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Sodium in PDB 5d4f: Crystal Structure of C-As Lyase with Fe(III)

Protein crystallography data

The structure of Crystal Structure of C-As Lyase with Fe(III), PDB code: 5d4f was solved by S.Venkadesh, M.Yoshinaga, B.Sankaran, P.Kandavelu, B.P.Rosen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.02 / 1.72
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 42.370, 42.370, 116.900, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 23.5

Other elements in 5d4f:

The structure of Crystal Structure of C-As Lyase with Fe(III) also contains other interesting chemical elements:

Iron (Fe) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of C-As Lyase with Fe(III) (pdb code 5d4f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of C-As Lyase with Fe(III), PDB code: 5d4f:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5d4f

Go back to Sodium Binding Sites List in 5d4f
Sodium binding site 1 out of 3 in the Crystal Structure of C-As Lyase with Fe(III)


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 C-As Lyase with Fe(III) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:45.2
occ:1.00
O A:HOH353 2.3 50.5 1.0
NH2 A:ARG82 3.8 37.7 1.0
CG2 A:VAL68 4.3 17.8 1.0
O A:HOH343 4.6 46.9 1.0
CG1 A:VAL68 4.6 21.1 1.0
CB A:VAL68 4.7 19.6 1.0
CG2 A:VAL118 4.9 25.1 1.0

Sodium binding site 2 out of 3 in 5d4f

Go back to Sodium Binding Sites List in 5d4f
Sodium binding site 2 out of 3 in the Crystal Structure of C-As Lyase with Fe(III)


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 C-As Lyase with Fe(III) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:59.3
occ:1.00
CG A:PRO36 2.7 42.6 1.0
CB A:PRO36 2.9 38.7 1.0
CA A:PRO36 3.0 27.0 1.0
CD A:PRO36 3.4 37.2 1.0
N A:PRO36 3.5 33.1 1.0
C A:ARG35 4.3 30.8 1.0
C A:PRO36 4.4 24.9 1.0
O A:ARG35 4.6 24.7 1.0
N A:GLY37 4.8 27.8 1.0

Sodium binding site 3 out of 3 in 5d4f

Go back to Sodium Binding Sites List in 5d4f
Sodium binding site 3 out of 3 in the Crystal Structure of C-As Lyase with Fe(III)


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 C-As Lyase with Fe(III) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:44.8
occ:1.00
N A:GLU45 3.2 29.1 1.0
N A:ALA44 3.4 25.2 1.0
O A:GLU45 3.6 34.6 1.0
CB A:ALA44 3.9 35.0 1.0
CG2 A:ILE43 3.9 21.2 1.0
CB A:GLU45 4.0 37.4 1.0
CA A:GLU45 4.0 29.2 1.0
CA A:ALA44 4.0 26.1 1.0
C A:ALA44 4.1 24.7 1.0
C A:GLU45 4.2 31.0 1.0
C A:ILE43 4.4 24.3 1.0
O A:PHE27 4.6 29.6 1.0
CA A:ILE43 4.6 16.3 1.0
CB A:ILE43 4.9 18.4 1.0

Reference:

S.Venkadesh, M.Yoshinaga, B.Sankaran, P.Kandavelu, B.P.Rosen. Crystal Structure of C-As Lyase with Mercaptoethonal To Be Published.
Page generated: Tue Dec 15 10:47:42 2020

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