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Potassium in PDB 4rvn: Crystal Structure of A Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.20 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.20 A Resolution, PDB code: 4rvn 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) 47.78 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 127.780, 211.300, 71.980, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 21.9

Other elements in 4rvn:

The structure of Crystal Structure of A Putative Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.20 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 2.20 A Resolution (pdb code 4rvn). 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 2.20 A Resolution, PDB code: 4rvn:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 4rvn

Go back to Potassium Binding Sites List in 4rvn
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 2.20 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 2.20 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K504

b:38.8
occ:1.00
 OD1 A:ASN339 2.6 32.6 1.0
O A:ALA214 2.8 40.7 1.0
O5' A:AMP502 2.8 31.6 1.0
O5 A:UNL507 2.9 45.4 1.0
O4' A:AMP502 2.9 34.8 1.0
O A:GLY337 3.1 45.8 1.0
O4 A:UNL507 3.3 26.2 1.0
O3P A:AMP502 3.5 36.2 1.0
CG A:ASN339 3.5 48.8 1.0
C5' A:AMP502 3.6 31.1 1.0
C4' A:AMP502 3.7 32.9 1.0
P A:AMP502 3.7 33.9 1.0
C A:ALA214 3.7 40.6 1.0
ND2 A:ASN339 3.9 41.4 1.0
C A:GLY337 3.9 46.5 1.0
CA A:ALA214 4.0 34.8 1.0
C1' A:AMP502 4.1 34.5 1.0
CB A:ALA214 4.1 35.5 1.0
O2P A:AMP502 4.1 29.1 1.0
CG2 A:ILE334 4.2 50.1 1.0
O A:HOH715 4.3 47.5 1.0
CD1 A:ILE334 4.4 57.3 1.0
N A:ASN339 4.6 39.7 1.0
N9 A:AMP502 4.6 32.5 1.0
C8 A:AMP502 4.7 32.1 1.0
CG1 A:ILE334 4.7 48.8 1.0
CA A:GLY337 4.7 45.7 1.0
N A:VAL338 4.7 41.5 1.0
CB A:ASN339 4.8 37.2 1.0
C A:VAL338 4.9 42.6 1.0
CA A:VAL338 4.9 39.9 1.0
N A:GLU215 5.0 38.6 1.0

Potassium binding site 2 out of 6 in 4rvn

Go back to Potassium Binding Sites List in 4rvn
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 2.20 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 2.20 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K505

b:43.8
occ:1.00
 O A:LYS128 2.5 44.5 1.0
O B:GLY87 2.6 44.4 1.0
O A:GLY155 2.8 45.1 1.0
O B:LYS84 2.8 51.6 1.0
N A:LEU157 3.4 40.5 1.0
O B:MSE83 3.4 45.7 1.0
C B:LYS84 3.6 52.0 1.0
C A:LYS128 3.7 45.6 1.0
C A:CYS156 3.7 42.6 1.0
C B:GLY87 3.7 44.5 1.0
C A:GLY155 3.9 44.5 1.0
CB A:LEU157 4.0 41.4 1.0
N B:GLY87 4.0 43.7 1.0
O B:ARG85 4.0 52.3 1.0
CA A:LEU157 4.0 40.2 1.0
CA A:CYS156 4.0 38.6 1.0
C B:ARG85 4.1 52.2 1.0
O A:HOH626 4.2 43.5 1.0
CA B:GLY87 4.3 41.8 1.0
N B:ARG85 4.3 49.7 1.0
O A:ASP130 4.4 39.8 1.0
CA B:LYS84 4.4 47.0 1.0
O A:CYS156 4.4 40.8 1.0
N A:CYS156 4.4 39.2 1.0
N B:ASP86 4.5 46.4 1.0
CA B:ARG85 4.5 50.3 0.5
CA B:ARG85 4.5 50.1 0.5
C B:MSE83 4.5 46.8 1.0
N A:THR129 4.5 42.9 1.0
C B:ASP86 4.6 46.6 1.0
CA A:THR129 4.6 43.8 1.0
CA A:LYS128 4.6 41.9 1.0
N B:VAL88 4.8 39.4 1.0
C A:THR129 4.8 46.6 1.0
CB A:LYS128 4.9 45.6 1.0
CA B:ASP86 5.0 44.7 1.0
N B:LYS84 5.0 46.1 1.0

