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Zinc 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:

Magnesium (Mg) 12 atoms
Iron (Fe) 12 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the The Structure of Mycobacterial Bacterioferritin (pdb code 3bkn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the The Structure of Mycobacterial Bacterioferritin, PDB code: 3bkn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in 3bkn

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Zinc binding site 1 out of 24 in the The Structure of Mycobacterial Bacterioferritin


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:40.0
occ:1.00
OE1 A:GLU51 2.0 51.7 1.0
OE1 A:GLU18 2.0 44.4 1.0
OE2 A:GLU127 2.0 50.7 1.0
ND1 A:HIS54 2.0 44.7 1.0
CD A:GLU18 2.7 45.8 1.0
CD A:GLU127 2.8 51.0 1.0
OE2 A:GLU18 2.9 47.9 1.0
CE1 A:HIS54 2.9 44.3 1.0
CD A:GLU51 3.0 50.0 1.0
CG A:HIS54 3.1 44.8 1.0
OE1 A:GLU127 3.2 52.1 1.0
OE2 A:GLU51 3.3 50.5 1.0
CB A:HIS54 3.5 43.8 1.0
ZN A:ZN202 3.9 53.4 1.0
NE2 A:HIS54 4.1 43.9 1.0
CG A:GLU127 4.1 48.6 1.0
CD2 A:HIS54 4.2 44.1 1.0
CG A:GLU18 4.2 44.1 1.0
CG A:GLU51 4.3 47.0 1.0
CG2 A:ILE123 4.4 42.8 1.0
CA A:GLU51 4.5 46.7 1.0
CB A:GLU51 4.7 44.8 1.0
CB A:GLU18 4.7 42.1 1.0
NE2 A:GLN14 4.9 43.0 1.0

Zinc binding site 2 out of 24 in 3bkn

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Zinc binding site 2 out of 24 in the The Structure of Mycobacterial Bacterioferritin


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:53.4
occ:1.00
OE1 A:GLU127 1.9 52.1 1.0
OE2 A:GLU94 2.0 52.7 1.0
OE2 A:GLU51 2.0 50.5 1.0
ND1 A:HIS130 2.1 65.7 1.0
CE1 A:HIS130 2.7 66.3 1.0
CD A:GLU94 2.8 51.9 1.0
OE1 A:GLU94 2.9 53.8 1.0
CD A:GLU127 2.9 51.0 1.0
CD A:GLU51 3.2 50.0 1.0
CG A:HIS130 3.3 61.9 1.0
OE2 A:GLU127 3.4 50.7 1.0
OE1 A:GLU51 3.7 51.7 1.0
ZN A:ZN201 3.9 40.0 1.0
CB A:HIS130 3.9 55.2 1.0
NE2 A:HIS130 3.9 66.8 1.0
OH A:TYR25 4.1 54.9 1.0
CG A:GLU127 4.1 48.6 1.0
CG A:GLU94 4.2 48.0 1.0
CB A:GLU127 4.2 48.0 1.0
CD2 A:HIS130 4.2 65.6 1.0
CA A:GLU127 4.3 48.8 1.0
CE2 A:TYR25 4.4 52.4 1.0
CG A:GLU51 4.4 47.0 1.0
CZ A:TYR25 4.7 54.1 1.0
CE1 A:HIS54 4.7 44.3 1.0
ND1 A:HIS54 4.9 44.7 1.0
N A:GLU127 4.9 48.9 1.0

