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Iron in PDB 1ngk: Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O

Protein crystallography data

The structure of Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O, PDB code: 1ngk was solved by M.Milani, P.-Y.Savard, H.Oullet, P.Ascenzi, M.Guertin, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.11
Space group I 41 2 2 1
Cell size a, b, c (Å), α, β, γ (°) 187.034, 187.034, 274.861, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.6

Iron Binding Sites:

Pages:

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

Binding sites:

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

Iron binding site 1 out of 12 in 1ngk

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Iron binding site 1 out of 12 in the Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe700

b:14.5
occ:1.00
FE A:HEM700 0.0 14.5 1.0
C A:CYN800 1.8 14.5 1.0
NC A:HEM700 2.0 13.3 1.0
NE2 A:HIS75 2.0 12.5 1.0
NA A:HEM700 2.0 14.3 1.0
NB A:HEM700 2.0 14.4 1.0
ND A:HEM700 2.1 14.0 1.0
N A:CYN800 3.0 11.3 1.0
CE1 A:HIS75 3.0 13.6 1.0
C4D A:HEM700 3.0 15.0 1.0
C1A A:HEM700 3.0 14.2 1.0
C4B A:HEM700 3.0 14.1 1.0
C1C A:HEM700 3.1 15.2 1.0
C4C A:HEM700 3.1 13.9 1.0
CD2 A:HIS75 3.1 13.0 1.0
C1B A:HEM700 3.1 13.8 1.0
C4A A:HEM700 3.1 15.6 1.0
C1D A:HEM700 3.1 11.6 1.0
CHA A:HEM700 3.4 13.3 1.0
CHC A:HEM700 3.4 14.7 1.0
CHD A:HEM700 3.5 13.2 1.0
CHB A:HEM700 3.5 14.5 1.0
ND1 A:HIS75 4.1 12.1 1.0
CG A:HIS75 4.2 14.4 1.0
C3C A:HEM700 4.3 13.8 1.0
C2C A:HEM700 4.3 13.7 1.0
C3B A:HEM700 4.3 13.5 1.0
C2A A:HEM700 4.3 13.4 1.0
C3D A:HEM700 4.3 13.8 1.0
C2B A:HEM700 4.3 15.0 1.0
C3A A:HEM700 4.3 14.9 1.0
C2D A:HEM700 4.3 13.1 1.0
NE1 A:TRP88 4.4 14.5 1.0
OH A:TYR36 4.8 14.5 1.0
O A:HOH2034 4.9 20.1 1.0

Iron binding site 2 out of 12 in 1ngk

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Iron binding site 2 out of 12 in the Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe700

b:16.1
occ:1.00
FE B:HEM700 0.0 16.1 1.0
C B:CYN800 1.8 19.0 1.0
NA B:HEM700 2.0 18.0 1.0
NB B:HEM700 2.0 15.9 1.0
NC B:HEM700 2.1 15.2 1.0
NE2 B:HIS75 2.1 18.0 1.0
ND B:HEM700 2.1 16.1 1.0
N B:CYN800 2.9 16.1 1.0
CE1 B:HIS75 3.0 17.4 1.0
C4A B:HEM700 3.1 17.1 1.0
C1A B:HEM700 3.1 16.6 1.0
C1B B:HEM700 3.1 16.8 1.0
C4C B:HEM700 3.1 16.1 1.0
C1D B:HEM700 3.1 15.2 1.0
CD2 B:HIS75 3.1 16.5 1.0
C4B B:HEM700 3.1 16.7 1.0
C4D B:HEM700 3.1 17.0 1.0
C1C B:HEM700 3.1 16.6 1.0
CHB B:HEM700 3.4 16.0 1.0
CHD B:HEM700 3.4 13.9 1.0
CHA B:HEM700 3.4 15.2 1.0
CHC B:HEM700 3.4 15.7 1.0
ND1 B:HIS75 4.1 15.3 1.0
CG B:HIS75 4.2 17.0 1.0
C2A B:HEM700 4.3 16.6 1.0
C3A B:HEM700 4.3 16.5 1.0
C3C B:HEM700 4.3 17.0 1.0
C2B B:HEM700 4.3 15.4 1.0
C3B B:HEM700 4.3 15.0 1.0
C2C B:HEM700 4.3 16.6 1.0
C2D B:HEM700 4.3 15.4 1.0
C3D B:HEM700 4.3 15.9 1.0
NE1 B:TRP88 4.4 17.1 1.0
OH B:TYR36 4.7 18.6 1.0
O B:HOH2020 4.8 20.9 1.0
CD1 B:LEU123 4.9 18.5 1.0

