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Magnesium in PDB 3bkn: The Structure of Mycobacterial Bacterioferritin

Protein crystallography data

The structure of The Structure of Mycobacterial Bacterioferritin, PDB code: 3bkn was solved by R.Janowski, T.Auerbach-Nevo, M.S.Weiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.64 / 2.72
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 181.523, 151.520, 116.715, 90.00, 128.08, 90.00
R / Rfree (%) 17.9 / 22.8

Other elements in 3bkn:

The structure of The Structure of Mycobacterial Bacterioferritin also contains other interesting chemical elements:

Iron (Fe) 12 atoms
Zinc (Zn) 24 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the The Structure of Mycobacterial Bacterioferritin (pdb code 3bkn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the The Structure of Mycobacterial Bacterioferritin, PDB code: 3bkn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 3bkn

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Magnesium binding site 1 out of 12 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:51.5
occ:1.00
OD1 A:ASP66 3.3 57.2 1.0
OD1 B:ASN34 3.7 59.4 1.0
OD1 K:ASP132 3.8 56.3 1.0
O A:LEU63 4.2 44.5 1.0
CG A:ASP66 4.4 53.9 1.0
NE2 K:GLN139 4.5 54.0 1.0
OE1 K:GLN139 4.6 55.6 1.0
O A:LEU64 4.6 47.3 1.0
OE1 K:GLU135 4.6 55.8 1.0
OG1 K:THR136 4.6 43.2 1.0
O B:ASN34 4.7 51.8 1.0
CG B:ASN34 4.8 57.4 1.0
OD2 A:ASP66 4.9 56.8 1.0
N A:MET1 5.0 60.8 1.0
CA A:LEU64 5.0 45.3 1.0
CG K:ASP132 5.0 53.4 1.0

Magnesium binding site 2 out of 12 in 3bkn

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Magnesium binding site 2 out of 12 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:58.0
occ:1.00
NE2 B:GLN139 4.1 53.2 1.0
OD1 B:ASP132 4.1 54.9 1.0
OE1 B:GLU135 4.9 53.5 1.0
OE1 B:GLN139 4.9 55.6 1.0
OG1 B:THR136 4.9 44.9 1.0
CD B:GLN139 5.0 54.0 1.0

Magnesium binding site 3 out of 12 in 3bkn

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Magnesium binding site 3 out of 12 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:50.1
occ:1.00
OD1 B:ASP66 3.6 54.3 1.0
OE1 G:GLN139 4.0 53.8 1.0
OD1 G:ASP132 4.1 54.9 1.0
OD1 A:ASN34 4.2 61.2 1.0
OG1 G:THR136 4.5 45.8 1.0
O A:ASN34 4.6 51.8 1.0
O B:LEU63 4.7 44.6 1.0
CG B:ASP66 4.8 53.0 1.0
OE1 G:GLU135 4.8 52.1 1.0
O B:LEU64 4.9 47.1 1.0
N B:MET1 4.9 60.8 1.0
CB G:GLU135 4.9 46.2 1.0

Magnesium binding site 4 out of 12 in 3bkn

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Magnesium binding site 4 out of 12 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:57.9
occ:1.00
OD1 C:ASN34 3.3 62.4 1.0
OD1 D:ASP66 3.6 57.2 1.0
OD1 A:ASP132 3.9 57.6 1.0
O C:ASN34 4.4 51.7 1.0
CG C:ASN34 4.4 59.5 1.0
NE2 A:GLN139 4.4 53.1 1.0
OE1 A:GLN139 4.4 55.7 1.0
OG1 A:THR136 4.6 43.5 1.0
O D:LEU63 4.6 44.6 1.0
CG D:ASP66 4.8 54.2 1.0
OE1 A:GLU135 4.8 54.2 1.0
CD A:GLN139 4.8 53.5 1.0
O D:LEU64 5.0 47.1 1.0

Magnesium binding site 5 out of 12 in 3bkn

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Magnesium binding site 5 out of 12 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:55.3
occ:1.00
OD1 C:ASP66 3.1 54.1 1.0
OD1 D:ASN34 3.6 60.1 1.0
OD1 F:ASP132 3.7 55.6 1.0
OE1 F:GLN139 4.2 54.6 1.0
CG C:ASP66 4.4 53.5 1.0
OG1 F:THR136 4.4 45.5 1.0
O C:LEU63 4.4 44.5 1.0
NE2 F:GLN139 4.6 55.7 1.0
O D:ASN34 4.7 51.5 1.0
O C:LEU64 4.8 47.2 1.0
CG D:ASN34 4.8 58.4 1.0
CD F:GLN139 4.9 54.1 1.0
OD2 C:ASP66 4.9 56.9 1.0
CG F:ASP132 4.9 53.2 1.0
N C:MET1 4.9 60.8 1.0
OE1 F:GLU135 4.9 54.0 1.0

