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Sodium in PDB 2otm: Crystal Structure of A Putative Endoribonuclease (SO_1960) From Shewanella Oneidensis Mr-1 at 1.85 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Endoribonuclease (SO_1960) From Shewanella Oneidensis Mr-1 at 1.85 A Resolution, PDB code: 2otm 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) 29.21 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.083, 62.908, 78.689, 90.00, 93.24, 90.00
R / Rfree (%) 15.1 / 17.7

Other elements in 2otm:

The structure of Crystal Structure of A Putative Endoribonuclease (SO_1960) From Shewanella Oneidensis Mr-1 at 1.85 A Resolution also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Putative Endoribonuclease (SO_1960) From Shewanella Oneidensis Mr-1 at 1.85 A Resolution (pdb code 2otm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of A Putative Endoribonuclease (SO_1960) From Shewanella Oneidensis Mr-1 at 1.85 A Resolution, PDB code: 2otm:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2otm

Go back to Sodium Binding Sites List in 2otm
Sodium binding site 1 out of 3 in the Crystal Structure of A Putative Endoribonuclease (SO_1960) From Shewanella Oneidensis Mr-1 at 1.85 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 Putative Endoribonuclease (SO_1960) From Shewanella Oneidensis Mr-1 at 1.85 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na155

b:16.5
occ:1.00
O A:HOH168 2.1 22.9 1.0
O A:ASP58 2.2 21.0 1.0
O A:HOH307 2.3 34.0 1.0
O A:HOH195 2.6 35.3 1.0
O A:HOH181 2.6 30.5 1.0
C A:ASP58 3.4 20.9 1.0
O A:HOH240 4.0 46.7 1.0
CA A:ASP58 4.1 21.7 1.0
OE1 A:GLU63 4.3 17.9 1.0
N A:TYR59 4.4 19.3 1.0
CA A:TYR59 4.6 18.9 1.0
CD1 A:TYR59 4.8 21.8 1.0
CB A:ASP58 4.8 19.9 1.0

Sodium binding site 2 out of 3 in 2otm

Go back to Sodium Binding Sites List in 2otm
Sodium binding site 2 out of 3 in the Crystal Structure of A Putative Endoribonuclease (SO_1960) From Shewanella Oneidensis Mr-1 at 1.85 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 Putative Endoribonuclease (SO_1960) From Shewanella Oneidensis Mr-1 at 1.85 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na154

b:24.7
occ:1.00
O B:ASP58 2.3 21.1 1.0
O B:HOH182 2.6 28.9 1.0
C B:ASP58 3.4 20.9 1.0
O B:HOH255 3.9 46.6 1.0
CA B:ASP58 4.2 21.8 1.0
N B:TYR59 4.4 19.2 1.0
OE1 B:GLU63 4.4 18.7 1.0
CA B:TYR59 4.7 18.6 1.0
O B:HOH206 4.8 34.7 1.0
CD1 B:TYR59 4.9 19.7 1.0
CB B:ASP58 4.9 23.5 1.0

Sodium binding site 3 out of 3 in 2otm

Go back to Sodium Binding Sites List in 2otm
Sodium binding site 3 out of 3 in the Crystal Structure of A Putative Endoribonuclease (SO_1960) From Shewanella Oneidensis Mr-1 at 1.85 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 Putative Endoribonuclease (SO_1960) From Shewanella Oneidensis Mr-1 at 1.85 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na154

b:28.1
occ:1.00
O C:HOH170 2.0 28.6 0.5
O C:ASP58 2.3 20.6 1.0
O C:HOH193 2.3 37.2 1.0
O C:HOH184 2.5 34.3 1.0
C C:ASP58 3.4 21.1 1.0
O C:HOH227 4.0 46.8 1.0
CA C:ASP58 4.2 21.6 1.0
OE1 C:GLU63 4.3 20.4 1.0
N C:TYR59 4.4 19.5 1.0
CA C:TYR59 4.6 18.6 1.0
CD1 C:TYR59 4.7 21.1 1.0
OE2 C:GLU63 4.8 31.4 1.0
O C:HOH175 4.9 30.4 1.0
CB C:ASP58 4.9 22.1 1.0
CE1 C:TYR59 5.0 20.7 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Tue Dec 15 05:52:53 2020

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