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Sodium in PDB 4had: Crystal Structure of Probable Oxidoreductase Protein From Rhizobium Etli Cfn 42

Protein crystallography data

The structure of Crystal Structure of Probable Oxidoreductase Protein From Rhizobium Etli Cfn 42, PDB code: 4had was solved by V.N.Malashkevich, R.Bhosle, R.Toro, B.Hillerich, A.Gizzi, S.Garforth, A.Kar, M.K.Chan, J.Lafluer, H.Patel, B.Matikainen, S.Chamala, S.Lim, A.Celikgil, G.Villegas, B.Evans, W.Zenchek, J.Love, A.Fiser, K.Khafizov, R.Seidel, J.B.Bonanno, S.C.Almo, New York Structural Genomics Researchconsortium (Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.01 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.662, 160.081, 192.646, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 20.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Probable Oxidoreductase Protein From Rhizobium Etli Cfn 42 (pdb code 4had). 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 Probable Oxidoreductase Protein From Rhizobium Etli Cfn 42, PDB code: 4had:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4had

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Sodium binding site 1 out of 4 in the Crystal Structure of Probable Oxidoreductase Protein From Rhizobium Etli Cfn 42


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 Probable Oxidoreductase Protein From Rhizobium Etli Cfn 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na500

b:22.6
occ:1.00
 O B:ARG46 2.2 24.9 1.0
O A:CYS27 2.3 22.9 1.0
O A:ALA24 2.3 24.9 1.0
O A:GLN22 2.5 24.2 1.0
O A:ILE21 2.6 21.9 1.0
C A:GLN22 3.1 24.2 1.0
C A:ALA24 3.4 23.1 1.0
N A:ALA24 3.4 21.3 1.0
C B:ARG46 3.4 26.8 1.0
C A:CYS27 3.5 25.4 1.0
CA A:GLN22 3.5 24.3 1.0
C A:ILE21 3.7 22.8 1.0
C A:ASP23 3.8 22.1 1.0
CA A:ALA24 3.8 21.6 1.0
N A:ASP23 3.9 23.6 1.0
CG B:ARG46 4.0 27.1 1.0
N A:GLN22 4.1 22.9 1.0
CB A:ALA24 4.2 21.7 1.0
CA A:VAL28 4.2 24.2 1.0
O A:ASP23 4.2 23.4 1.0
CA B:ARG46 4.3 28.8 1.0
N A:VAL28 4.3 24.9 1.0
CA A:ASP23 4.4 22.3 1.0
N B:PHE47 4.4 26.0 1.0
CA B:PHE47 4.5 25.5 1.0
CB A:VAL28 4.5 27.3 1.0
N A:CYS27 4.5 26.4 1.0
N A:GLU25 4.6 24.0 1.0
CA A:CYS27 4.6 27.0 1.0
CG2 A:VAL28 4.7 28.0 1.0
CB B:ARG46 4.8 28.8 1.0
OE1 A:GLN22 4.8 23.4 1.0
CB A:GLN22 4.9 25.0 1.0
CA A:ILE21 5.0 21.9 1.0

Sodium binding site 2 out of 4 in 4had

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Sodium binding site 2 out of 4 in the Crystal Structure of Probable Oxidoreductase Protein From Rhizobium Etli Cfn 42


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 Probable Oxidoreductase Protein From Rhizobium Etli Cfn 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na500

b:21.4
occ:1.00
 O B:CYS27 2.2 25.3 1.0
O A:ARG46 2.3 26.2 1.0
O B:ALA24 2.3 24.4 1.0
O B:ILE21 2.5 24.8 1.0
O B:GLN22 2.5 27.3 1.0
C B:GLN22 3.1 23.8 1.0
C B:ALA24 3.3 23.7 1.0
N B:ALA24 3.4 24.9 1.0
C B:CYS27 3.4 27.2 1.0
C A:ARG46 3.5 27.5 1.0
CA B:GLN22 3.6 23.2 1.0
C B:ILE21 3.6 22.9 1.0
CA B:ALA24 3.8 24.8 1.0
C B:ASP23 3.8 24.4 1.0
N B:ASP23 3.9 22.0 1.0
CG A:ARG46 4.1 27.5 1.0
N B:GLN22 4.1 22.4 1.0
CB B:ALA24 4.1 23.5 1.0
CA B:VAL28 4.1 24.7 1.0
N B:VAL28 4.2 25.6 1.0
O B:ASP23 4.3 23.5 1.0
CA A:ARG46 4.3 29.9 1.0
CA B:ASP23 4.4 23.2 1.0
N B:CYS27 4.4 27.2 1.0
N A:PHE47 4.5 27.9 1.0
CB B:VAL28 4.5 25.6 1.0
CA B:CYS27 4.5 29.0 1.0
N B:GLU25 4.5 24.7 1.0
CA A:PHE47 4.6 25.9 1.0
CG2 B:VAL28 4.7 25.5 1.0
OE1 B:GLN22 4.8 24.2 1.0
CB A:ARG46 4.8 28.2 1.0
CA B:ILE21 4.9 22.1 1.0
CB B:GLN22 4.9 22.9 1.0
CA B:GLU25 5.0 26.8 1.0

