B:LYS84 3.6 48.9 1.0
C B:GLY87 3.7 39.5 1.0
C A:CYS156 3.7 42.0 1.0
C A:LYS128 3.7 45.4 1.0
N B:GLY87 3.9 38.1 1.0
CB A:LEU157 4.0 38.2 1.0
C A:GLY155 4.0 43.8 1.0
CA A:LEU157 4.0 38.0 1.0
CA A:CYS156 4.1 37.9 1.0
O B:ARG85 4.1 50.0 1.0
C B:ARG85 4.1 48.4 1.0
CA B:GLY87 4.2 36.9 1.0
O A:HOH624 4.2 38.8 1.0
N B:ARG85 4.3 45.8 1.0
CA B:LYS84 4.3 44.9 1.0
O A:CYS156 4.4 40.4 1.0
O A:ASP130 4.4 37.6 1.0
C B:MSE83 4.4 45.1 1.0
N B:ASP86 4.5 40.5 1.0
N A:CYS156 4.5 38.5 1.0
CA B:ARG85 4.5 46.3 0.5
CA B:ARG85 4.5 46.1 0.5
C B:ASP86 4.5 39.9 1.0
N A:THR129 4.6 40.2 1.0
CA A:LYS128 4.6 39.0 1.0
CA A:THR129 4.7 40.9 1.0
N B:VAL88 4.8 33.0 1.0
CB A:LYS128 4.8 41.5 1.0
N B:LYS84 4.9 44.6 1.0
CA B:ASP86 4.9 38.6 1.0
C A:THR129 5.0 45.4 1.0

Potassium binding site 4 out of 6 in 4r1l

Go back to Potassium Binding Sites List in 4r1l
Potassium binding site 4 out of 6 in the Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.42 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 A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.42 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K504

b:45.4
occ:1.00
 OD1 C:ASN339 2.6 45.9 1.0
O C:GLY337 2.9 48.0 1.0
O C:ALA214 2.9 49.4 1.0
O4' C:AMP502 2.9 50.2 1.0
O5' C:AMP502 3.0 53.5 1.0
CG C:ASN339 3.5 54.1 1.0
C4' C:AMP502 3.7 50.7 1.0
C5' C:AMP502 3.8 52.4 1.0
O2P C:AMP502 3.8 52.5 1.0
P C:AMP502 3.8 56.0 1.0
C C:ALA214 3.8 49.7 1.0
O3P C:AMP502 3.9 61.9 1.0
C C:GLY337 3.9 47.9 1.0
ND2 C:ASN339 3.9 44.8 1.0
CG2 C:ILE334 4.0 52.6 1.0
CA C:ALA214 4.0 43.9 1.0
C1' C:AMP502 4.0 46.4 1.0
CB C:ALA214 4.1 43.4 1.0
N C:ASN339 4.5 41.6 1.0
CD1 C:ILE334 4.5 64.6 1.0
N9 C:AMP502 4.6 44.4 1.0
O C:HOH635 4.6 45.1 1.0
CA C:GLY337 4.6 47.7 1.0
CG1 C:ILE334 4.7 54.0 1.0
C8 C:AMP502 4.7 43.1 1.0
N C:VAL338 4.7 41.8 1.0
CB C:ASN339 4.7 38.1 1.0
C C:VAL338 4.8 43.2 1.0
CA C:VAL338 4.8 39.4 1.0
CB C:ILE334 5.0 53.0 1.0

Potassium binding site 5 out of 6 in 4r1l

Go back to Potassium Binding Sites List in 4r1l
Potassium binding site 5 out of 6 in the Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.42 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 A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.42 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K505

b:42.0
occ:1.00
 O D:LYS128 2.5 40.7 1.0
O C:LYS84 2.6 49.3 1.0
O C:GLY87 2.7 38.1 1.0
O D:GLY155 2.8 38.1 1.0
O C:HOH612 2.9 45.9 1.0
O C:MSE83 3.2 47.8 1.0
N D:LEU157 3.4 33.4 1.0
C C:LYS84 3.4 48.6 1.0
C D:LYS128 3.7 40.2 1.0
C D:CYS156 3.7 37.8 1.0
C C:GLY87 3.8 39.4 1.0
C D:GLY155 3.9 38.2 1.0
N C:GLY87 4.0 42.1 1.0
C C:ARG85 4.0 49.0 1.0
CB D:LEU157 4.0 31.9 1.0
CA D:LEU157 4.1 31.5 1.0
CA D:CYS156 4.1 33.4 1.0
N C:ARG85 4.1 45.9 1.0
O C:ARG85 4.1 50.7 1.0
O C:HOH649 4.2 36.5 1.0
CA C:ARG85 4.2 44.8 1.0
CA C:LYS84 4.2 43.0 1.0
C C:MSE83 4.3 47.1 1.0
CA C:GLY87 4.3 39.3 1.0
O D:CYS156 4.4 36.8 1.0
N C:ASP86 4.4 44.2 1.0
N D:CYS156 4.5 33.3 1.0
O D:ASP130 4.6 36.1 1.0
N D:THR129 4.6 36.8 1.0
CA D:LYS128 4.6 33.4 1.0
CA D:THR129 4.6 36.3 1.0
C C:ASP86 4.6 46.2 1.0
N C:LYS84 4.7 43.8 1.0
CB D:LYS128 4.9 34.9 1.0
C D:THR129 4.9 40.3 1.0
N C:VAL88 4.9 34.0 1.0
CA C:ASP86 5.0 42.9 1.0

Potassium binding site 6 out of 6 in 4r1l

Go back to Potassium Binding Sites List in 4r1l
Potassium binding site 6 out of 6 in the Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.42 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.42 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K503

b:37.8
occ:1.00
 O C:LYS128 2.5 39.3 1.0
O D:LYS84 2.7 48.0 1.0
O D:HOH736 2.7 41.8 1.0
O D:GLY87 2.7 38.2 1.0
O C:GLY155 2.8 37.2 1.0
O D:MSE83 3.3 39.0 1.0
N C:LEU157 3.4 33.3 1.0
C D:LYS84 3.4 46.4 1.0
C C:LYS128 3.6 41.9 1.0
C C:CYS156 3.7 36.6 1.0
C D:GLY87 3.8 38.4 1.0
C C:GLY155 3.9 40.0 1.0
O D:HOH697 4.0 36.1 1.0
N D:GLY87 4.0 35.1 1.0
CA C:CYS156 4.1 35.8 1.0
CB C:LEU157 4.1 32.9 1.0
CA C:LEU157 4.1 32.4 1.0
CA D:LYS84 4.2 40.8 1.0
C D:ARG85 4.2 47.0 1.0
N D:ARG85 4.3 42.8 1.0
O D:ARG85 4.3 50.1 1.0
C D:MSE83 4.3 40.4 1.0
CA D:GLY87 4.3 34.7 1.0
O C:CYS156 4.4 34.8 1.0
N C:CYS156 4.4 36.1 1.0
O C:ASP130 4.5 38.9 1.0
N D:ASP86 4.5 37.9 1.0
N C:THR129 4.5 41.7 1.0
CA C:LYS128 4.5 38.5 1.0
CA D:ARG85 4.6 43.3 1.0
CA C:THR129 4.6 41.9 1.0
C D:ASP86 4.7 37.3 1.0
CB C:LYS128 4.7 41.3 1.0
N D:LYS84 4.7 39.5 1.0
C C:THR129 4.9 46.7 1.0
N D:VAL88 5.0 34.6 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Mon Aug 12 11:55:32 2024

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