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Potassium in PDB 4rvo: Crystal Structure of A Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.41 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.41 A Resolution, PDB code: 4rvo 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) 46.57 / 2.41
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 127.237, 210.223, 71.504, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.4

Other elements in 4rvo:

The structure of Crystal Structure of A Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.41 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 Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.41 A Resolution (pdb code 4rvo). 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 Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.41 A Resolution, PDB code: 4rvo:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 4rvo

Go back to Potassium Binding Sites List in 4rvo
Potassium binding site 1 out of 6 in the Crystal Structure of A Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.41 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 Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.41 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:49.1
occ:1.00
 OD1 A:ASN339 2.3 50.4 1.0
O1B A:ADP502 2.5 55.1 1.0
O A:ALA214 2.8 45.2 1.0
O A:GLY337 2.9 55.3 1.0
O4' A:ADP502 3.0 37.7 1.0
O5' A:ADP502 3.2 41.7 1.0
CG A:ASN339 3.4 63.1 1.0
C A:ALA214 3.7 44.7 1.0
PB A:ADP502 3.8 54.6 1.0
C A:GLY337 3.8 56.1 1.0
C4' A:ADP502 3.8 38.1 1.0
ND2 A:ASN339 3.9 61.5 1.0
C5' A:ADP502 3.9 39.5 1.0
CG2 A:ILE334 4.0 59.8 1.0
PA A:ADP502 4.0 43.0 1.0
CA A:ALA214 4.1 38.2 1.0
C1' A:ADP502 4.1 34.2 1.0
O2A A:ADP502 4.1 41.6 1.0
CD1 A:ILE334 4.1 64.3 1.0
O3A A:ADP502 4.2 46.2 1.0
CB A:ALA214 4.3 39.2 1.0
N A:ASN339 4.3 49.1 1.0
O A:HOH719 4.3 55.7 1.0
CG1 A:ILE334 4.4 57.8 1.0
O2B A:ADP502 4.4 53.6 1.0
CA A:GLY337 4.6 55.0 1.0
N A:VAL338 4.6 50.8 1.0
N9 A:ADP502 4.6 29.5 1.0
CB A:ASN339 4.6 45.7 1.0
C A:VAL338 4.6 52.6 1.0
C8 A:ADP502 4.7 26.6 1.0
CA A:VAL338 4.7 49.5 1.0
CA A:ASN339 4.8 47.5 1.0
CB A:ILE334 4.9 58.4 1.0
O3B A:ADP502 4.9 56.6 1.0
N A:GLU215 5.0 42.8 1.0

Potassium binding site 2 out of 6 in 4rvo

Go back to Potassium Binding Sites List in 4rvo
Potassium binding site 2 out of 6 in the Crystal Structure of A Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.41 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 Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.41 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K504

b:42.8
occ:1.00
 O A:LYS128 2.5 45.9 1.0
O B:GLY87 2.6 44.4 1.0
O A:GLY155 2.7 42.8 1.0
O B:HOH656 2.9 44.1 1.0
O B:LYS84 3.0 52.9 1.0
N A:LEU157 3.3 39.3 1.0
C A:CYS156 3.6 43.4 1.0
O B:MSE83 3.7 48.0 1.0
C A:LYS128 3.7 46.4 1.0
C B:GLY87 3.7 43.4 1.0
C B:LYS84 3.8 52.8 1.0
O B:ARG85 3.8 48.4 1.0
C A:GLY155 3.8 43.0 1.0
CA A:CYS156 4.0 39.4 1.0
C B:ARG85 4.0 49.5 1.0
N B:GLY87 4.0 42.0 1.0
O A:HOH625 4.1 46.1 1.0
CA A:LEU157 4.1 38.8 1.0
CB A:LEU157 4.1 39.9 1.0
CA B:GLY87 4.3 40.7 1.0
O A:CYS156 4.3 41.9 1.0
N A:CYS156 4.4 39.0 1.0
N B:ARG85 4.4 49.2 1.0
N B:ASP86 4.4 44.3 1.0
O A:ASP130 4.5 37.5 1.0
CA B:ARG85 4.5 49.2 1.0
CA A:LYS128 4.6 41.9 1.0
C B:ASP86 4.6 43.9 1.0
N A:THR129 4.6 43.2 1.0
CA B:LYS84 4.7 48.7 1.0
CA A:THR129 4.7 43.6 1.0
CB A:LYS128 4.8 44.3 1.0
C B:MSE83 4.8 48.2 1.0
N B:VAL88 4.8 37.5 1.0
CA B:ASP86 5.0 42.4 1.0

