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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

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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

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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

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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

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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

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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

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