Zinc binding site 3 out of 24 in 3bkn

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Zinc binding site 3 out of 24 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:41.9
occ:1.00
OE2 B:GLU127 1.8 53.3 1.0
OE1 B:GLU51 1.8 51.7 1.0
OE1 B:GLU18 2.1 47.2 1.0
ND1 B:HIS54 2.1 44.9 1.0
OE2 B:GLU18 2.6 47.8 1.0
CD B:GLU18 2.7 46.5 1.0
CD B:GLU127 2.9 51.4 1.0
CD B:GLU51 3.0 50.0 1.0
CE1 B:HIS54 3.1 44.2 1.0
CG B:HIS54 3.2 45.4 1.0
OE1 B:GLU127 3.3 51.9 1.0
OE2 B:GLU51 3.4 50.6 1.0
CB B:HIS54 3.5 44.7 1.0
CG2 B:ILE123 4.1 43.1 1.0
CG B:GLU18 4.1 44.2 1.0
ZN B:ZN202 4.1 53.3 1.0
CG B:GLU127 4.2 49.7 1.0
NE2 B:HIS54 4.2 44.5 1.0
CG B:GLU51 4.3 48.5 1.0
CD2 B:HIS54 4.3 43.2 1.0
CA B:GLU51 4.4 47.0 1.0
CB B:GLU51 4.5 46.1 1.0
CB B:GLU18 4.7 42.7 1.0
NE2 B:GLN14 4.8 43.9 1.0
CA B:HIS54 5.0 44.8 1.0

Zinc binding site 4 out of 24 in 3bkn

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Zinc binding site 4 out of 24 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:53.3
occ:1.00
OE2 B:GLU51 1.9 50.6 1.0
OE1 B:GLU127 2.0 51.9 1.0
ND1 B:HIS130 2.1 64.9 1.0
OE2 B:GLU94 2.2 54.6 1.0
CD B:GLU94 2.7 54.5 1.0
OE1 B:GLU94 2.7 57.2 1.0
CE1 B:HIS130 2.9 65.9 1.0
CD B:GLU127 3.0 51.4 1.0
CD B:GLU51 3.1 50.0 1.0
CG B:HIS130 3.3 61.9 1.0
OE2 B:GLU127 3.6 53.3 1.0
OE1 B:GLU51 3.6 51.7 1.0
CB B:HIS130 3.8 55.1 1.0
NE2 B:HIS130 4.1 65.1 1.0
CG B:GLU94 4.1 50.3 1.0
ZN B:ZN201 4.1 41.9 1.0
OH B:TYR25 4.1 54.1 1.0
CG B:GLU127 4.2 49.7 1.0
CG B:GLU51 4.2 48.5 1.0
CA B:GLU127 4.2 48.6 1.0
CB B:GLU127 4.3 48.1 1.0
CD2 B:HIS130 4.3 65.2 1.0
CE2 B:TYR25 4.3 52.2 1.0
CZ B:TYR25 4.7 53.8 1.0
N B:GLU127 4.9 48.8 1.0

Zinc binding site 5 out of 24 in 3bkn

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Zinc binding site 5 out of 24 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:44.9
occ:1.00
OE1 C:GLU51 1.8 51.6 1.0
ND1 C:HIS54 2.0 45.8 1.0
OE2 C:GLU127 2.0 53.1 1.0
OE1 C:GLU18 2.1 44.9 1.0
CD C:GLU18 2.8 46.2 1.0
OE2 C:GLU18 2.8 49.3 1.0
CE1 C:HIS54 2.9 45.2 1.0
CD C:GLU51 2.9 50.6 1.0
CD C:GLU127 2.9 52.6 1.0
CG C:HIS54 3.1 46.2 1.0
OE1 C:GLU127 3.2 55.0 1.0
OE2 C:GLU51 3.4 52.7 1.0
CB C:HIS54 3.6 45.9 1.0
NE2 C:HIS54 4.0 45.5 1.0
CG C:GLU127 4.1 49.5 1.0
ZN C:ZN202 4.1 49.7 1.0
CG C:GLU51 4.1 47.9 1.0
CD2 C:HIS54 4.2 44.4 1.0
CG2 C:ILE123 4.2 43.8 1.0
CG C:GLU18 4.2 44.6 1.0
CA C:GLU51 4.4 47.0 1.0
CB C:GLU51 4.5 47.1 1.0
NE2 C:GLN14 4.7 43.6 1.0
CB C:GLU18 4.8 43.8 1.0
O C:GLU50 5.0 50.4 1.0