Potassium binding site 3 out of 6 in 4rvo

Go back to Potassium Binding Sites List in 4rvo
Potassium binding site 3 out of 6 in the Crystal Structure of A Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.41 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 Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.41 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K505

b:29.2
occ:1.00
 O A:HOH650 2.5 15.3 1.0
O B:LYS128 2.5 40.2 1.0
O B:GLY155 2.6 38.6 1.0
O A:GLY87 2.7 40.2 1.0
O A:LYS84 2.9 42.8 1.0
O B:HOH603 3.4 29.0 1.0
O A:MSE83 3.5 42.2 1.0
N B:LEU157 3.5 35.4 1.0
C B:LYS128 3.6 41.0 1.0
C A:LYS84 3.6 43.0 1.0
C B:CYS156 3.8 38.2 1.0
C A:GLY87 3.8 40.1 1.0
C B:GLY155 3.8 38.3 1.0
N A:GLY87 4.0 36.7 1.0
CA B:CYS156 4.1 34.8 1.0
C A:ARG85 4.1 43.7 1.0
O A:ARG85 4.2 43.5 1.0
CA B:LEU157 4.3 35.0 1.0
CB B:LEU157 4.3 35.6 1.0
CA A:GLY87 4.3 36.1 1.0
N A:ARG85 4.3 40.8 1.0
N B:CYS156 4.4 33.6 1.0
CA A:LYS84 4.4 38.8 1.0
O B:CYS156 4.4 36.5 1.0
N A:ASP86 4.5 38.3 1.0
CA B:LYS128 4.5 35.8 0.5
CA B:LYS128 4.5 35.9 0.5
CA A:ARG85 4.5 40.8 1.0
C A:MSE83 4.6 40.8 1.0
N B:THR129 4.6 39.4 1.0
CB B:LYS128 4.6 38.7 0.5
CB B:LYS128 4.6 38.5 0.5
C A:ASP86 4.7 39.8 1.0
O B:ASP130 4.7 39.5 1.0
CA B:THR129 4.7 39.5 1.0
N A:VAL88 4.9 36.4 1.0
N A:LYS84 5.0 39.1 1.0
CA B:GLY155 5.0 35.3 1.0

Potassium binding site 4 out of 6 in 4rvo

Go back to Potassium Binding Sites List in 4rvo
Potassium binding site 4 out of 6 in the Crystal Structure of A Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.41 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 Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.41 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K503

b:54.5
occ:1.00
 OD1 C:ASN339 2.4 64.5 1.0
O3B C:ADP502 2.6 59.3 1.0
O4' C:ADP502 2.9 46.6 1.0
O C:GLY337 3.0 56.4 1.0
O C:ALA214 3.2 47.5 1.0
O5' C:ADP502 3.3 49.7 1.0
CG C:ASN339 3.5 71.4 1.0
C4' C:ADP502 3.9 46.0 1.0
C C:ALA214 3.9 47.9 1.0
C C:GLY337 3.9 56.4 1.0
PB C:ADP502 3.9 57.1 1.0
C1' C:ADP502 4.0 44.0 1.0
CG2 C:ILE334 4.0 64.0 1.0
CA C:ALA214 4.0 43.2 1.0
ND2 C:ASN339 4.0 67.0 1.0
C5' C:ADP502 4.0 47.8 1.0
CD1 C:ILE334 4.0 69.0 1.0
CB C:ALA214 4.1 43.2 1.0
PA C:ADP502 4.2 50.4 1.0
O1A C:ADP502 4.3 53.1 1.0
O3A C:ADP502 4.3 50.6 1.0
N C:ASN339 4.4 49.2 1.0
CG1 C:ILE334 4.4 63.7 1.0
N9 C:ADP502 4.4 42.6 1.0
O2B C:ADP502 4.5 58.0 1.0
C8 C:ADP502 4.6 43.0 1.0
CA C:GLY337 4.6 55.4 1.0
O C:HOH630 4.7 38.8 1.0
N C:VAL338 4.7 50.5 1.0
CB C:ASN339 4.7 50.8 1.0
C C:VAL338 4.8 51.9 1.0
CB C:ILE334 4.8 63.1 1.0
CA C:VAL338 4.9 48.9 1.0
CA C:ASN339 5.0 48.2 1.0

