Atomistry » Sodium » PDB 3icf-3ivu » 3ij6
Atomistry »
  Sodium »
    PDB 3icf-3ivu »
      3ij6 »

Sodium in PDB 3ij6: Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus

Protein crystallography data

The structure of Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus, PDB code: 3ij6 was solved by Y.Patskovsky, R.Toro, M.Dickey, S.Chang, J.M.Sauder, F.M.Raushel, S.K.Burley, S.C.Almo, New York Sgx Research Center For Structuralgenomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 170.717, 96.433, 96.033, 90.00, 90.40, 90.00
R / Rfree (%) 22.1 / 26.8

Other elements in 3ij6:

The structure of Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus (pdb code 3ij6). 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 An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus, PDB code: 3ij6:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3ij6

Go back to Sodium Binding Sites List in 3ij6
Sodium binding site 1 out of 4 in the Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus


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 An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na313

b:58.1
occ:1.00
O A:LEU124 2.5 44.5 1.0
O A:ILE118 2.5 34.0 1.0
O A:ASP121 2.6 49.0 1.0
OE2 A:GLU304 3.6 96.5 1.0
C A:ASP121 3.6 43.9 1.0
C A:ILE118 3.7 42.1 1.0
C A:LEU124 3.7 41.0 1.0
CG2 A:ILE118 4.1 34.0 1.0
CA A:GLU122 4.1 48.0 1.0
O A:GLU122 4.2 45.8 1.0
C A:GLU122 4.2 46.3 1.0
N A:GLU122 4.3 43.3 1.0
N A:LYS119 4.6 50.6 1.0
N A:LEU124 4.6 42.1 1.0
CA A:VAL125 4.6 38.5 1.0
N A:VAL125 4.6 32.3 1.0
CA A:LYS119 4.6 60.9 1.0
CA A:LEU124 4.6 40.0 1.0
CA A:ILE118 4.6 44.5 1.0
CD A:GLU304 4.7 92.7 1.0
O A:LYS119 4.7 62.2 1.0
N A:ASP121 4.8 46.6 1.0
CA A:ASP121 4.8 45.7 1.0
C A:LYS119 4.8 59.0 1.0
CB A:ILE118 5.0 45.2 1.0
N A:ASN123 5.0 44.7 1.0
CB A:LEU124 5.0 28.7 1.0

Sodium binding site 2 out of 4 in 3ij6

Go back to Sodium Binding Sites List in 3ij6
Sodium binding site 2 out of 4 in the Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus


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 An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na313

b:49.0
occ:1.00
O B:ILE118 2.4 33.5 1.0
O B:HOH354 2.5 46.2 1.0
O B:ASP121 2.6 50.4 1.0
O B:LEU124 2.6 35.7 1.0
C B:ILE118 3.6 37.9 1.0
C B:ASP121 3.6 39.6 1.0
C B:LEU124 3.8 39.2 1.0
OE2 B:GLU304 4.0 65.4 1.0
CG2 B:ILE118 4.1 36.3 1.0
CA B:GLU122 4.1 48.7 1.0
O B:GLU122 4.2 35.5 1.0
N B:GLU122 4.3 42.5 1.0
C B:GLU122 4.3 43.5 1.0
N B:LYS119 4.4 31.0 1.0
CA B:LYS119 4.4 46.7 1.0
OE1 B:GLU304 4.4 85.5 1.0
O B:HOH395 4.5 26.1 1.0
N B:ASP121 4.6 34.0 1.0
CA B:ILE118 4.6 34.4 1.0
C B:LYS119 4.6 45.6 1.0
N B:LEU124 4.7 35.0 1.0
CD B:GLU304 4.7 78.8 1.0
CA B:ASP121 4.7 35.6 1.0
N B:VAL125 4.7 43.6 1.0
CA B:LEU124 4.7 35.6 1.0
O B:LYS119 4.7 49.1 1.0
CA B:VAL125 4.7 38.8 1.0
CB B:ILE118 5.0 37.3 1.0

Sodium binding site 3 out of 4 in 3ij6

Go back to Sodium Binding Sites List in 3ij6
Sodium binding site 3 out of 4 in the Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus


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 An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na313

b:61.1
occ:1.00
O C:ILE118 2.5 41.8 1.0
O C:ASP121 2.8 46.8 1.0
O C:LEU124 2.8 41.5 1.0
C C:ASP121 3.5 46.8 1.0
CA C:GLU122 3.7 48.9 1.0
C C:ILE118 3.7 43.9 1.0
N C:GLU122 4.0 48.6 1.0
C C:GLU122 4.0 49.4 1.0
C C:LEU124 4.0 43.5 1.0
CA C:LYS119 4.0 53.4 0.5
CA C:LYS119 4.0 51.3 0.5
O C:GLU122 4.1 43.8 1.0
N C:LYS119 4.3 49.7 1.0
C C:LYS119 4.3 52.9 1.0
O C:LYS119 4.4 51.6 1.0
CG2 C:ILE118 4.4 35.8 0.5
CG2 C:ILE118 4.4 37.9 0.5
N C:ASP121 4.6 45.7 1.0
N C:LEU124 4.7 47.8 1.0
CA C:ASP121 4.7 42.4 1.0
N C:ASN123 4.8 42.6 1.0
CA C:ILE118 4.8 43.5 0.5
CA C:ILE118 4.8 42.7 0.5
CA C:LEU124 4.9 42.5 1.0
CB C:GLU122 4.9 56.5 1.0
CA C:VAL125 4.9 32.3 1.0
N C:VAL125 4.9 38.3 1.0

Sodium binding site 4 out of 4 in 3ij6

Go back to Sodium Binding Sites List in 3ij6
Sodium binding site 4 out of 4 in the Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus


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 An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na313

b:43.5
occ:1.00
O D:HOH394 2.4 41.5 1.0
O D:LEU124 2.5 38.3 1.0
O D:ASP121 2.5 59.5 1.0
O D:ILE118 2.6 45.5 1.0
C D:ASP121 3.7 57.3 1.0
C D:LEU124 3.7 40.7 1.0
C D:ILE118 3.8 48.9 1.0
CG2 D:ILE118 4.1 35.5 1.0
O D:GLU122 4.1 49.1 1.0
CA D:GLU122 4.3 52.6 1.0
C D:GLU122 4.3 51.9 1.0
O D:HOH346 4.3 27.9 1.0
N D:GLU122 4.4 51.4 1.0
CA D:VAL125 4.5 33.5 1.0
N D:VAL125 4.6 33.8 1.0
O D:LYS119 4.6 56.8 1.0
N D:LEU124 4.7 42.0 1.0
CA D:LEU124 4.7 40.0 1.0
CA D:ILE118 4.7 45.6 1.0
N D:LYS119 4.7 49.3 1.0
CA D:LYS119 4.8 57.7 1.0
C D:LYS119 4.8 57.6 1.0
CA D:ASP121 4.8 54.9 1.0
N D:ASP121 4.8 57.7 1.0

Reference:

Y.Patskovsky, R.Toro, M.Dickey, S.Chang, J.M.Sauder, F.M.Raushel, S.K.Burley, S.C.Almo. Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidopphilus To Be Published.
Page generated: Tue Dec 15 06:14:59 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy