Atomistry » Sodium » PDB 7jr6-7kka » 7k26
Atomistry »
  Sodium »
    PDB 7jr6-7kka »
      7k26 »

Sodium in PDB 7k26: Crystal Structure of Human H-Chain Ferritin Variant Infused with Sodium Acrylate

Enzymatic activity of Crystal Structure of Human H-Chain Ferritin Variant Infused with Sodium Acrylate

All present enzymatic activity of Crystal Structure of Human H-Chain Ferritin Variant Infused with Sodium Acrylate:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of Human H-Chain Ferritin Variant Infused with Sodium Acrylate, PDB code: 7k26 was solved by J.B.Bailey, L.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.99 / 2.70
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 131.570, 131.570, 306.560, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 25.4

Other elements in 7k26:

The structure of Crystal Structure of Human H-Chain Ferritin Variant Infused with Sodium Acrylate also contains other interesting chemical elements:

Iron (Fe) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human H-Chain Ferritin Variant Infused with Sodium Acrylate (pdb code 7k26). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of Human H-Chain Ferritin Variant Infused with Sodium Acrylate, PDB code: 7k26:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 7k26

Go back to Sodium Binding Sites List in 7k26
Sodium binding site 1 out of 7 in the Crystal Structure of Human H-Chain Ferritin Variant Infused with Sodium Acrylate


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 Human H-Chain Ferritin Variant Infused with Sodium Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:82.0
occ:1.00
 OE2 G:GLU134 2.4 77.6 1.0
OE2 A:GLU134 2.6 77.4 1.0
OE1 C:GLU134 2.7 73.6 1.0
O G:HOH320 2.9 65.6 1.0
OE1 G:GLU134 2.9 75.1 1.0
CD G:GLU134 3.0 75.7 1.0
O C:HOH302 3.3 61.5 1.0
OE1 A:GLU134 3.3 81.0 1.0
CD A:GLU134 3.3 75.5 1.0
OE2 C:GLU134 3.4 78.7 1.0
CD C:GLU134 3.4 76.9 1.0
CG G:GLU134 4.5 70.3 1.0
OD1 G:ASP131 4.6 63.1 1.0
OD2 C:ASP131 4.8 68.9 1.0
CG A:GLU134 4.8 68.9 1.0
CG C:GLU134 4.9 74.0 1.0
OD1 A:ASP131 5.0 63.9 1.0

Sodium binding site 2 out of 7 in 7k26

Go back to Sodium Binding Sites List in 7k26
Sodium binding site 2 out of 7 in the Crystal Structure of Human H-Chain Ferritin Variant Infused with Sodium Acrylate


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 Human H-Chain Ferritin Variant Infused with Sodium Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:32.3
occ:1.00
 CE1 E:HIS173 2.8 51.6 1.0
CE1 L:HIS173 3.0 54.6 1.0
CE1 F:HIS173 3.0 47.3 1.0
CE1 A:HIS173 3.0 56.5 1.0
NE2 A:HIS173 3.5 57.8 1.0
NE2 E:HIS173 3.5 50.7 1.0
NE2 L:HIS173 3.5 55.8 1.0
NE2 F:HIS173 3.6 45.8 1.0
ND1 E:HIS173 3.9 52.4 1.0
CD2 L:LEU169 4.0 47.6 1.0
ND1 A:HIS173 4.1 57.7 1.0
ND1 L:HIS173 4.1 55.0 1.0
ND1 F:HIS173 4.1 47.2 1.0
CD2 E:LEU169 4.2 52.6 1.0
CD2 F:LEU169 4.3 44.2 1.0
CD2 A:LEU169 4.3 46.1 1.0
CD1 L:LEU169 4.5 48.0 1.0
CD1 E:LEU169 4.5 54.4 1.0
CD2 A:HIS173 4.7 58.4 1.0
CD2 E:HIS173 4.7 50.6 1.0
CD2 L:HIS173 4.8 53.3 1.0
CG L:LEU169 4.9 49.5 1.0
CD2 F:HIS173 4.9 46.5 1.0
CG E:HIS173 4.9 48.1 1.0
CG E:LEU169 5.0 53.4 1.0
CD1 A:LEU169 5.0 46.8 1.0

Sodium binding site 3 out of 7 in 7k26

Go back to Sodium Binding Sites List in 7k26
Sodium binding site 3 out of 7 in the Crystal Structure of Human H-Chain Ferritin Variant Infused with Sodium Acrylate


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 Human H-Chain Ferritin Variant Infused with Sodium Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:54.2
occ:1.00
 OE2 F:GLU134 2.5 62.9 1.0
OD1 D:ASP131 2.9 55.7 1.0
OD2 F:ASP131 2.9 71.9 1.0
OE2 D:GLU134 3.0 81.1 1.0
OE2 B:GLU134 3.0 65.4 1.0
OD1 B:ASP131 3.3 45.7 1.0
CD F:GLU134 3.7 64.0 1.0
CG D:ASP131 4.0 54.1 1.0
CG F:ASP131 4.1 65.1 1.0
CD D:GLU134 4.2 73.4 1.0
CD B:GLU134 4.2 61.5 1.0
O D:HOH346 4.3 56.7 1.0
O B:HOH322 4.3 55.8 1.0
OE1 F:GLU134 4.4 64.8 1.0
CG B:ASP131 4.5 47.7 1.0
CB F:ASP131 4.6 56.6 1.0
CB F:GLU134 4.7 47.3 1.0
CB D:ASP131 4.7 51.8 1.0
CB B:GLU134 4.8 47.6 1.0
CA F:ASP131 4.8 50.5 1.0
CG F:GLU134 4.8 57.9 1.0
CB D:GLU134 4.9 54.9 1.0
OE1 D:GLU134 4.9 77.5 1.0
CB B:ASP131 4.9 47.7 1.0
OE1 B:GLU134 5.0 58.5 1.0

