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Sodium in PDB 4r1m: Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.48 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.48 A Resolution, PDB code: 4r1m 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) 48.89 / 2.48
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 127.060, 211.870, 72.250, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 20

Other elements in 4r1m:

The structure of Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.48 A Resolution also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.48 A Resolution (pdb code 4r1m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.48 A Resolution, PDB code: 4r1m:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4r1m

Go back to Sodium Binding Sites List in 4r1m
Sodium binding site 1 out of 4 in the Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.48 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.48 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:51.9
occ:1.00
 O B:HOH665 2.3 51.9 1.0
O A:GLY155 2.3 57.5 1.0
O B:GLY87 2.3 50.0 1.0
O A:LYS128 2.4 57.1 1.0
N A:LEU157 3.2 49.2 1.0
C A:CYS156 3.3 53.8 1.0
C A:GLY155 3.5 55.1 1.0
C A:LYS128 3.5 57.5 1.0
C B:GLY87 3.6 51.1 1.0
CA A:CYS156 3.8 49.8 1.0
CA A:LEU157 3.9 47.5 1.0
O A:CYS156 3.9 52.9 1.0
CB A:LEU157 4.0 48.3 1.0
N A:CYS156 4.1 49.6 1.0
O B:LYS84 4.1 62.3 1.0
N B:GLY87 4.1 50.8 1.0
CA A:LYS128 4.2 52.9 1.0
CB A:LYS128 4.3 55.8 1.0
CA B:GLY87 4.3 49.2 1.0
O B:MSE83 4.4 58.6 1.0
C B:ASP86 4.5 53.9 1.0
O A:ASP130 4.5 47.7 1.0
N B:VAL88 4.6 46.2 1.0
N A:THR129 4.6 54.1 1.0
CA B:VAL88 4.6 45.2 1.0
CA A:GLY155 4.7 50.6 1.0
CG1 B:VAL88 4.8 49.7 1.0
N B:ASP86 4.8 54.8 1.0
C B:LYS84 4.9 62.7 1.0
C B:ARG85 4.9 60.7 1.0
O B:ARG85 4.9 61.0 1.0
CA A:THR129 4.9 54.0 1.0
CA B:ASP86 5.0 52.7 1.0

Sodium binding site 2 out of 4 in 4r1m

Go back to Sodium Binding Sites List in 4r1m
Sodium binding site 2 out of 4 in the Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.48 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.48 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:51.3
occ:1.00
 O B:GLY155 2.3 52.6 1.0
O B:HOH601 2.4 50.3 1.0
O B:LYS128 2.4 54.0 1.0
O A:GLY87 2.4 50.3 1.0
O A:HOH638 2.5 41.2 1.0
C B:LYS128 3.5 54.0 1.0
C B:GLY155 3.5 52.0 1.0
C A:GLY87 3.6 48.8 1.0
N B:LEU157 3.7 44.2 1.0
C B:CYS156 3.7 47.2 1.0
O A:LYS84 3.9 57.3 1.0
N A:GLY87 3.9 46.6 1.0
CB B:LYS128 4.0 51.9 1.0
CA B:CYS156 4.1 47.5 1.0
CA B:LYS128 4.1 49.6 1.0
N B:CYS156 4.2 46.8 1.0
O A:MSE83 4.2 51.6 1.0
O B:CYS156 4.3 43.5 1.0
O A:ARG85 4.3 54.6 1.0
CA A:GLY87 4.3 44.5 1.0
C A:ASP86 4.3 49.8 1.0
CA B:LEU157 4.4 43.6 1.0
CB B:LEU157 4.4 44.4 1.0
C A:ARG85 4.4 55.7 1.0
N B:THR129 4.5 50.5 1.0
CA B:GLY155 4.6 49.3 1.0
N A:ASP86 4.6 50.3 1.0
C A:LYS84 4.6 57.2 1.0
N A:VAL88 4.6 44.9 1.0
CG B:LYS128 4.7 52.0 1.0
CA A:ASP86 4.7 48.2 1.0
CA A:VAL88 4.8 44.1 1.0
CG1 A:VAL88 4.8 47.1 1.0
CA B:THR129 4.8 50.2 1.0
O A:ASP86 4.9 47.3 1.0
O B:ASP130 5.0 47.4 1.0

