Atomistry » Sodium » PDB 5ccb-5cvp » 5cmr
Atomistry »
  Sodium »
    PDB 5ccb-5cvp »
      5cmr »

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: Tue Dec 15 10:46:19 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