Zinc binding site 6 out of 24 in 3bkn

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Zinc binding site 6 out of 24 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:49.7
occ:1.00
OE2 C:GLU51 2.0 52.7 1.0
OE1 C:GLU127 2.1 55.0 1.0
ND1 C:HIS130 2.2 65.1 1.0
OE2 C:GLU94 2.2 55.2 1.0
CD C:GLU94 2.7 53.6 1.0
OE1 C:GLU94 2.7 55.5 1.0
CD C:GLU127 2.9 52.6 1.0
CE1 C:HIS130 3.0 66.0 1.0
CD C:GLU51 3.1 50.6 1.0
CG C:HIS130 3.3 61.3 1.0
OE2 C:GLU127 3.3 53.1 1.0
OE1 C:GLU51 3.6 51.6 1.0
CB C:HIS130 3.7 54.7 1.0
OH C:TYR25 4.0 55.3 1.0
ZN C:ZN201 4.1 44.9 1.0
CG C:GLU94 4.1 50.3 1.0
NE2 C:HIS130 4.2 65.8 1.0
CG C:GLU127 4.2 49.5 1.0
CA C:GLU127 4.2 48.9 1.0
CB C:GLU127 4.3 48.6 1.0
CD2 C:HIS130 4.3 64.4 1.0
CG C:GLU51 4.3 47.9 1.0
CE2 C:TYR25 4.4 52.8 1.0
CZ C:TYR25 4.6 54.8 1.0
N C:GLU127 4.9 48.7 1.0

Zinc binding site 7 out of 24 in 3bkn

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Zinc binding site 7 out of 24 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:39.1
occ:1.00
OE1 D:GLU51 1.9 50.7 1.0
OE1 D:GLU18 1.9 46.2 1.0
OE2 D:GLU127 2.0 50.8 1.0
ND1 D:HIS54 2.1 44.9 1.0
OE2 D:GLU18 2.5 47.5 1.0
CD D:GLU18 2.5 45.8 1.0
CD D:GLU127 3.0 50.2 1.0
CE1 D:HIS54 3.0 43.6 1.0
CD D:GLU51 3.0 49.6 1.0
CG D:HIS54 3.2 44.6 1.0
OE1 D:GLU127 3.5 48.7 1.0
CB D:HIS54 3.5 43.8 1.0
OE2 D:GLU51 3.5 48.8 1.0
ZN D:ZN202 4.0 48.5 1.0
CG D:GLU18 4.0 44.2 1.0
NE2 D:HIS54 4.1 43.5 1.0
CG D:GLU127 4.2 50.0 1.0
CG2 D:ILE123 4.2 42.5 1.0
CD2 D:HIS54 4.2 42.3 1.0
CG D:GLU51 4.3 48.9 1.0
CA D:GLU51 4.4 46.9 1.0
CB D:GLU51 4.5 46.9 1.0
CB D:GLU18 4.7 42.8 1.0
NE2 D:GLN14 4.9 43.0 1.0

Zinc binding site 8 out of 24 in 3bkn

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Zinc binding site 8 out of 24 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:48.5
occ:1.00
OE1 D:GLU127 1.8 48.7 1.0
OE2 D:GLU51 2.0 48.8 1.0
OE2 D:GLU94 2.0 53.9 1.0
ND1 D:HIS130 2.2 63.7 1.0
OE1 D:GLU94 2.5 55.4 1.0
CD D:GLU94 2.6 52.6 1.0
CE1 D:HIS130 2.9 64.7 1.0
CD D:GLU127 3.0 50.2 1.0
CD D:GLU51 3.1 49.6 1.0
CG D:HIS130 3.3 59.5 1.0
OE2 D:GLU127 3.4 50.8 1.0
OE1 D:GLU51 3.5 50.7 1.0
CB D:HIS130 3.8 53.8 1.0
ZN D:ZN201 4.0 39.1 1.0
NE2 D:HIS130 4.1 64.0 1.0
CG D:GLU94 4.1 48.7 1.0
OH D:TYR25 4.2 52.0 1.0
CG D:GLU127 4.2 50.0 1.0
CA D:GLU127 4.2 48.8 1.0
CD2 D:HIS130 4.3 62.3 1.0
CE2 D:TYR25 4.4 51.9 1.0
CB D:GLU127 4.4 48.3 1.0
CG D:GLU51 4.4 48.9 1.0
CZ D:TYR25 4.7 52.5 1.0
CE1 D:HIS54 4.9 43.6 1.0
O D:ASP126 5.0 50.6 1.0