Sodium binding site 3 out of 4 in 4had

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Sodium binding site 3 out of 4 in the Crystal Structure of Probable Oxidoreductase Protein From Rhizobium Etli Cfn 42


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 Probable Oxidoreductase Protein From Rhizobium Etli Cfn 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na500

b:30.0
occ:1.00
 O C:ALA24 2.3 34.9 1.0
O C:CYS27 2.3 35.2 1.0
O D:ARG46 2.3 33.7 1.0
O C:ILE21 2.5 29.9 1.0
O C:GLN22 2.5 35.6 1.0
C C:GLN22 3.1 32.9 1.0
C C:ALA24 3.3 32.4 1.0
N C:ALA24 3.3 28.9 1.0
C C:CYS27 3.5 35.9 1.0
C D:ARG46 3.5 35.6 1.0
CA C:GLN22 3.6 33.1 1.0
C C:ILE21 3.6 31.9 1.0
CA C:ALA24 3.7 29.8 1.0
C C:ASP23 3.8 31.6 1.0
N C:ASP23 3.9 31.4 1.0
CG D:ARG46 4.0 35.5 1.0
CB C:ALA24 4.1 29.2 1.0
N C:GLN22 4.1 32.3 1.0
CA C:VAL28 4.2 36.7 1.0
O C:ASP23 4.2 30.0 1.0
N C:VAL28 4.3 35.7 1.0
CA D:ARG46 4.3 37.8 1.0
CA C:ASP23 4.4 29.7 1.0
N C:CYS27 4.5 37.4 1.0
N D:PHE47 4.5 34.3 1.0
N C:GLU25 4.5 34.6 1.0
CA C:CYS27 4.5 37.2 1.0
CB C:VAL28 4.6 42.3 1.0
CA D:PHE47 4.6 33.0 1.0
CG2 C:VAL28 4.8 46.9 1.0
CB D:ARG46 4.8 37.4 1.0
OE1 C:GLN22 4.8 31.0 1.0
CA C:ILE21 4.9 29.7 1.0
CB C:GLN22 4.9 32.4 1.0
CA C:GLU25 5.0 37.3 1.0

Sodium binding site 4 out of 4 in 4had

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Sodium binding site 4 out of 4 in the Crystal Structure of Probable Oxidoreductase Protein From Rhizobium Etli Cfn 42


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 Probable Oxidoreductase Protein From Rhizobium Etli Cfn 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na500

b:28.8
occ:1.00
 O C:ARG46 2.2 32.4 1.0
O D:CYS27 2.3 30.7 1.0
O D:ALA24 2.4 31.2 1.0
O D:GLN22 2.5 28.4 1.0
O D:ILE21 2.7 32.4 1.0
C D:GLN22 3.1 29.2 1.0
C C:ARG46 3.4 33.2 1.0
C D:ALA24 3.4 29.4 1.0
N D:ALA24 3.5 28.1 1.0
C D:CYS27 3.5 32.1 1.0
CA D:GLN22 3.6 29.2 1.0
C D:ILE21 3.8 29.2 1.0
C D:ASP23 3.9 27.5 1.0
CA D:ALA24 3.9 30.1 1.0
N D:ASP23 4.0 28.5 1.0
CG C:ARG46 4.0 35.2 1.0
CA D:VAL28 4.2 32.2 1.0
N D:GLN22 4.2 29.7 1.0
CA C:ARG46 4.2 35.2 1.0
N D:VAL28 4.3 30.8 1.0
CB D:ALA24 4.3 28.6 1.0
O D:ASP23 4.3 28.6 1.0
N C:PHE47 4.3 31.5 1.0
CA D:ASP23 4.4 28.4 1.0
CB D:VAL28 4.4 35.1 1.0
CA C:PHE47 4.5 31.0 1.0
N D:CYS27 4.6 32.9 1.0
N D:GLU25 4.6 29.0 1.0
CG2 D:VAL28 4.6 36.7 1.0
CA D:CYS27 4.6 35.4 1.0
CB C:ARG46 4.8 35.9 1.0
OE1 D:GLN22 4.8 30.2 1.0
CB D:GLN22 4.9 29.6 1.0

Reference:

V.N.Malashkevich, R.Bhosle, R.Toro, B.Hillerich, A.Gizzi, S.Garforth, A.Kar, M.K.Chan, J.Lafluer, H.Patel, B.Matikainen, S.Chamala, S.Lim, A.Celikgil, G.Villegas, B.Evans, W.Zenchek, J.Love, A.Fiser, K.Khafizov, R.Seidel, J.B.Bonanno, S.C.Almo. Crystal Structure of Probable Oxidoreductase Protein From Rhizobium Etli Cfn 42 To Be Published.
Page generated: Mon Oct 7 15:45:31 2024

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