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Iron in PDB 2wtl: Crystal Structure of Bfra From M. Tuberculosis

Protein crystallography data

The structure of Crystal Structure of Bfra From M. Tuberculosis, PDB code: 2wtl was solved by V.Gupta, R.K.Gupta, G.Khare, D.M.Salunke, A.K.Tyagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.05 / 2.59
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 125.960, 125.960, 175.840, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.8

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Bfra From M. Tuberculosis (pdb code 2wtl). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of Bfra From M. Tuberculosis, PDB code: 2wtl:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 2wtl

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Iron binding site 1 out of 12 in the Crystal Structure of Bfra From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Bfra From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:33.6
occ:0.30
 OE1 A:GLU51 2.3 29.3 1.0
OE2 A:GLU127 2.4 33.8 1.0
OE2 A:GLU18 2.6 28.2 1.0
OE1 A:GLU18 3.0 29.2 1.0
CD A:GLU127 3.1 33.7 1.0
CD A:GLU51 3.1 32.8 1.0
CD A:GLU18 3.2 27.8 1.0
OE2 A:GLU51 3.2 35.9 1.0
ND1 A:HIS54 3.3 30.2 1.0
OE1 A:GLU127 3.7 34.4 1.0
CG A:GLU127 3.9 30.6 1.0
CG2 A:ILE123 4.0 25.9 1.0
CE1 A:HIS54 4.1 30.5 1.0
NE2 A:GLN14 4.1 28.7 1.0
CG A:HIS54 4.3 30.4 1.0
CG A:GLU51 4.5 29.4 1.0
CB A:HIS54 4.5 28.1 1.0
CG A:GLU18 4.7 26.7 1.0
CG2 A:VAL97 4.8 29.1 1.0
O A:HOH2023 4.8 35.0 1.0
CG1 A:VAL97 4.9 28.3 1.0
FE A:FE202 4.9 34.2 0.3

Iron binding site 2 out of 12 in 2wtl

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Iron binding site 2 out of 12 in the Crystal Structure of Bfra From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Bfra From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:34.2
occ:0.30
 OE2 A:GLU51 2.4 35.9 1.0
O A:HOH2008 2.5 36.3 1.0
OE2 A:GLU94 2.5 35.8 1.0
OE1 A:GLU127 2.5 34.4 1.0
O A:HOH2023 2.7 35.0 1.0
ND1 A:HIS130 2.9 32.3 1.0
CD A:GLU94 3.4 33.8 1.0
CG A:HIS130 3.5 31.7 1.0
CD A:GLU127 3.6 33.7 1.0
CD A:GLU51 3.6 32.8 1.0
CB A:HIS130 3.7 29.3 1.0
CE1 A:HIS130 3.7 31.6 1.0
OE1 A:GLU94 3.7 34.8 1.0
CE2 A:TYR25 3.9 30.5 1.0
OE2 A:GLU127 3.9 33.8 1.0
OH A:TYR25 4.2 31.1 1.0
CG A:GLU51 4.3 29.4 1.0
CD2 A:HIS130 4.4 30.7 1.0
O A:HOH2007 4.4 38.8 1.0
CZ A:TYR25 4.5 30.2 1.0
OE1 A:GLU51 4.5 29.3 1.0
NE2 A:HIS130 4.5 30.7 1.0
OE1 A:GLU47 4.6 35.6 1.0
CG A:GLU94 4.6 30.9 1.0
CD2 A:TYR25 4.8 29.1 1.0
CG A:GLU127 4.9 30.6 1.0
CA A:GLU127 4.9 29.2 1.0
FE A:FE201 4.9 33.6 0.3

