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Sodium in PDB 6p8k: Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX

Enzymatic activity of Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX

All present enzymatic activity of Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX:
1.16.3.1;

Protein crystallography data

The structure of Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX, PDB code: 6p8k was solved by A.B.Taylor, D.Cioloboc, D.M.Kurtz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 1.70
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 207.852, 207.852, 142.657, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 21.8

Other elements in 6p8k:

The structure of Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX also contains other interesting chemical elements:

Zinc (Zn) 24 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX (pdb code 6p8k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX, PDB code: 6p8k:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6p8k

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Sodium binding site 1 out of 4 in the Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:37.9
occ:0.50
 O C:HOH349 2.1 31.1 0.5
O C:HOH449 2.3 29.9 0.5
OD1 C:ASN148 2.4 21.3 1.0
OD1 A:ASN148 2.5 21.8 1.0
CG C:ASN148 3.4 21.6 1.0
CG A:ASN148 3.4 20.9 1.0
ND2 C:ASN148 3.7 22.9 1.0
ND2 A:ASN148 3.8 22.5 1.0
OE1 C:GLN151 4.1 34.7 1.0
OE1 A:GLN151 4.2 36.4 1.0
O C:HOH440 4.3 28.9 1.0
O A:HOH438 4.4 33.2 1.0
CB C:ASN148 4.7 18.0 1.0
CB A:ASN148 4.8 17.4 1.0

Sodium binding site 2 out of 4 in 6p8k

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Sodium binding site 2 out of 4 in the Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:31.4
occ:1.00
 O K:HOH442 2.2 25.9 1.0
O K:HOH342 2.3 25.3 1.0
OD1 G:ASN148 2.4 21.2 1.0
OD1 B:ASN148 2.4 24.1 1.0
OD1 J:ASN148 2.5 21.7 1.0
OD1 K:ASN148 2.5 22.1 1.0
CG B:ASN148 3.4 22.0 1.0
CG G:ASN148 3.4 22.0 1.0
CG J:ASN148 3.4 21.3 1.0
CG K:ASN148 3.5 21.0 1.0
ND2 B:ASN148 3.7 23.6 1.0
ND2 J:ASN148 3.7 23.0 1.0
ND2 G:ASN148 3.7 26.0 1.0
ND2 K:ASN148 3.9 24.0 1.0
OE1 G:GLN151 4.2 32.9 1.0
OE1 J:GLN151 4.2 38.6 1.0
O G:HOH449 4.2 31.2 1.0
O B:HOH429 4.3 26.1 1.0
OE1 K:GLN151 4.3 36.5 1.0
O J:HOH435 4.3 26.8 1.0
O K:HOH417 4.4 28.1 1.0
OE1 B:GLN151 4.5 32.5 1.0
CB G:ASN148 4.7 19.8 1.0
CB B:ASN148 4.7 17.7 1.0
CB J:ASN148 4.8 18.3 1.0
CB K:ASN148 4.8 17.8 1.0

Sodium binding site 3 out of 4 in 6p8k

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Sodium binding site 3 out of 4 in the Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na202

b:32.2
occ:1.00
 OD1 H:ASN148 2.4 21.8 1.0
OD1 D:ASN148 2.4 21.9 1.0
CG H:ASN148 3.4 22.5 1.0
CG D:ASN148 3.4 21.4 1.0
ND2 D:ASN148 3.8 23.3 1.0
ND2 H:ASN148 3.8 26.5 1.0
O D:HOH425 4.4 33.1 1.0
OE1 D:GLN151 4.4 36.1 1.0
OE1 H:GLN151 4.5 35.5 1.0
O H:HOH423 4.5 30.4 1.0
CB D:ASN148 4.8 17.2 1.0
CB H:ASN148 4.8 19.5 1.0

Sodium binding site 4 out of 4 in 6p8k

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Sodium binding site 4 out of 4 in the Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na202

b:34.1
occ:0.50
 O L:HOH451 2.1 25.8 0.5
O F:HOH403 2.4 33.6 0.5
OD1 F:ASN148 2.5 21.0 1.0
OD1 L:ASN148 2.5 24.0 1.0
CG F:ASN148 3.4 20.6 1.0
CG L:ASN148 3.4 23.3 1.0
ND2 F:ASN148 3.7 23.0 1.0
ND2 L:ASN148 3.7 25.2 1.0
O L:HOH430 4.2 30.3 1.0
O F:HOH438 4.3 31.1 1.0
OE1 F:GLN151 4.5 35.1 1.0
CB F:ASN148 4.8 17.6 1.0
CB L:ASN148 4.8 20.9 1.0
OE1 L:GLN151 4.9 35.4 1.0

Reference:

B.S.Benavides, S.Valandro, D.Cioloboc, A.B.Taylor, K.S.Schanze, D.M.Kurtz Jr.. Structure of A Zinc Porphyrin-Substituted Bacterioferritin and Photophysical Properties of Iron Reduction. Biochemistry V. 59 1618 2020.
ISSN: ISSN 0006-2960
PubMed: 32283930
DOI: 10.1021/ACS.BIOCHEM.9B01103
Page generated: Mon Aug 18 06:34:06 2025

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