Potassium binding site 5 out of 6 in 4rvo

Go back to Potassium Binding Sites List in 4rvo
Potassium binding site 5 out of 6 in the Crystal Structure of A Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.41 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 Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.41 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K504

b:38.9
occ:1.00
 O D:LYS128 2.5 41.0 1.0
O C:GLY87 2.7 42.4 1.0
O D:GLY155 2.8 43.6 1.0
O C:LYS84 2.8 47.3 1.0
O C:HOH690 3.1 31.1 1.0
N D:LEU157 3.4 38.6 1.0
O C:MSE83 3.4 40.9 1.0
C C:LYS84 3.5 46.0 1.0
C D:LYS128 3.7 41.2 1.0
C D:CYS156 3.7 41.3 1.0
O C:ARG85 3.7 47.5 1.0
C C:GLY87 3.8 42.4 1.0
C C:ARG85 3.9 47.6 1.0
C D:GLY155 3.9 43.2 1.0
N C:GLY87 4.1 43.8 1.0
CA D:CYS156 4.1 38.0 1.0
CB D:LEU157 4.1 38.4 1.0
CA D:LEU157 4.1 37.8 1.0
N C:ARG85 4.1 42.6 1.0
CA C:ARG85 4.1 42.5 1.0
CA C:GLY87 4.3 41.5 1.0
O D:CYS156 4.4 39.8 1.0
N C:ASP86 4.4 44.6 1.0
CA C:LYS84 4.4 39.7 1.0
N D:CYS156 4.5 38.7 1.0
O C:HOH638 4.5 34.9 1.0
C C:MSE83 4.5 41.6 1.0
O D:ASP130 4.6 40.2 1.0
N D:THR129 4.6 38.2 1.0
CA D:LYS128 4.6 36.5 0.5
CA D:LYS128 4.6 36.7 0.5
CA D:THR129 4.6 38.4 1.0
C C:ASP86 4.7 48.2 1.0
CB D:LYS128 4.8 39.6 0.5
CB D:LYS128 4.8 39.2 0.5
C D:THR129 4.9 41.7 1.0
N C:VAL88 4.9 36.9 1.0
N C:LYS84 5.0 39.6 1.0

Potassium binding site 6 out of 6 in 4rvo

Go back to Potassium Binding Sites List in 4rvo
Potassium binding site 6 out of 6 in the Crystal Structure of A Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.41 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 Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.41 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K503

b:42.9
occ:1.00
 O C:LYS128 2.5 48.8 1.0
O D:GLY87 2.7 47.2 1.0
O D:LYS84 2.8 54.1 1.0
O C:GLY155 2.8 38.9 1.0
O D:MSE83 3.3 46.5 1.0
O C:HOH670 3.4 36.3 1.0
N C:LEU157 3.5 38.5 1.0
C D:LYS84 3.5 53.0 1.0
C C:LYS128 3.7 49.7 1.0
C C:CYS156 3.8 41.5 1.0
C D:GLY87 3.8 46.1 1.0
C C:GLY155 4.0 41.4 1.0
N D:GLY87 4.1 44.0 1.0
CB C:LEU157 4.1 38.3 1.0
CA C:CYS156 4.1 38.7 1.0
CA C:LEU157 4.1 37.4 1.0
CA D:LYS84 4.2 47.5 1.0
N D:ARG85 4.2 49.8 1.0
CA D:GLY87 4.3 42.7 1.0
C D:MSE83 4.4 47.1 1.0
C D:ARG85 4.4 53.9 1.0
CA D:ARG85 4.5 50.3 1.0
O C:CYS156 4.5 40.4 1.0
N D:ASP86 4.5 47.6 1.0
N C:CYS156 4.5 38.4 1.0
O C:ASP130 4.6 42.5 1.0
N C:THR129 4.6 47.2 1.0
CA C:THR129 4.6 47.8 1.0
CA C:LYS128 4.6 45.0 1.0
C D:ASP86 4.8 47.2 1.0
N D:LYS84 4.8 46.8 1.0
CB C:LYS128 4.8 47.5 1.0
C C:THR129 4.9 51.3 1.0
O D:ARG85 4.9 55.1 1.0
N D:VAL88 5.0 40.8 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Mon Aug 12 12:04:56 2024

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