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Sodium in PDB 3grd: Crystal Structure of NTF2-Superfamily Protein with Unknown Function (NP_977240.1) From Bacillus Cereus Atcc 10987 at 1.25 A Resolution

Protein crystallography data

The structure of Crystal Structure of NTF2-Superfamily Protein with Unknown Function (NP_977240.1) From Bacillus Cereus Atcc 10987 at 1.25 A Resolution, PDB code: 3grd 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) 29.57 / 1.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.090, 47.140, 151.790, 90.00, 90.00, 90.00
R / Rfree (%) 13.3 / 16.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of NTF2-Superfamily Protein with Unknown Function (NP_977240.1) From Bacillus Cereus Atcc 10987 at 1.25 A Resolution (pdb code 3grd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of NTF2-Superfamily Protein with Unknown Function (NP_977240.1) From Bacillus Cereus Atcc 10987 at 1.25 A Resolution, PDB code: 3grd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3grd

Go back to Sodium Binding Sites List in 3grd
Sodium binding site 1 out of 2 in the Crystal Structure of NTF2-Superfamily Protein with Unknown Function (NP_977240.1) From Bacillus Cereus Atcc 10987 at 1.25 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 NTF2-Superfamily Protein with Unknown Function (NP_977240.1) From Bacillus Cereus Atcc 10987 at 1.25 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na135

b:11.9
occ:1.00
O A:TRP64 2.4 10.8 1.0
O A:HOH297 2.4 13.1 1.0
O A:GLY61 2.4 11.3 1.0
O A:HOH158 2.4 20.7 1.0
O A:HOH253 2.5 10.7 1.0
C A:GLY61 3.4 9.7 1.0
C A:TRP64 3.5 9.1 1.0
CA A:GLY61 3.7 9.5 1.0
CA A:ASN65 4.0 8.7 1.0
N A:ASP66 4.1 8.8 1.0
O A:LEU60 4.1 9.8 1.0
N A:ASN65 4.2 9.2 1.0
NZ A:LYS94 4.3 20.9 1.0
CE A:LYS94 4.4 17.2 1.0
C A:ASN65 4.5 8.6 1.0
O A:HOH317 4.5 21.9 1.0
N A:SER62 4.6 10.1 1.0
CA A:TRP64 4.6 8.4 1.0
N A:TRP64 4.7 9.1 1.0
O A:HOH170 4.7 22.8 1.0
N A:GLY61 4.8 9.0 1.0
C A:LEU60 4.9 7.9 1.0
OD1 A:ASN65 4.9 13.8 1.0

Sodium binding site 2 out of 2 in 3grd

Go back to Sodium Binding Sites List in 3grd
Sodium binding site 2 out of 2 in the Crystal Structure of NTF2-Superfamily Protein with Unknown Function (NP_977240.1) From Bacillus Cereus Atcc 10987 at 1.25 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 NTF2-Superfamily Protein with Unknown Function (NP_977240.1) From Bacillus Cereus Atcc 10987 at 1.25 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na135

b:6.3
occ:1.00
O B:VAL77 2.3 7.2 1.0
O A:HOH222 2.3 8.5 1.0
O B:LYS80 2.4 6.5 1.0
O B:HOH158 2.5 8.3 1.0
C B:VAL77 3.4 6.5 1.0
C B:LYS80 3.6 6.2 1.0
O B:HOH175 3.9 16.4 1.0
N B:VAL77 4.0 6.6 1.0
N B:LYS80 4.0 6.7 1.0
CA B:VAL77 4.2 6.4 1.0
O B:HOH152 4.3 11.9 1.0
N B:SER78 4.3 6.1 1.0
N B:GLY79 4.3 7.2 1.0
CA B:LYS80 4.4 7.3 1.0
CA B:SER78 4.4 6.6 1.0
C B:GLU76 4.5 6.5 1.0
OG A:SER78 4.5 8.6 1.0
N B:ASP81 4.6 6.1 0.5
N B:ASP81 4.6 7.1 0.5
C B:SER78 4.7 6.9 1.0
O B:HOH159 4.7 13.8 1.0
O B:VAL82 4.7 6.9 1.0
CA B:ASP81 4.7 6.2 0.5
O B:HOH170 4.7 14.0 1.0
CA B:ASP81 4.8 7.5 0.5
N B:VAL82 4.8 7.1 1.0
CB B:GLU76 4.8 8.5 1.0
CB B:VAL77 5.0 6.6 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Tue Dec 15 06:12:41 2020

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