Sodium binding site 3 out of 4 in 4r1m

Go back to Sodium Binding Sites List in 4r1m
Sodium binding site 3 out of 4 in the Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.48 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.48 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:53.0
occ:1.00
 O D:LYS128 2.4 45.8 1.0
O C:GLY87 2.4 45.4 1.0
O C:LYS84 2.5 62.8 1.0
O D:GLY155 2.5 50.8 1.0
O C:ARG85 2.8 60.7 1.0
C C:ARG85 3.4 61.1 1.0
N D:LEU157 3.4 43.6 1.0
C D:LYS128 3.5 47.2 1.0
C D:CYS156 3.6 48.4 1.0
C C:LYS84 3.6 64.0 1.0
C C:GLY87 3.6 46.5 1.0
C D:GLY155 3.7 50.9 1.0
N C:GLY87 3.8 50.1 1.0
CA C:ARG85 3.8 56.3 1.0
O C:MSE83 4.0 61.6 1.0
CA D:CYS156 4.0 46.0 1.0
CB D:LEU157 4.0 43.3 1.0
CA D:LEU157 4.0 42.9 1.0
N C:ARG85 4.1 57.2 1.0
CA C:GLY87 4.1 47.0 1.0
O D:CYS156 4.2 47.4 1.0
N C:ASP86 4.3 58.2 1.0
N D:CYS156 4.3 46.1 1.0
CA D:LYS128 4.3 41.6 1.0
C C:ASP86 4.4 55.7 1.0
CB D:LYS128 4.4 43.7 1.0
N D:THR129 4.5 45.0 1.0
CA D:THR129 4.7 44.8 1.0
O D:ASP130 4.7 46.8 1.0
N C:VAL88 4.7 41.4 1.0
CA C:ASP86 4.8 56.1 1.0
CA D:GLY155 4.9 48.6 1.0
CA C:LYS84 4.9 63.2 1.0
CA C:VAL88 4.9 39.8 1.0
C C:MSE83 5.0 61.5 1.0

Sodium binding site 4 out of 4 in 4r1m

Go back to Sodium Binding Sites List in 4r1m
Sodium binding site 4 out of 4 in the Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.48 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of A Hypothetical Acyl-Coa Ligase (BT_0428) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.48 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:52.5
occ:1.00
 O D:HOH613 2.4 51.0 1.0
O C:GLY155 2.5 62.8 1.0
O C:LYS128 2.5 59.6 1.0
O D:GLY87 2.5 53.2 1.0
O C:HOH653 2.7 58.0 1.0
C C:LYS128 3.6 61.0 1.0
O D:LYS84 3.7 60.1 1.0
C D:GLY87 3.7 50.8 1.0
C C:GLY155 3.7 61.5 1.0
N C:LEU157 3.7 50.4 1.0
C C:CYS156 3.8 54.3 1.0
N D:GLY87 4.0 45.1 1.0
O D:MSE83 4.0 57.1 1.0
CA C:CYS156 4.2 55.1 1.0
CB C:LYS128 4.3 56.6 1.0
CA D:GLY87 4.3 45.0 1.0
CA C:LYS128 4.3 54.8 1.0
CA C:LEU157 4.3 49.1 1.0
CB C:LEU157 4.3 50.1 1.0
O C:CYS156 4.3 51.3 1.0
N C:CYS156 4.4 55.2 1.0
C D:LYS84 4.4 59.4 1.0
C D:ASP86 4.5 48.8 1.0
N C:THR129 4.6 61.0 1.0
C D:ARG85 4.6 56.2 1.0
N D:ASP86 4.6 50.4 1.0
O D:ARG85 4.7 56.9 1.0
N D:VAL88 4.8 46.4 1.0
CA C:GLY155 4.8 58.0 1.0
CA C:THR129 4.8 61.9 1.0
CA D:ASP86 4.9 48.5 1.0
CG C:LYS128 4.9 70.0 1.0
O C:ASP130 5.0 51.6 1.0
CA D:VAL88 5.0 46.4 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Mon Oct 7 18:08:48 2024

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