Zinc binding site 9 out of 24 in 3bkn

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Zinc binding site 9 out of 24 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:44.6
occ:1.00
OE2 E:GLU127 1.9 50.1 1.0
OE1 E:GLU51 2.0 51.1 1.0
ND1 E:HIS54 2.1 46.4 1.0
OE1 E:GLU18 2.1 43.2 1.0
OE2 E:GLU18 2.6 44.4 1.0
CD E:GLU18 2.7 43.1 1.0
CD E:GLU127 2.9 50.7 1.0
CD E:GLU51 2.9 50.5 1.0
CE1 E:HIS54 3.0 46.4 1.0
OE2 E:GLU51 3.1 51.7 1.0
CG E:HIS54 3.1 45.5 1.0
OE1 E:GLU127 3.4 52.4 1.0
CB E:HIS54 3.5 44.5 1.0
ZN E:ZN202 4.0 55.5 1.0
CG E:GLU127 4.1 49.2 1.0
NE2 E:HIS54 4.1 46.5 1.0
CG E:GLU18 4.2 42.7 1.0
CD2 E:HIS54 4.2 45.7 1.0
CG2 E:ILE123 4.3 43.8 1.0
CG E:GLU51 4.3 48.6 1.0
CA E:GLU51 4.5 47.1 1.0
NE2 E:GLN14 4.6 43.3 1.0
CB E:GLU51 4.7 48.0 1.0
CB E:GLU18 4.9 42.1 1.0
OE1 E:GLU94 4.9 53.4 1.0

Zinc binding site 10 out of 24 in 3bkn

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Zinc binding site 10 out of 24 in the The Structure of Mycobacterial Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Structure of Mycobacterial Bacterioferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn202

b:55.5
occ:1.00
OE2 E:GLU94 1.8 54.3 1.0
OE1 E:GLU127 1.8 52.4 1.0
OE2 E:GLU51 1.9 51.7 1.0
ND1 E:HIS130 2.2 65.4 1.0
CD E:GLU94 2.7 52.3 1.0
CD E:GLU127 2.9 50.7 1.0
OE1 E:GLU94 2.9 53.4 1.0
CE1 E:HIS130 2.9 67.2 1.0
CD E:GLU51 3.1 50.5 1.0
OE2 E:GLU127 3.3 50.1 1.0
CG E:HIS130 3.4 61.5 1.0
OE1 E:GLU51 3.8 51.1 1.0
CB E:HIS130 3.9 55.1 1.0
ZN E:ZN201 4.0 44.6 1.0
CG E:GLU94 4.1 49.4 1.0
CG E:GLU127 4.1 49.2 1.0
CG E:GLU51 4.1 48.6 1.0
NE2 E:HIS130 4.1 67.1 1.0
OH E:TYR25 4.3 53.9 1.0
CE2 E:TYR25 4.3 53.2 1.0
CA E:GLU127 4.3 48.7 1.0
CB E:GLU127 4.4 48.0 1.0
CD2 E:HIS130 4.4 65.1 1.0
CZ E:TYR25 4.7 54.3 1.0
CE1 E:HIS54 4.8 46.4 1.0
N E:GLU127 4.9 48.9 1.0
ND1 E:HIS54 4.9 46.4 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: Wed Dec 16 04:09:05 2020

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