Iron binding site 3 out of 12 in 1ngk

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Iron binding site 3 out of 12 in the Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe700

b:13.1
occ:1.00
FE C:HEM700 0.0 13.1 1.0
C C:CYN800 1.9 10.6 1.0
NA C:HEM700 2.0 11.6 1.0
NC C:HEM700 2.0 13.0 1.0
ND C:HEM700 2.0 12.2 1.0
NB C:HEM700 2.1 9.8 1.0
NE2 C:HIS75 2.1 13.1 1.0
CD2 C:HIS75 3.0 12.6 1.0
C1A C:HEM700 3.0 13.7 1.0
C4C C:HEM700 3.0 14.0 1.0
N C:CYN800 3.0 8.6 1.0
C4A C:HEM700 3.0 11.4 1.0
C4D C:HEM700 3.0 11.8 1.0
C1D C:HEM700 3.0 11.3 1.0
C1C C:HEM700 3.1 12.6 1.0
C1B C:HEM700 3.1 11.5 1.0
C4B C:HEM700 3.1 10.1 1.0
CE1 C:HIS75 3.1 15.4 1.0
CHD C:HEM700 3.4 11.9 1.0
CHA C:HEM700 3.4 10.8 1.0
CHB C:HEM700 3.4 10.0 1.0
CHC C:HEM700 3.5 11.5 1.0
CG C:HIS75 4.2 13.1 1.0
ND1 C:HIS75 4.2 11.7 1.0
C2A C:HEM700 4.2 12.2 1.0
C3C C:HEM700 4.2 15.6 1.0
C3A C:HEM700 4.2 10.8 1.0
C2C C:HEM700 4.3 13.5 1.0
C3D C:HEM700 4.3 12.3 1.0
C2D C:HEM700 4.3 11.3 1.0
C2B C:HEM700 4.3 9.1 1.0
C3B C:HEM700 4.3 9.3 1.0
NE1 C:TRP88 4.4 13.1 1.0
O C:HOH2036 4.8 16.0 1.0
OH C:TYR36 4.9 16.0 1.0
CD1 C:LEU123 4.9 10.8 1.0

Iron binding site 4 out of 12 in 1ngk

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Iron binding site 4 out of 12 in the Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe700

b:16.2
occ:1.00
FE D:HEM700 0.0 16.2 1.0
NC D:HEM700 2.0 15.5 1.0
NA D:HEM700 2.0 16.1 1.0
C D:CYN800 2.0 14.0 1.0
NB D:HEM700 2.1 16.1 1.0
ND D:HEM700 2.1 16.8 1.0
NE2 D:HIS75 2.1 17.0 1.0
CE1 D:HIS75 3.0 15.5 1.0
C4C D:HEM700 3.0 15.3 1.0
C1C D:HEM700 3.0 14.7 1.0
C4A D:HEM700 3.0 18.0 1.0
C1A D:HEM700 3.1 17.1 1.0
C1D D:HEM700 3.1 17.1 1.0
C1B D:HEM700 3.1 14.1 1.0
C4D D:HEM700 3.1 14.9 1.0
CD2 D:HIS75 3.1 15.4 1.0
C4B D:HEM700 3.1 13.8 1.0
N D:CYN800 3.2 14.8 1.0
CHD D:HEM700 3.4 16.0 1.0
CHB D:HEM700 3.4 15.7 1.0
CHA D:HEM700 3.4 14.9 1.0
CHC D:HEM700 3.4 15.4 1.0
ND1 D:HIS75 4.1 14.5 1.0
CG D:HIS75 4.2 17.2 1.0
C3C D:HEM700 4.2 14.4 1.0
C2C D:HEM700 4.2 13.8 1.0
C2A D:HEM700 4.3 18.5 1.0
C3A D:HEM700 4.3 17.4 1.0
C2B D:HEM700 4.3 12.6 1.0
C2D D:HEM700 4.3 15.4 1.0
C3D D:HEM700 4.3 15.7 1.0
C3B D:HEM700 4.3 13.4 1.0
NE1 D:TRP88 4.4 12.5 1.0
OH D:TYR36 4.9 16.1 1.0
O D:HOH2049 4.9 20.7 1.0

Iron binding site 5 out of 12 in 1ngk

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Iron binding site 5 out of 12 in the Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe700

b:19.2
occ:1.00
FE E:HEM700 0.0 19.2 1.0
C E:CYN800 1.9 23.0 1.0
NA E:HEM700 2.0 19.2 1.0
NB E:HEM700 2.0 16.9 1.0
NC E:HEM700 2.0 17.8 1.0
NE2 E:HIS75 2.0 18.4 1.0
ND E:HEM700 2.1 18.5 1.0
N E:CYN800 2.9 19.1 1.0
CD2 E:HIS75 3.0 18.4 1.0
C1A E:HEM700 3.0 21.0 1.0
C4B E:HEM700 3.0 16.9 1.0
C4A E:HEM700 3.0 20.3 1.0
C1C E:HEM700 3.0 18.3 1.0
C1B E:HEM700 3.0 17.3 1.0
CE1 E:HIS75 3.0 18.1 1.0
C4C E:HEM700 3.1 20.0 1.0
C4D E:HEM700 3.1 18.3 1.0
C1D E:HEM700 3.1 18.3 1.0
CHC E:HEM700 3.4 18.1 1.0
CHB E:HEM700 3.4 17.6 1.0
CHA E:HEM700 3.4 18.6 1.0
CHD E:HEM700 3.5 19.5 1.0
CG E:HIS75 4.1 18.1 1.0
ND1 E:HIS75 4.1 19.3 1.0
C2A E:HEM700 4.2 21.6 1.0
C3A E:HEM700 4.2 21.0 1.0
C3B E:HEM700 4.2 17.3 1.0
C2B E:HEM700 4.3 17.1 1.0
C2C E:HEM700 4.3 20.2 1.0
C3C E:HEM700 4.3 19.1 1.0
C3D E:HEM700 4.4 19.9 1.0
NE1 E:TRP88 4.4 19.8 1.0
C2D E:HEM700 4.4 18.0 1.0
O E:HOH308 4.7 28.1 1.0
OH E:TYR36 4.7 21.5 1.0

Iron binding site 6 out of 12 in 1ngk

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Iron binding site 6 out of 12 in the Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe700

b:16.2
occ:1.00
FE F:HEM700 0.0 16.2 1.0
C F:CYN800 1.9 21.8 1.0
NA F:HEM700 2.0 14.3 1.0
NC F:HEM700 2.0 14.6 1.0
ND F:HEM700 2.0 17.3 1.0
NB F:HEM700 2.1 13.9 1.0
NE2 F:HIS75 2.1 19.5 1.0
N F:CYN800 2.9 17.3 1.0
C1A F:HEM700 3.0 17.1 1.0
CD2 F:HIS75 3.0 19.0 1.0
C4C F:HEM700 3.0 14.3 1.0
C4D F:HEM700 3.0 17.1 1.0
C4A F:HEM700 3.1 16.8 1.0
C1C F:HEM700 3.1 15.4 1.0
C4B F:HEM700 3.1 14.6 1.0
C1D F:HEM700 3.1 17.9 1.0
C1B F:HEM700 3.1 14.4 1.0
CE1 F:HIS75 3.1 18.3 1.0
CHA F:HEM700 3.4 16.3 1.0
CHD F:HEM700 3.4 17.9 1.0
CHC F:HEM700 3.4 14.1 1.0
CHB F:HEM700 3.5 14.0 1.0
ND1 F:HIS75 4.2 17.7 1.0
CG F:HIS75 4.2 16.5 1.0
C2A F:HEM700 4.2 17.1 1.0
C3C F:HEM700 4.3 15.8 1.0
C3A F:HEM700 4.3 15.6 1.0
C2C F:HEM700 4.3 15.1 1.0
C3D F:HEM700 4.3 16.7 1.0
C3B F:HEM700 4.3 13.1 1.0
C2B F:HEM700 4.3 15.1 1.0
C2D F:HEM700 4.3 16.7 1.0
NE1 F:TRP88 4.4 14.7 1.0
O F:HOH842 4.8 25.9 1.0
OH F:TYR36 4.8 17.8 1.0

Iron binding site 7 out of 12 in 1ngk

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Iron binding site 7 out of 12 in the Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe700

b:15.7
occ:1.00
FE G:HEM700 0.0 15.7 1.0
C G:CYN800 1.8 23.7 1.0
NA G:HEM700 2.0 17.0 1.0
NC G:HEM700 2.0 14.2 1.0
NB G:HEM700 2.1 13.6 1.0
NE2 G:HIS75 2.1 17.6 1.0
ND G:HEM700 2.1 17.1 1.0
N G:CYN800 2.9 20.1 1.0
C4A G:HEM700 3.0 17.9 1.0
C4C G:HEM700 3.0 15.0 1.0
CD2 G:HIS75 3.0 13.4 1.0
C1A G:HEM700 3.0 17.7 1.0
C1B G:HEM700 3.0 15.1 1.0
C1D G:HEM700 3.1 14.6 1.0
CE1 G:HIS75 3.1 17.7 1.0
C1C G:HEM700 3.1 14.8 1.0
C4D G:HEM700 3.1 16.6 1.0
C4B G:HEM700 3.1 14.4 1.0
CHB G:HEM700 3.4 17.2 1.0
CHD G:HEM700 3.4 14.4 1.0
CHA G:HEM700 3.4 16.4 1.0
CHC G:HEM700 3.5 14.4 1.0
ND1 G:HIS75 4.2 19.2 1.0
CG G:HIS75 4.2 15.5 1.0
C3A G:HEM700 4.2 18.7 1.0
C2A G:HEM700 4.2 19.7 1.0
C3C G:HEM700 4.3 16.1 1.0
C2B G:HEM700 4.3 15.9 1.0
C2C G:HEM700 4.3 13.4 1.0
C2D G:HEM700 4.3 16.5 1.0
C3B G:HEM700 4.3 13.1 1.0
C3D G:HEM700 4.3 16.4 1.0
NE1 G:TRP88 4.5 17.9 1.0
OH G:TYR36 4.6 31.0 1.0

Iron binding site 8 out of 12 in 1ngk

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Iron binding site 8 out of 12 in the Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe700

b:17.5
occ:1.00
FE H:HEM700 0.0 17.5 1.0
C H:CYN800 1.8 14.1 1.0
NA H:HEM700 2.0 16.5 1.0
NE2 H:HIS75 2.0 21.1 1.0
NC H:HEM700 2.0 18.1 1.0
ND H:HEM700 2.1 17.3 1.0
NB H:HEM700 2.1 16.3 1.0
N H:CYN800 2.9 16.2 1.0
CD2 H:HIS75 3.0 18.5 1.0
C1A H:HEM700 3.0 15.7 1.0
C4A H:HEM700 3.0 17.3 1.0
C4C H:HEM700 3.0 19.0 1.0
CE1 H:HIS75 3.0 20.1 1.0
C4D H:HEM700 3.0 16.3 1.0
C1D H:HEM700 3.1 16.6 1.0
C1C H:HEM700 3.1 18.5 1.0
C1B H:HEM700 3.1 16.4 1.0
C4B H:HEM700 3.1 18.6 1.0
CHA H:HEM700 3.4 15.7 1.0
CHD H:HEM700 3.4 18.4 1.0
CHB H:HEM700 3.4 17.0 1.0
CHC H:HEM700 3.5 19.4 1.0
CG H:HIS75 4.1 20.9 1.0
ND1 H:HIS75 4.1 19.6 1.0
C2A H:HEM700 4.2 18.6 1.0
C3A H:HEM700 4.2 16.1 1.0
C3C H:HEM700 4.3 19.6 1.0
C2C H:HEM700 4.3 17.7 1.0
C3D H:HEM700 4.3 15.6 1.0
C2D H:HEM700 4.3 16.5 1.0
C3B H:HEM700 4.3 16.8 1.0
C2B H:HEM700 4.3 16.8 1.0
NE1 H:TRP88 4.5 17.3 1.0
OH H:TYR36 4.7 31.7 1.0
CD1 H:LEU123 4.8 20.2 1.0

Iron binding site 9 out of 12 in 1ngk

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Iron binding site 9 out of 12 in the Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe700

b:15.7
occ:1.00
FE I:HEM700 0.0 15.7 1.0
C I:CYN800 1.8 22.8 1.0
NA I:HEM700 2.0 13.6 1.0
NB I:HEM700 2.0 14.1 1.0
NC I:HEM700 2.0 14.5 1.0
NE2 I:HIS75 2.0 13.7 1.0
ND I:HEM700 2.1 14.2 1.0
N I:CYN800 2.9 16.7 1.0
CD2 I:HIS75 3.0 13.6 1.0
C4A I:HEM700 3.0 16.0 1.0
C1A I:HEM700 3.0 14.5 1.0
C1B I:HEM700 3.0 14.3 1.0
CE1 I:HIS75 3.0 14.7 1.0
C4C I:HEM700 3.1 16.1 1.0
C1C I:HEM700 3.1 15.0 1.0
C4B I:HEM700 3.1 15.5 1.0
C4D I:HEM700 3.1 14.0 1.0
C1D I:HEM700 3.1 14.1 1.0
CHB I:HEM700 3.4 13.7 1.0
CHA I:HEM700 3.4 13.7 1.0
CHD I:HEM700 3.4 13.7 1.0
CHC I:HEM700 3.4 15.2 1.0
ND1 I:HIS75 4.1 15.4 1.0
CG I:HIS75 4.1 14.9 1.0
C2A I:HEM700 4.2 15.8 1.0
C3A I:HEM700 4.2 14.5 1.0
C2B I:HEM700 4.3 12.0 1.0
C3C I:HEM700 4.3 12.9 1.0
C2C I:HEM700 4.3 14.3 1.0
C3B I:HEM700 4.3 12.9 1.0
C3D I:HEM700 4.3 14.1 1.0
C2D I:HEM700 4.3 14.7 1.0
NE1 I:TRP88 4.5 17.2 1.0
OH I:TYR36 4.6 21.6 1.0

Iron binding site 10 out of 12 in 1ngk

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Iron binding site 10 out of 12 in the Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystallographic Structure of Mycobacterium Tuberculosis Hemoglobin O within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe700

b:20.7
occ:1.00
FE J:HEM700 0.0 20.7 1.0
C J:CYN800 1.9 16.9 1.0
NA J:HEM700 2.0 20.6 1.0
NE2 J:HIS75 2.0 23.0 1.0
NC J:HEM700 2.0 19.6 1.0
ND J:HEM700 2.1 21.1 1.0
NB J:HEM700 2.1 18.1 1.0
CE1 J:HIS75 3.0 21.1 1.0
C1A J:HEM700 3.0 20.8 1.0
CD2 J:HIS75 3.0 19.4 1.0
C4A J:HEM700 3.0 22.9 1.0
C4C J:HEM700 3.0 21.4 1.0
C4D J:HEM700 3.0 19.6 1.0
C1C J:HEM700 3.0 19.6 1.0
N J:CYN800 3.1 21.0 1.0
C1D J:HEM700 3.1 22.1 1.0
C4B J:HEM700 3.1 17.8 1.0
C1B J:HEM700 3.1 18.0 1.0
CHA J:HEM700 3.4 20.8 1.0
CHD J:HEM700 3.4 20.4 1.0
CHC J:HEM700 3.4 20.5 1.0
CHB J:HEM700 3.5 18.8 1.0
ND1 J:HIS75 4.1 21.0 1.0
CG J:HIS75 4.2 20.6 1.0
C2A J:HEM700 4.2 23.1 1.0
C3A J:HEM700 4.2 22.6 1.0
C3C J:HEM700 4.3 20.1 1.0
C2C J:HEM700 4.3 21.4 1.0
C3D J:HEM700 4.3 21.4 1.0
C2D J:HEM700 4.3 22.0 1.0
C2B J:HEM700 4.3 17.8 1.0
C3B J:HEM700 4.3 17.3 1.0
NE1 J:TRP88 4.4 24.4 1.0
OH J:TYR36 4.5 33.5 1.0

Reference:

M.Milani, P.-Y.Savard, H.Oullet, P.Ascenzi, M.Guertin, M.Bolognesi. A TYRCD1/TRPG8 Hydrogen Bond Network and A TYRB10-TYRCD1 Covalent Link Shape the Heme Distal Site of Mycobacterium Tuberculosis Hemoglobin O Proc.Natl.Acad.Sci.Usa V. 100 5766 2003.
ISSN: ISSN 0027-8424
PubMed: 12719529
DOI: 10.1073/PNAS.1037676100
Page generated: Sat Aug 3 11:35:06 2024

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