Sodium binding site 4 out of 7 in 7k26

Go back to Sodium Binding Sites List in 7k26
Sodium binding site 4 out of 7 in the Crystal Structure of Human H-Chain Ferritin Variant Infused with Sodium Acrylate


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 Human H-Chain Ferritin Variant Infused with Sodium Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:35.7
occ:1.00
 NE2 H:HIS173 3.0 57.8 1.0
NE2 B:HIS173 3.1 53.7 1.0
CE1 H:HIS173 3.8 55.4 1.0
CD2 H:LEU169 3.9 45.0 1.0
CE1 B:HIS173 3.9 51.4 1.0
CD2 B:LEU169 3.9 49.0 1.0
CD2 B:HIS173 4.0 52.8 1.0
CD2 H:HIS173 4.0 58.2 1.0
CD1 B:LEU169 4.7 53.4 1.0
CD1 H:LEU169 4.9 49.9 1.0
CG B:LEU169 4.9 50.2 1.0
ND1 H:HIS173 4.9 56.1 1.0
CG H:LEU169 5.0 48.2 1.0

Sodium binding site 5 out of 7 in 7k26

Go back to Sodium Binding Sites List in 7k26
Sodium binding site 5 out of 7 in the Crystal Structure of Human H-Chain Ferritin Variant Infused with Sodium Acrylate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Human H-Chain Ferritin Variant Infused with Sodium Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:49.0
occ:1.00
 NE2 C:HIS173 2.8 61.4 1.0
CE1 K:HIS173 2.8 57.5 1.0
CE1 J:HIS173 3.1 59.0 1.0
NE2 K:HIS173 3.4 57.4 1.0
CE1 C:HIS173 3.4 61.9 1.0
NE2 J:HIS173 3.6 57.4 1.0
CD2 C:LEU169 3.7 54.3 1.0
ND1 K:HIS173 3.9 57.2 1.0
CD2 C:HIS173 3.9 60.8 1.0
CD2 K:LEU169 3.9 53.5 1.0
CD2 J:LEU169 4.0 46.1 1.0
ND1 J:HIS173 4.2 58.1 1.0
ND1 C:HIS173 4.6 61.2 1.0
CD2 K:HIS173 4.6 56.3 1.0
CD1 K:LEU169 4.7 54.2 1.0
CD1 J:LEU169 4.9 52.3 1.0
CG K:HIS173 4.9 55.0 1.0
CG C:HIS173 4.9 57.0 1.0
CG C:LEU169 4.9 55.6 1.0
CD1 C:LEU169 4.9 55.1 1.0
CD2 J:HIS173 4.9 56.3 1.0
CG K:LEU169 4.9 53.8 1.0

Sodium binding site 6 out of 7 in 7k26

Go back to Sodium Binding Sites List in 7k26
Sodium binding site 6 out of 7 in the Crystal Structure of Human H-Chain Ferritin Variant Infused with Sodium Acrylate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Human H-Chain Ferritin Variant Infused with Sodium Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na202

b:74.7
occ:1.00
 O H:HOH301 2.6 46.7 1.0
OD1 L:ASP131 2.9 61.6 1.0
OE1 H:GLU134 3.1 75.7 1.0
NA L:NA202 3.2 1.0 1.0
OD1 H:ASP131 3.2 82.2 1.0
OE1 L:GLU134 3.4 81.3 1.0
CG L:ASP131 4.1 58.8 1.0
CD L:GLU134 4.3 76.5 1.0
CG H:ASP131 4.3 78.4 1.0
CD H:GLU134 4.4 76.8 1.0
CG2 H:THR135 4.6 56.5 1.0
CB L:ASP131 4.8 56.8 1.0
OE2 L:GLU134 4.8 75.6 1.0
CB H:ASP131 4.9 72.7 1.0
CB H:GLU134 4.9 68.4 1.0
CB L:GLU134 5.0 67.8 1.0

Sodium binding site 7 out of 7 in 7k26

Go back to Sodium Binding Sites List in 7k26
Sodium binding site 7 out of 7 in the Crystal Structure of Human H-Chain Ferritin Variant Infused with Sodium Acrylate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Human H-Chain Ferritin Variant Infused with Sodium Acrylate within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na202

b:1.0
occ:1.00
 NA H:NA202 3.2 74.7 1.0
OD1 L:ASP131 3.6 61.6 1.0
OG1 L:THR135 4.1 65.7 1.0
CG2 H:THR135 4.2 56.5 1.0
OD1 H:ASP131 4.3 82.2 1.0
CG L:ASP131 4.6 58.8 1.0
OD2 L:ASP131 4.8 55.3 1.0
CG2 L:THR135 4.8 59.5 1.0

Reference:

K.Han, J.B.Bailey, L.Zhang, F.A.Tezcan. Anisotropic Dynamics and Mechanics of Macromolecular Crystals Containing Lattice-Patterned Polymer Networks. J.Am.Chem.Soc. V. 142 19402 2020.
ISSN: ESSN 1520-5126
PubMed: 33124805
DOI: 10.1021/JACS.0C10065
Page generated: Tue Oct 8 17:06:47 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy