Atomistry » Sodium » PDB 5gwl-5hn2 » 5h9v
Atomistry »
  Sodium »
    PDB 5gwl-5hn2 »
      5h9v »

Sodium in PDB 5h9v: Crystal Structure of Regnase Pin Domain, Form I

Protein crystallography data

The structure of Crystal Structure of Regnase Pin Domain, Form I, PDB code: 5h9v was solved by M.Yokogawa, T.Tsushima, W.Adachi, N.N.Noda, F.Inagaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.49 / 2.75
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.370, 113.370, 187.438, 90.00, 90.00, 120.00
R / Rfree (%) 18.9 / 22.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Regnase Pin Domain, Form I (pdb code 5h9v). 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 Regnase Pin Domain, Form I, PDB code: 5h9v:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5h9v

Go back to Sodium Binding Sites List in 5h9v
Sodium binding site 1 out of 4 in the Crystal Structure of Regnase Pin Domain, Form I


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 Regnase Pin Domain, Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:73.4
occ:1.00
 O A:ASN151 2.1 67.2 1.0
O A:HIS149 2.2 55.6 1.0
O A:VAL154 2.2 58.4 1.0
O A:MSE147 2.3 61.4 1.0
O A:ALA146 2.7 56.3 1.0
C A:MSE147 3.0 60.8 1.0
C A:ASN151 3.3 70.4 1.0
C A:VAL154 3.4 57.4 1.0
C A:HIS149 3.4 57.8 1.0
CA A:MSE147 3.4 59.7 1.0
C A:ALA146 3.7 55.8 1.0
CB A:SER156 3.9 59.2 1.0
N A:HIS149 3.9 56.4 1.0
N A:SER156 3.9 55.5 1.0
N A:ASN151 4.0 72.8 1.0
N A:VAL154 4.0 61.8 1.0
C A:SER148 4.0 59.3 1.0
C A:GLY150 4.0 67.9 1.0
N A:SER148 4.1 59.4 1.0
N A:MSE147 4.1 56.9 1.0
CA A:VAL154 4.1 59.8 1.0
CA A:LYS152 4.1 70.0 1.0
N A:LYS152 4.2 70.3 1.0
CA A:HIS149 4.3 57.9 1.0
C A:LYS152 4.3 71.6 1.0
CB A:VAL154 4.3 59.9 1.0
CA A:ASN151 4.3 74.1 1.0
N A:GLY150 4.3 61.5 1.0
O A:SER148 4.4 60.8 1.0
O A:GLY150 4.4 69.1 1.0
CA A:GLY150 4.4 65.9 1.0
N A:PHE155 4.4 58.1 1.0
O A:LYS152 4.5 78.4 1.0
CB A:MSE147 4.6 62.5 1.0
CA A:SER148 4.6 60.4 1.0
CA A:SER156 4.6 57.7 1.0
CA A:PHE155 4.6 56.9 1.0
C A:PHE155 4.7 57.3 1.0
N A:GLU153 4.8 69.9 1.0
CB A:ASN151 4.8 79.1 1.0
CG1 A:VAL154 4.9 59.5 1.0

Sodium binding site 2 out of 4 in 5h9v

Go back to Sodium Binding Sites List in 5h9v
Sodium binding site 2 out of 4 in the Crystal Structure of Regnase Pin Domain, Form I


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 Regnase Pin Domain, Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:79.6
occ:1.00
 O B:HIS149 2.0 56.1 1.0
O B:ASN151 2.0 71.3 1.0
O B:MSE147 2.3 63.2 1.0
O B:VAL154 2.3 62.8 1.0
O B:ALA146 2.7 54.2 1.0
C B:MSE147 3.1 63.3 1.0
C B:ASN151 3.2 73.5 1.0
C B:HIS149 3.2 55.7 1.0
C B:VAL154 3.5 65.2 1.0
CA B:MSE147 3.7 61.6 1.0
CB B:SER156 3.7 58.6 1.0
C B:GLY150 3.7 67.8 1.0
N B:HIS149 3.7 55.4 1.0
N B:ASN151 3.8 71.4 1.0
C B:ALA146 3.8 55.1 1.0
O B:GLY150 3.9 72.9 1.0
C B:SER148 4.0 58.4 1.0
N B:VAL154 4.0 72.7 1.0
CA B:ASN151 4.0 73.2 1.0
CA B:HIS149 4.0 54.0 1.0
N B:LYS152 4.1 74.3 1.0
N B:GLY150 4.1 58.6 1.0
N B:SER156 4.1 60.0 1.0
N B:SER148 4.1 62.1 1.0
CA B:VAL154 4.1 67.6 1.0
CA B:LYS152 4.2 74.6 1.0
CA B:GLY150 4.2 63.9 1.0
CB B:VAL154 4.2 66.2 1.0
N B:MSE147 4.3 58.1 1.0
O B:SER148 4.4 57.6 1.0
C B:LYS152 4.5 76.6 1.0
CB B:ASN151 4.5 74.4 1.0
CA B:SER148 4.6 62.2 1.0
N B:PHE155 4.6 66.7 1.0
CA B:SER156 4.6 58.9 1.0
OG B:SER156 4.7 58.9 1.0
CB B:HIS149 4.8 52.1 1.0
CG1 B:VAL154 4.9 65.5 1.0
O B:LYS152 4.9 73.7 1.0
CA B:PHE155 4.9 61.7 1.0
N B:GLU153 4.9 79.7 1.0
C B:PHE155 4.9 60.9 1.0
CB B:MSE147 5.0 64.9 1.0