Iron binding site 3 out of 12 in 2wtl

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Iron binding site 3 out of 12 in the Crystal Structure of Bfra From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Bfra From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:34.0
occ:0.30
 OE1 B:GLU51 2.4 32.1 1.0
OE2 B:GLU127 2.5 36.0 1.0
OE2 B:GLU18 2.7 31.0 1.0
O B:HOH2007 2.9 31.3 1.0
OE1 B:GLU18 3.0 31.6 1.0
CD B:GLU18 3.2 30.3 1.0
CD B:GLU127 3.2 34.7 1.0
CD B:GLU51 3.4 33.4 1.0
OE2 B:GLU51 3.7 35.7 1.0
ND1 B:HIS54 3.7 32.8 1.0
OE1 B:GLU127 3.8 34.0 1.0
CG B:GLU127 3.8 31.1 1.0
NE2 B:GLN14 3.9 28.4 1.0
CG2 B:ILE123 4.1 27.5 1.0
CE1 B:HIS54 4.4 31.9 1.0
CG B:GLU18 4.6 27.6 1.0
CG B:HIS54 4.6 32.8 1.0
CG2 B:VAL97 4.6 29.9 1.0
CG B:GLU51 4.6 30.8 1.0
OE1 B:GLU94 4.7 35.8 1.0
CG1 B:VAL97 4.7 29.1 1.0
CB B:HIS54 4.8 30.3 1.0
FE B:FE202 4.9 35.9 0.3

Iron binding site 4 out of 12 in 2wtl

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Iron binding site 4 out of 12 in the Crystal Structure of Bfra From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Bfra From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:35.9
occ:0.30
 OE1 B:GLU127 2.4 34.0 1.0
OE2 B:GLU51 2.4 35.7 1.0
OE2 B:GLU94 2.4 33.5 1.0
ND1 B:HIS130 3.1 31.1 1.0
CD B:GLU127 3.3 34.7 1.0
OE2 B:GLU127 3.4 36.0 1.0
CD B:GLU94 3.5 33.2 1.0
CD B:GLU51 3.5 33.4 1.0
CG B:HIS130 3.6 29.9 1.0
CB B:HIS130 3.7 28.8 1.0
OE1 B:GLU94 3.9 35.8 1.0
CE1 B:HIS130 3.9 32.0 1.0
CE2 B:TYR25 4.1 28.6 1.0
OE1 B:GLU47 4.2 37.3 1.0
CG B:GLU51 4.3 30.8 1.0
OE1 B:GLU51 4.3 32.1 1.0
OH B:TYR25 4.4 31.9 1.0
CD2 B:HIS130 4.5 30.2 1.0
O B:HOH2013 4.6 43.4 1.0
NE2 B:HIS130 4.7 29.6 1.0
CG B:GLU127 4.7 31.1 1.0
CG B:GLU94 4.7 31.3 1.0
CZ B:TYR25 4.7 29.4 1.0
CA B:GLU127 4.8 29.0 1.0
FE B:FE201 4.9 34.0 0.3

Iron binding site 5 out of 12 in 2wtl

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Iron binding site 5 out of 12 in the Crystal Structure of Bfra From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Bfra From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:35.6
occ:0.30
 OE1 C:GLU51 2.3 32.7 1.0
OE1 C:GLU127 2.4 40.2 1.0
OE2 C:GLU18 2.7 30.3 1.0
CD C:GLU127 3.0 37.2 1.0
ND1 C:HIS54 3.0 33.0 1.0
OE1 C:GLU18 3.0 31.9 1.0
CD C:GLU51 3.1 34.8 1.0
OE2 C:GLU51 3.2 36.0 1.0
CD C:GLU18 3.2 30.2 1.0
OE2 C:GLU127 3.3 36.2 1.0
CE1 C:HIS54 3.7 33.6 1.0
CG2 C:ILE123 3.9 28.4 1.0
CG C:HIS54 4.0 32.0 1.0
CG C:GLU127 4.0 32.5 1.0
NE2 C:GLN14 4.3 30.9 1.0
CB C:HIS54 4.3 31.8 1.0
CG C:GLU51 4.6 33.3 1.0
FE C:FE202 4.7 48.1 0.5
CG C:GLU18 4.8 28.5 1.0
NE2 C:HIS54 4.8 33.5 1.0