Potassium binding site 3 out of 6 in 4rvn

Go back to Potassium Binding Sites List in 4rvn
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 2.20 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 2.20 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K506

b:30.6
occ:1.00
 O A:HOH661 2.3 25.4 1.0
O B:LYS128 2.5 42.3 1.0
O A:GLY87 2.6 36.1 1.0
O B:GLY155 2.6 39.9 1.0
O A:LYS84 2.8 43.5 1.0
O B:HOH601 3.2 40.3 1.0
O A:MSE83 3.4 39.6 1.0
C A:LYS84 3.6 43.4 1.0
N B:LEU157 3.6 34.8 1.0
C B:LYS128 3.7 43.6 1.0
C A:GLY87 3.7 36.1 1.0
C B:GLY155 3.8 40.1 1.0
C B:CYS156 3.8 37.8 1.0
N A:GLY87 3.9 32.8 1.0
O A:ARG85 3.9 42.5 1.0
C A:ARG85 4.0 42.7 1.0
CA B:CYS156 4.1 36.0 1.0
CA A:GLY87 4.2 31.6 1.0
N A:ARG85 4.3 39.7 1.0
CB B:LEU157 4.3 35.0 1.0
CA B:LEU157 4.3 34.5 1.0
CA A:LYS84 4.4 39.9 1.0
N A:ASP86 4.4 37.4 1.0
N B:CYS156 4.4 36.4 1.0
CA A:ARG85 4.4 40.0 0.3
CA A:ARG85 4.4 40.0 0.7
O B:CYS156 4.5 35.5 1.0
C A:MSE83 4.5 39.5 1.0
C A:ASP86 4.5 36.4 1.0
CA B:LYS128 4.5 39.9 1.0
N B:THR129 4.6 40.7 1.0
CB B:LYS128 4.7 43.5 1.0
O B:ASP130 4.7 38.9 1.0
CA B:THR129 4.7 40.5 1.0
N A:VAL88 4.8 33.0 1.0
CA A:ASP86 4.8 35.7 1.0
N A:LYS84 4.9 39.0 1.0
CA B:GLY155 5.0 36.8 1.0

Potassium binding site 4 out of 6 in 4rvn

Go back to Potassium Binding Sites List in 4rvn
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 2.20 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 2.20 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K504

b:44.6
occ:1.00
 OD1 C:ASN339 2.5 48.4 1.0
O C:ALA214 2.7 48.3 1.0
O C:GLY337 2.9 51.1 1.0
O5' C:AMP502 2.9 42.9 1.0
O4' C:AMP502 3.0 41.7 1.0
O1 C:UNL507 3.3 40.7 1.0
CG C:ASN339 3.5 58.6 1.0
C C:ALA214 3.7 49.2 1.0
O3P C:AMP502 3.7 45.3 1.0
C4' C:AMP502 3.8 42.0 1.0
C C:GLY337 3.8 52.0 1.0
C5' C:AMP502 3.8 42.6 1.0
P C:AMP502 3.9 43.3 1.0
CA C:ALA214 4.0 44.2 1.0
ND2 C:ASN339 4.0 52.1 1.0
CG2 C:ILE334 4.0 56.1 1.0
CB C:ALA214 4.1 43.8 1.0
C1' C:AMP502 4.1 41.4 1.0
O2P C:AMP502 4.3 42.2 1.0
CD1 C:ILE334 4.4 63.3 1.0
O C:HOH633 4.4 49.0 1.0
N C:ASN339 4.5 45.6 1.0
CA C:GLY337 4.5 50.3 1.0
CG1 C:ILE334 4.6 55.9 1.0
N C:VAL338 4.6 47.3 1.0
N9 C:AMP502 4.7 42.4 1.0
C8 C:AMP502 4.7 42.4 1.0
C C:VAL338 4.8 48.7 1.0
CA C:VAL338 4.8 45.6 1.0
CB C:ASN339 4.8 44.7 1.0
N C:GLU215 4.9 47.0 1.0
CB C:ILE334 5.0 55.4 1.0

