Sodium in PDB 6p8l: Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX (Zn Absorption Edge X-Ray Data)

Enzymatic activity of Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX (Zn Absorption Edge X-Ray Data)

All present enzymatic activity of Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX (Zn Absorption Edge X-Ray Data):
1.16.3.1;

Protein crystallography data

The structure of Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX (Zn Absorption Edge X-Ray Data), PDB code: 6p8l 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) 92.65 / 2.10
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 207.918, 207.918, 143.046, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 24

Other elements in 6p8l:

The structure of Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX (Zn Absorption Edge X-Ray Data) 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 (Zn Absorption Edge X-Ray Data) (pdb code 6p8l). 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 (Zn Absorption Edge X-Ray Data), PDB code: 6p8l:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6p8l

Go back to Sodium Binding Sites List in 6p8l
Sodium binding site 1 out of 4 in the Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX (Zn Absorption Edge X-Ray Data)


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 (Zn Absorption Edge X-Ray Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:48.2
occ:0.50
 OD1 C:ASN148 2.5 43.0 1.0
OD1 A:ASN148 2.5 49.5 1.0
O C:HOH331 2.7 47.3 0.5
CG C:ASN148 3.4 38.2 1.0
CG A:ASN148 3.4 45.7 1.0
ND2 C:ASN148 3.5 44.5 1.0
O C:HOH391 3.7 51.0 1.0
ND2 A:ASN148 3.7 42.6 1.0
O A:HOH388 3.9 45.9 1.0
NE2 A:GLN151 4.6 34.6 1.0
OE1 C:GLN151 4.7 38.1 1.0
CB C:ASN148 4.8 27.0 1.0
CB A:ASN148 4.8 36.4 1.0

Sodium binding site 2 out of 4 in 6p8l

Go back to Sodium Binding Sites List in 6p8l
Sodium binding site 2 out of 4 in the Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX (Zn Absorption Edge X-Ray Data)


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 (Zn Absorption Edge X-Ray Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:41.0
occ:1.00
 O G:HOH410 2.2 41.3 1.0
OD1 B:ASN148 2.4 43.1 1.0
O K:HOH340 2.4 45.9 1.0
OD1 J:ASN148 2.4 36.2 1.0
OD1 G:ASN148 2.5 39.2 1.0
OD1 K:ASN148 2.6 44.9 1.0
CG J:ASN148 3.3 41.6 1.0
CG B:ASN148 3.4 42.1 1.0
CG G:ASN148 3.5 45.3 1.0
ND2 J:ASN148 3.5 37.2 1.0
CG K:ASN148 3.5 36.8 1.0
ND2 B:ASN148 3.7 36.6 1.0
ND2 K:ASN148 3.7 38.6 1.0
ND2 G:ASN148 3.8 38.4 1.0
O B:HOH413 3.8 43.4 1.0
O B:HOH407 3.8 46.5 1.0
OE1 B:GLN151 4.4 38.5 1.0
OE1 G:GLN151 4.5 41.6 1.0
NE2 K:GLN151 4.5 41.3 1.0
NE2 J:GLN151 4.5 43.8 1.0
CB J:ASN148 4.7 30.6 1.0
CB B:ASN148 4.7 31.5 1.0
CB G:ASN148 4.8 32.4 1.0
CB K:ASN148 4.9 33.3 1.0

Sodium binding site 3 out of 4 in 6p8l

Go back to Sodium Binding Sites List in 6p8l
Sodium binding site 3 out of 4 in the Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX (Zn Absorption Edge X-Ray Data)


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 (Zn Absorption Edge X-Ray Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na203

b:48.1
occ:1.00
 O H:HOH412 2.3 42.5 1.0
OD1 D:ASN148 2.4 36.1 1.0
OD1 H:ASN148 2.4 36.1 1.0
CG H:ASN148 3.3 39.0 1.0
CG D:ASN148 3.3 35.7 1.0
ND2 H:ASN148 3.6 45.2 1.0
ND2 D:ASN148 3.6 41.6 1.0
O H:HOH407 3.9 47.3 1.0
O D:HOH392 4.0 44.6 1.0
NE2 D:GLN151 4.5 43.3 1.0
OE1 H:GLN151 4.6 46.1 1.0
CB H:ASN148 4.7 33.8 1.0
CB D:ASN148 4.7 36.8 1.0

Sodium binding site 4 out of 4 in 6p8l

Go back to Sodium Binding Sites List in 6p8l
Sodium binding site 4 out of 4 in the Escherichia Coli Bacterioferritin Substituted with Zinc Protoporphyrin IX (Zn Absorption Edge X-Ray Data)


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 (Zn Absorption Edge X-Ray Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na203

b:40.5
occ:0.50
 O F:HOH417 2.4 40.5 0.5
OD1 L:ASN148 2.5 44.5 1.0
OD1 F:ASN148 2.5 41.9 1.0
CG L:ASN148 3.4 38.8 1.0
CG F:ASN148 3.5 41.0 1.0
ND2 L:ASN148 3.6 37.4 1.0
ND2 F:ASN148 3.7 37.5 1.0
O L:HOH389 4.1 42.5 1.0
OE1 L:GLN151 4.5 56.8 1.0
OE1 F:GLN151 4.7 44.2 1.0
CB L:ASN148 4.8 37.1 1.0
CB F:ASN148 4.8 34.5 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: Tue Dec 15 12:44:37 2020

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