Iron binding site 6 out of 12 in 2wtl

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Iron binding site 6 out of 12 in the Crystal Structure of Bfra From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Bfra From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:48.1
occ:0.50
 O C:HOH2015 2.6 38.0 1.0
OE2 C:GLU127 2.9 36.2 1.0
OE2 C:GLU51 3.0 36.0 1.0
O C:HOH2006 3.0 43.4 1.0
OD2 C:ASP50 3.5 45.2 1.0
CE1 C:HIS54 3.8 33.6 1.0
CD C:GLU51 3.9 34.8 1.0
OE1 C:GLU47 3.9 38.3 1.0
CD C:GLU127 4.1 37.2 1.0
CB C:ASP126 4.3 31.8 1.0
ND1 C:HIS54 4.3 33.0 1.0
CG C:ASP50 4.4 43.3 1.0
OE1 C:GLU51 4.5 32.7 1.0
CB C:ASP50 4.5 36.4 1.0
O C:ASP126 4.5 32.2 1.0
C C:ASP126 4.6 31.5 1.0
FE C:FE201 4.7 35.6 0.3
CB C:HIS130 4.7 30.8 1.0
CG C:GLU51 4.8 33.3 1.0
OE1 C:GLU127 4.8 40.2 1.0
N C:GLU127 4.8 30.8 1.0
NE2 C:HIS54 4.8 33.5 1.0
OE2 C:GLU94 4.9 38.2 1.0
CA C:GLU127 4.9 30.9 1.0

Iron binding site 7 out of 12 in 2wtl

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Iron binding site 7 out of 12 in the Crystal Structure of Bfra From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Bfra From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:36.1
occ:0.30
 OE1 D:GLU51 2.3 35.1 1.0
OE1 D:GLU127 2.4 40.0 1.0
OE2 D:GLU18 2.8 33.4 1.0
OE1 D:GLU18 2.8 33.1 1.0
CD D:GLU127 3.0 36.7 1.0
ND1 D:HIS54 3.0 33.6 1.0
O D:HOH2017 3.0 37.0 1.0
CD D:GLU51 3.1 35.6 1.0
OE2 D:GLU51 3.1 38.5 1.0
CD D:GLU18 3.2 33.3 1.0
OE2 D:GLU127 3.3 36.3 1.0
CE1 D:HIS54 3.7 34.5 1.0
CG2 D:ILE123 3.8 29.7 1.0
CG D:HIS54 4.0 33.9 1.0
CG D:GLU127 4.1 31.7 1.0
CB D:HIS54 4.4 32.6 1.0
NE2 D:GLN14 4.4 31.4 1.0
CG D:GLU51 4.5 32.4 1.0
CG D:GLU18 4.7 31.2 1.0
FE D:FE202 4.8 47.0 0.5
NE2 D:HIS54 4.9 34.4 1.0

Iron binding site 8 out of 12 in 2wtl

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Iron binding site 8 out of 12 in the Crystal Structure of Bfra From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Bfra From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:47.0
occ:0.50
 OE2 D:GLU51 2.3 38.5 1.0
O D:HOH2004 2.8 42.0 1.0
OE2 D:GLU94 3.0 37.5 1.0
OE2 D:GLU127 3.0 36.3 1.0
OE1 D:GLU47 3.3 37.1 1.0
ND1 D:HIS130 3.3 32.2 1.0
CD D:GLU51 3.5 35.6 1.0
CG D:HIS130 3.7 31.8 1.0
CB D:HIS130 3.9 30.0 1.0
CE1 D:HIS130 4.0 32.2 1.0
CD D:GLU94 4.1 35.9 1.0
CG D:GLU51 4.1 32.4 1.0
CD D:GLU127 4.1 36.7 1.0
CE2 D:TYR25 4.3 30.4 1.0
OE1 D:GLU51 4.4 35.1 1.0
CD D:GLU47 4.5 35.8 1.0
OE1 D:GLU94 4.5 36.5 1.0
CD2 D:HIS130 4.5 30.6 1.0
OE1 D:GLU127 4.6 40.0 1.0
NE2 D:HIS130 4.7 30.4 1.0
O D:GLU47 4.7 32.4 1.0
FE D:FE201 4.8 36.1 0.3
OH D:TYR25 4.8 32.2 1.0

Iron binding site 9 out of 12 in 2wtl

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Iron binding site 9 out of 12 in the Crystal Structure of Bfra From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Bfra From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:34.0
occ:0.30
 OE1 E:GLU51 2.6 32.5 1.0
OE2 E:GLU127 2.6 35.5 1.0
OE2 E:GLU18 2.8 30.9 1.0
O E:HOH2011 2.8 36.4 1.0
CD E:GLU127 2.9 34.3 1.0
O E:HOH2003 3.0 33.9 1.0
OE1 E:GLU127 3.3 36.0 1.0
OE1 E:GLU18 3.4 32.2 1.0
CD E:GLU18 3.4 31.5 1.0
CD E:GLU51 3.4 34.7 1.0
OE2 E:GLU51 3.6 37.2 1.0
CG E:GLU127 3.6 30.6 1.0
ND1 E:HIS54 3.6 33.6 1.0
CG2 E:ILE123 3.9 28.1 1.0
NE2 E:GLN14 4.0 28.5 1.0
CE1 E:HIS54 4.2 32.5 1.0
CG2 E:VAL97 4.4 31.8 1.0
CG1 E:VAL97 4.5 28.5 1.0
FE E:FE202 4.5 42.9 0.5
OE1 E:GLU94 4.6 35.8 1.0
CG E:HIS54 4.7 33.3 1.0
CG E:GLU51 4.8 33.2 1.0
CG E:GLU18 4.9 29.6 1.0
CB E:VAL97 5.0 32.1 1.0

Iron binding site 10 out of 12 in 2wtl

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Iron binding site 10 out of 12 in the Crystal Structure of Bfra From M. Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Bfra From M. Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe202

b:42.9
occ:0.50
 OE2 E:GLU51 2.4 37.2 1.0
OE2 E:GLU94 2.4 37.2 1.0
OE1 E:GLU127 2.6 36.0 1.0
ND1 E:HIS130 3.1 31.9 1.0
CD E:GLU127 3.3 34.3 1.0
O E:HOH2011 3.4 36.4 1.0
OE2 E:GLU127 3.4 35.5 1.0
CD E:GLU94 3.4 35.7 1.0
CD E:GLU51 3.5 34.7 1.0
CG E:HIS130 3.7 32.2 1.0
OE1 E:GLU94 3.7 35.8 1.0
CB E:HIS130 3.8 29.6 1.0
CE1 E:HIS130 3.9 32.1 1.0
OH E:TYR25 4.1 34.7 1.0
CE2 E:TYR25 4.1 30.8 1.0
OE1 E:GLU51 4.3 32.5 1.0
CG E:GLU51 4.4 33.2 1.0
CZ E:TYR25 4.5 31.3 1.0
FE E:FE201 4.5 34.0 0.3
CD2 E:HIS130 4.7 31.2 1.0
OE1 E:GLU47 4.7 35.2 1.0
CG E:GLU127 4.7 30.6 1.0
CG E:GLU94 4.8 33.2 1.0
NE2 E:HIS130 4.8 31.2 1.0
CA E:GLU127 4.8 30.1 1.0

Reference:

V.Gupta, R.K.Gupta, G.Khare, D.M.Salunke, A.K.Tyagi. Crystal Structure of Bfra From Mycobacterium Tuberculosis:Incorporation of Selenomethionine Results in Cleavage and Demetallation of Haem Plos One V. 4 E8028 2009.
ISSN: ESSN 1932-6203
PubMed: 19946376
DOI: 10.1371/JOURNAL.PONE.0008028
Page generated: Sun Aug 4 04:08:57 2024

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