Potassium binding site 5 out of 6 in 4rvn

Go back to Potassium Binding Sites List in 4rvn
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 2.20 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 2.20 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K505

b:37.7
occ:1.00
 O D:LYS128 2.5 39.1 1.0
O C:LYS84 2.7 47.1 1.0
O C:GLY87 2.7 40.4 1.0
O D:GLY155 2.8 38.4 1.0
O D:HOH602 3.1 42.9 1.0
O C:MSE83 3.2 42.8 1.0
C C:LYS84 3.4 48.0 1.0
N D:LEU157 3.5 35.6 1.0
C D:LYS128 3.7 39.9 1.0
C C:GLY87 3.8 41.3 1.0
C D:CYS156 3.8 37.5 1.0
O C:ARG85 3.9 48.1 1.0
C C:ARG85 3.9 48.2 1.0
N C:GLY87 4.0 41.1 1.0
C D:GLY155 4.0 38.1 1.0
CB D:LEU157 4.0 36.7 1.0
N C:ARG85 4.1 45.8 1.0
CA D:LEU157 4.1 35.4 1.0
CA D:CYS156 4.1 32.4 1.0
CA C:ARG85 4.2 45.1 1.0
CA C:LYS84 4.2 43.0 1.0
CA C:GLY87 4.3 39.4 1.0
C C:MSE83 4.3 43.8 1.0
O C:HOH646 4.3 38.3 1.0
N C:ASP86 4.4 44.0 1.0
O D:CYS156 4.5 36.5 1.0
N D:CYS156 4.5 33.0 1.0
O D:ASP130 4.5 36.3 1.0
N D:THR129 4.6 37.2 1.0
CA D:THR129 4.6 37.4 1.0
C C:ASP86 4.6 45.2 1.0
CA D:LYS128 4.6 35.2 1.0
N C:LYS84 4.7 42.7 1.0
CB D:LYS128 4.9 38.0 1.0
C D:THR129 4.9 39.9 1.0
N C:VAL88 4.9 36.8 1.0
CA C:ASP86 5.0 42.6 1.0

Potassium binding site 6 out of 6 in 4rvn

Go back to Potassium Binding Sites List in 4rvn
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 2.20 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 2.20 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K506

b:38.9
occ:1.00
 O D:HOH621 2.4 44.4 1.0
O C:LYS128 2.5 45.2 1.0
O D:GLY87 2.7 41.1 1.0
O C:GLY155 2.7 42.2 1.0
O D:LYS84 2.8 49.1 1.0
O D:MSE83 3.3 39.6 1.0
N C:LEU157 3.5 37.5 1.0
C D:LYS84 3.6 48.4 1.0
C C:LYS128 3.7 46.8 1.0
C C:CYS156 3.7 41.3 1.0
C D:GLY87 3.8 40.6 1.0
C C:GLY155 3.9 43.1 1.0
O D:ARG85 4.0 48.9 1.0
N D:GLY87 4.0 38.6 1.0
CA C:CYS156 4.1 39.7 1.0
CB C:LEU157 4.1 36.8 1.0
CA C:LEU157 4.1 36.0 1.0
C D:ARG85 4.1 47.8 1.0
O D:HOH709 4.2 39.3 1.0
CA D:LYS84 4.3 42.6 1.0
CA D:GLY87 4.3 37.4 1.0
N D:ARG85 4.3 45.3 1.0
O C:CYS156 4.4 40.0 1.0
N C:CYS156 4.4 39.7 1.0
C D:MSE83 4.4 41.1 1.0
O C:ASP130 4.5 43.5 1.0
N D:ASP86 4.5 40.6 1.0
N C:THR129 4.6 45.9 1.0
CA D:ARG85 4.6 45.3 1.0
CA C:LYS128 4.6 42.5 1.0
C D:ASP86 4.6 41.9 1.0
CA C:THR129 4.6 46.5 1.0
CB C:LYS128 4.8 45.9 1.0
N D:LYS84 4.8 40.8 1.0
N D:VAL88 4.9 36.4 1.0
C C:THR129 4.9 49.7 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Sat Aug 9 07:50:46 2025

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