Magnesium binding site 6 out of 12 in 3bkn

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Magnesium binding site 6 out of 12 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:60.7
occ:1.00
OD1 E:ASP132 3.5 56.6 1.0
OE1 E:GLN139 4.4 56.5 1.0
OG1 E:THR136 4.4 44.1 1.0
CG E:ASP132 4.8 54.5 1.0
OE1 E:GLU135 4.9 53.0 1.0

Magnesium binding site 7 out of 12 in 3bkn

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Magnesium binding site 7 out of 12 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:46.8
occ:1.00
OD1 E:ASN34 3.6 61.0 1.0
OD1 J:ASP132 3.6 55.7 1.0
OD1 F:ASP66 3.9 55.2 1.0
OE1 J:GLN139 4.1 54.6 1.0
OE1 J:GLU135 4.4 53.9 1.0
OG1 J:THR136 4.5 44.7 1.0
O E:ASN34 4.5 51.7 1.0
O F:LEU63 4.5 44.5 1.0
O F:LEU64 4.7 47.2 1.0
CG E:ASN34 4.7 58.2 1.0
CG J:ASP132 4.9 53.7 1.0
N F:MET1 4.9 60.9 1.0
CG F:ASP66 4.9 52.9 1.0

Magnesium binding site 8 out of 12 in 3bkn

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Magnesium binding site 8 out of 12 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg401

b:47.5
occ:1.00
OD1 H:ASP66 3.3 54.8 1.0
OD1 G:ASN34 3.8 60.6 1.0
OE1 I:GLN139 4.1 53.9 1.0
O H:LEU63 4.3 44.5 1.0
OD1 I:ASP132 4.3 55.8 1.0
OE1 I:GLU135 4.5 53.8 1.0
CG H:ASP66 4.5 53.5 1.0
O G:ASN34 4.7 51.3 1.0
O H:LEU64 4.7 47.4 1.0
OG1 I:THR136 4.9 44.0 1.0
CG G:ASN34 4.9 58.3 1.0
N H:MET1 5.0 60.9 1.0

Magnesium binding site 9 out of 12 in 3bkn

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Magnesium binding site 9 out of 12 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg401

b:51.2
occ:1.00
OD1 I:ASP66 2.9 54.5 1.0
OD1 L:ASP132 3.7 56.2 1.0
CG I:ASP66 4.0 53.7 1.0
OD1 J:ASN34 4.1 58.1 1.0
OD2 I:ASP66 4.2 56.5 1.0
OE1 L:GLN139 4.4 56.5 1.0
O I:LEU63 4.4 44.4 1.0
OE1 L:GLU135 4.5 54.1 1.0
NE2 L:GLN139 4.7 55.7 1.0
OG1 L:THR136 4.7 46.4 1.0
ND2 J:ASN34 4.7 58.2 1.0
CG J:ASN34 4.7 56.8 1.0
N I:MET1 4.8 60.9 1.0
O I:LEU64 4.8 47.5 1.0
CG L:ASP132 4.9 54.2 1.0
O J:ASN34 4.9 51.7 1.0
CD L:GLN139 5.0 54.7 1.0

Magnesium binding site 10 out of 12 in 3bkn

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Magnesium binding site 10 out of 12 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg401

b:57.1
occ:1.00
OD1 J:ASP66 3.5 55.5 1.0
OD1 I:ASN34 3.5 61.5 1.0
OD1 C:ASP132 3.7 57.5 1.0
O J:LEU63 4.4 44.6 1.0
O I:ASN34 4.5 51.6 1.0
OG1 C:THR136 4.5 43.3 1.0
OE1 C:GLN139 4.5 55.3 1.0
OE1 C:GLU135 4.6 54.1 1.0
O J:LEU64 4.6 47.1 1.0
CG J:ASP66 4.7 53.6 1.0
CG I:ASN34 4.7 58.8 1.0
CG C:ASP132 4.9 54.9 1.0

Reference:

R.Janowski, T.Auerbach-Nevo, M.S.Weiss. Bacterioferritin From Mycobacterium Smegmatis Contains Zinc in Its Di-Nuclear Site. Protein Sci. V. 17 1138 2008.
ISSN: ISSN 0961-8368
PubMed: 18445621
DOI: 10.1110/PS.034819.108
Page generated: Mon Dec 14 07:55:59 2020

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