Sodium binding site 3 out of 4 in 5h9v

Go back to Sodium Binding Sites List in 5h9v
Sodium binding site 3 out of 4 in the Crystal Structure of Regnase Pin Domain, Form I


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 Regnase Pin Domain, Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:85.5
occ:1.00
 O C:HIS149 2.0 69.3 1.0
O C:ASN151 2.0 77.0 1.0
O C:MSE147 2.4 72.1 1.0
O C:VAL154 2.4 76.8 1.0
O C:ALA146 2.8 70.2 1.0
C C:ASN151 3.2 77.9 1.0
C C:HIS149 3.2 67.1 1.0
C C:MSE147 3.3 73.8 1.0
C C:VAL154 3.5 79.1 1.0
CB C:SER156 3.6 73.2 1.0
C C:GLY150 3.7 76.1 1.0
N C:ASN151 3.7 78.0 1.0
CA C:MSE147 3.8 76.1 1.0
C C:ALA146 3.9 69.0 1.0
CA C:GLY150 4.0 72.6 1.0
N C:GLY150 4.0 68.5 1.0
N C:VAL154 4.0 83.8 1.0
CA C:ASN151 4.0 78.4 1.0
N C:SER156 4.0 72.7 1.0
O C:GLY150 4.1 78.8 1.0
N C:LYS152 4.1 78.9 1.0
N C:HIS149 4.1 63.9 1.0
C C:SER148 4.1 68.2 1.0
CA C:VAL154 4.1 81.8 1.0
CA C:LYS152 4.2 80.8 1.0
CB C:VAL154 4.2 80.6 1.0
CA C:HIS149 4.2 64.4 1.0
O C:SER148 4.3 71.2 1.0
N C:SER148 4.3 70.2 1.0
N C:MSE147 4.4 70.7 1.0
CB C:ASN151 4.4 80.3 1.0
CA C:SER156 4.5 71.8 1.0
C C:LYS152 4.5 83.6 1.0
N C:PHE155 4.6 81.2 1.0
OG C:SER156 4.7 72.9 1.0
CA C:SER148 4.7 68.7 1.0
CG1 C:VAL154 4.8 79.5 1.0
N C:GLU153 4.8 86.6 1.0
C C:PHE155 4.8 76.9 1.0
CA C:PHE155 4.9 78.4 1.0
O C:LYS152 4.9 83.0 1.0

Sodium binding site 4 out of 4 in 5h9v

Go back to Sodium Binding Sites List in 5h9v
Sodium binding site 4 out of 4 in the Crystal Structure of Regnase Pin Domain, Form I


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 Regnase Pin Domain, Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:88.7
occ:1.00
 O D:ASN151 1.8 75.0 1.0
O D:HIS149 1.9 59.7 1.0
O D:VAL154 2.5 63.5 1.0
O D:MSE147 2.6 66.0 1.0
O D:ALA146 2.9 60.0 1.0
C D:ASN151 3.0 81.6 1.0
C D:HIS149 3.1 62.1 1.0
C D:MSE147 3.2 64.1 1.0
C D:VAL154 3.6 66.7 1.0
C D:GLY150 3.6 82.3 1.0
CA D:MSE147 3.7 63.5 1.0
O D:GLY150 3.7 88.3 1.0
N D:HIS149 3.8 60.6 1.0
N D:ASN151 3.8 89.0 1.0
CB D:SER156 3.9 66.4 1.0
C D:SER148 3.9 62.5 1.0
C D:ALA146 3.9 60.7 1.0
CA D:HIS149 4.0 61.1 1.0
N D:LYS152 4.0 82.1 1.0
CA D:ASN151 4.0 86.8 1.0
N D:GLY150 4.0 66.8 1.0
O D:SER148 4.1 64.2 1.0
N D:SER156 4.1 62.7 1.0
CA D:LYS152 4.1 81.3 1.0
N D:VAL154 4.1 73.2 1.0
CA D:GLY150 4.2 76.8 1.0
N D:SER148 4.2 61.2 1.0
CA D:VAL154 4.3 69.8 1.0
N D:MSE147 4.3 61.1 1.0
CB D:VAL154 4.4 70.2 1.0
C D:LYS152 4.4 80.1 1.0
CB D:ASN151 4.6 88.8 1.0
CA D:SER148 4.6 61.7 1.0
CA D:SER156 4.6 63.7 1.0
N D:PHE155 4.7 67.1 1.0
N D:GLU153 4.7 81.7 1.0
CB D:HIS149 4.7 60.9 1.0
CA D:PHE155 4.9 63.9 1.0
CB D:MSE147 4.9 67.5 1.0
C D:PHE155 4.9 64.1 1.0
O D:LYS152 4.9 77.7 1.0
CG1 D:VAL154 5.0 69.9 1.0
OG D:SER156 5.0 70.8 1.0

Reference:

M.Yokogawa, T.Tsushima, N.N.Noda, H.Kumeta, Y.Enokizono, K.Yamashita, D.M.Standley, O.Takeuchi, S.Akira, F.Inagaki. Structural Basis For the Regulation of Enzymatic Activity of Regnase-1 By Domain-Domain Interactions Sci Rep V. 6 22324 2016.
ISSN: ESSN 2045-2322
PubMed: 26927947
DOI: 10.1038/SREP22324
Page generated: Mon Oct 7 21:20:52 2024

Last articles

Cl in 5S8X
Cl in 5S9A
Cl in 5S4P
Cl in 5S95
Cl in 5S93
Cl in 5S8J
Cl in 5S5M
Cl in 5S8O
Cl in 5S5V
Cl in 5S5B
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy