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Sodium in PDB 5cmr: Crystal Structure of Linker-Mediated Zn-Bound Human H-Ferritin Variant 122H-Delta C-Star

Enzymatic activity of Crystal Structure of Linker-Mediated Zn-Bound Human H-Ferritin Variant 122H-Delta C-Star

All present enzymatic activity of Crystal Structure of Linker-Mediated Zn-Bound Human H-Ferritin Variant 122H-Delta C-Star:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of Linker-Mediated Zn-Bound Human H-Ferritin Variant 122H-Delta C-Star, PDB code: 5cmr was solved by P.A.Sontz, J.B.Bailey, S.Ahn, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.91 / 3.79
Space group I 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 155.320, 155.320, 155.320, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.6

Other elements in 5cmr:

The structure of Crystal Structure of Linker-Mediated Zn-Bound Human H-Ferritin Variant 122H-Delta C-Star also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Linker-Mediated Zn-Bound Human H-Ferritin Variant 122H-Delta C-Star (pdb code 5cmr). 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 Linker-Mediated Zn-Bound Human H-Ferritin Variant 122H-Delta C-Star, PDB code: 5cmr:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5cmr

Go back to Sodium Binding Sites List in 5cmr
Sodium binding site 1 out of 3 in the Crystal Structure of Linker-Mediated Zn-Bound Human H-Ferritin Variant 122H-Delta C-Star


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 Linker-Mediated Zn-Bound Human H-Ferritin Variant 122H-Delta C-Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:70.0
occ:0.33
OD1 A:ASP131 2.4 84.3 1.0
OE1 A:GLU134 2.5 75.1 1.0
NA A:NA204 2.5 72.4 0.3
CG A:ASP131 3.5 82.0 1.0
CD A:GLU134 3.7 76.7 1.0
CB A:ASP131 4.3 74.1 1.0
OE2 A:GLU134 4.3 64.2 1.0
OD2 A:ASP131 4.5 77.1 1.0
CB A:GLU134 4.5 76.9 1.0
CA A:ASP131 4.5 79.8 1.0
CG A:GLU134 4.7 90.5 1.0

Sodium binding site 2 out of 3 in 5cmr

Go back to Sodium Binding Sites List in 5cmr
Sodium binding site 2 out of 3 in the Crystal Structure of Linker-Mediated Zn-Bound Human H-Ferritin Variant 122H-Delta C-Star


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 Linker-Mediated Zn-Bound Human H-Ferritin Variant 122H-Delta C-Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:72.4
occ:0.33
OE1 A:GLU134 2.4 75.1 1.0
NA A:NA203 2.5 70.0 0.3
OE2 A:GLU134 2.8 64.2 1.0
CD A:GLU134 3.0 76.7 1.0
OD1 A:ASP131 4.1 84.3 1.0
CG A:GLU134 4.4 90.5 1.0
CA A:ASP131 4.9 79.8 1.0
CB A:ASP131 4.9 74.1 1.0
CG A:ASP131 4.9 82.0 1.0

Sodium binding site 3 out of 3 in 5cmr

Go back to Sodium Binding Sites List in 5cmr
Sodium binding site 3 out of 3 in the Crystal Structure of Linker-Mediated Zn-Bound Human H-Ferritin Variant 122H-Delta C-Star


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 Linker-Mediated Zn-Bound Human H-Ferritin Variant 122H-Delta C-Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:47.0
occ:1.00
OE2 A:GLU62 2.3 65.8 1.0
OE1 A:GLU107 2.3 0.2 1.0
OE2 A:GLU107 2.5 57.0 1.0
CD A:GLU107 2.7 82.2 1.0
OE1 A:GLN141 2.8 73.3 1.0
ZN A:ZN201 2.9 61.2 1.0
CD A:GLU62 2.9 66.6 1.0
OE1 A:GLU62 2.9 48.7 1.0
NE2 A:GLN141 3.5 72.6 1.0
CD A:GLN141 3.6 82.3 1.0
CE1 A:HIS65 3.9 91.3 1.0
ND1 A:HIS65 4.0 73.7 1.0
CG A:GLU107 4.3 92.5 1.0
CG A:GLU62 4.4 92.2 1.0
OE1 A:GLU27 4.5 83.8 1.0
CG1 A:VAL110 4.5 0.3 1.0
CB A:VAL110 4.9 89.1 1.0
CE2 A:TYR34 5.0 60.9 1.0

Reference:

P.A.Sontz, J.B.Bailey, S.Ahn, F.A.Tezcan. A Metal Organic Framework with Spherical Protein Nodes: Rational Chemical Design of 3D Protein Crystals. J.Am.Chem.Soc. V. 137 11598 2015.
ISSN: ESSN 1520-5126
PubMed: 26305584
DOI: 10.1021/JACS.5B07463
Page generated: Mon Oct 7 20:23:02 2024

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