Atomistry » Potassium » PDB 4qxg-4tog » 4rvn
Atomistry »
  Potassium »
    PDB 4qxg-4tog »
      4rvn »

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: Mon Aug 12 12:04:18 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy