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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

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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

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