Atomistry » Sodium » PDB 5gu8-5hl0 » 5h9v
Atomistry »
  Sodium »
    PDB 5gu8-5hl0 »
      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: Tue Dec 15 11:02:36 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