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Iron in PDB 4y1q: Crystal Structure of Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis

Protein crystallography data

The structure of Crystal Structure of Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis, PDB code: 4y1q was solved by S.Nagano, T.Hino, M.Kanadani, S.Ozaki, T.Sato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.85 / 3.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.660, 70.320, 77.030, 89.35, 89.75, 90.46
R / Rfree (%) 22 / 27.6

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis (pdb code 4y1q). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis, PDB code: 4y1q:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4y1q

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Iron binding site 1 out of 8 in the Crystal Structure of Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis


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 Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:97.5
occ:1.00
FE A:HEM301 0.0 97.5 1.0
NA A:HEM301 2.0 70.7 1.0
NC A:HEM301 2.1 72.6 1.0
NB A:HEM301 2.1 66.0 1.0
ND A:HEM301 2.1 71.8 1.0
C4C A:HEM301 3.1 64.8 1.0
C1A A:HEM301 3.1 65.0 1.0
C1D A:HEM301 3.1 63.6 1.0
C4A A:HEM301 3.1 67.4 1.0
C1B A:HEM301 3.1 62.0 1.0
C1C A:HEM301 3.1 66.6 1.0
C4B A:HEM301 3.1 61.6 1.0
C4D A:HEM301 3.1 68.5 1.0
CHD A:HEM301 3.4 61.1 1.0
CHA A:HEM301 3.4 62.7 1.0
CHB A:HEM301 3.4 59.5 1.0
CHC A:HEM301 3.5 61.1 1.0
CD2 A:HIS81 4.0 46.5 1.0
C3C A:HEM301 4.3 58.0 1.0
C2A A:HEM301 4.3 65.4 1.0
C2C A:HEM301 4.3 57.2 1.0
C2B A:HEM301 4.3 62.7 1.0
C3A A:HEM301 4.3 68.9 1.0
C3B A:HEM301 4.3 55.1 1.0
C2D A:HEM301 4.3 59.4 1.0
C3D A:HEM301 4.3 64.6 1.0
NH1 A:ARG40 4.4 59.9 1.0
CG A:HIS81 4.4 41.5 1.0
CB A:HIS81 4.5 35.5 1.0
NE2 A:HIS81 4.9 44.7 1.0

Iron binding site 2 out of 8 in 4y1q

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Iron binding site 2 out of 8 in the Crystal Structure of Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis


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 Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:97.8
occ:1.00
FE B:HEM301 0.0 97.8 1.0
NA B:HEM301 2.0 66.3 1.0
NC B:HEM301 2.0 63.3 1.0
NB B:HEM301 2.1 64.4 1.0
ND B:HEM301 2.1 67.7 1.0
C4C B:HEM301 3.1 58.8 1.0
C1A B:HEM301 3.1 68.7 1.0
C4A B:HEM301 3.1 67.0 1.0
C1D B:HEM301 3.1 58.5 1.0
C1B B:HEM301 3.1 62.8 1.0
C1C B:HEM301 3.1 60.0 1.0
C4B B:HEM301 3.1 61.3 1.0
C4D B:HEM301 3.1 64.9 1.0
CHD B:HEM301 3.4 54.9 1.0
CHA B:HEM301 3.4 63.9 1.0
CHB B:HEM301 3.4 64.2 1.0
CHC B:HEM301 3.5 61.1 1.0
ND1 B:HIS81 4.1 48.7 1.0
CB B:HIS81 4.2 41.9 1.0
C2A B:HEM301 4.3 70.2 1.0
C3A B:HEM301 4.3 69.1 1.0
C3C B:HEM301 4.3 59.0 1.0
C2D B:HEM301 4.3 56.2 1.0
C2C B:HEM301 4.3 54.5 1.0
C2B B:HEM301 4.3 59.4 1.0
CG B:HIS81 4.3 44.2 1.0
C3B B:HEM301 4.3 54.3 1.0
C3D B:HEM301 4.3 65.1 1.0
CE1 B:HIS81 4.8 46.6 1.0
NH1 B:ARG40 4.9 54.0 1.0

Iron binding site 3 out of 8 in 4y1q

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Iron binding site 3 out of 8 in the Crystal Structure of Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis


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 Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe301

b:94.6
occ:1.00
FE D:HEM301 0.0 94.6 1.0
NA D:HEM301 2.0 70.5 1.0
NC D:HEM301 2.1 69.7 1.0
NB D:HEM301 2.1 57.9 1.0
ND D:HEM301 2.1 68.4 1.0
C4C D:HEM301 3.1 59.2 1.0
C1A D:HEM301 3.1 65.8 1.0
C1D D:HEM301 3.1 61.6 1.0
C4A D:HEM301 3.1 68.3 1.0
C1B D:HEM301 3.1 59.9 1.0
C1C D:HEM301 3.1 65.5 1.0
C4B D:HEM301 3.1 57.7 1.0
C4D D:HEM301 3.1 64.1 1.0
CHD D:HEM301 3.4 56.2 1.0
CHA D:HEM301 3.4 63.0 1.0
CHB D:HEM301 3.4 63.1 1.0
CHC D:HEM301 3.5 56.2 1.0
ND1 D:HIS81 4.2 48.0 1.0
C3C D:HEM301 4.3 55.0 1.0
C2A D:HEM301 4.3 65.8 1.0
C2C D:HEM301 4.3 56.8 1.0
C3A D:HEM301 4.3 71.2 1.0
C2B D:HEM301 4.3 54.2 1.0
C2D D:HEM301 4.3 61.1 1.0
C3B D:HEM301 4.3 52.7 1.0
C3D D:HEM301 4.3 64.0 1.0
CB D:HIS81 4.5 42.0 1.0
CG D:HIS81 4.5 42.2 1.0
CD D:ARG40 4.9 51.2 1.0
CE1 D:HIS81 5.0 48.2 1.0

Iron binding site 4 out of 8 in 4y1q

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Iron binding site 4 out of 8 in the Crystal Structure of Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis


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 Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:96.3
occ:1.00
FE G:HEM301 0.0 96.3 1.0
NA G:HEM301 2.1 68.1 1.0
NC G:HEM301 2.1 62.0 1.0
NB G:HEM301 2.1 60.3 1.0
ND G:HEM301 2.1 64.7 1.0
C4C G:HEM301 3.1 54.3 1.0
C1A G:HEM301 3.1 63.4 1.0
C1D G:HEM301 3.1 59.0 1.0
C1C G:HEM301 3.1 59.8 1.0
C4A G:HEM301 3.1 66.0 1.0
C1B G:HEM301 3.1 61.0 1.0
C4B G:HEM301 3.1 56.0 1.0
C4D G:HEM301 3.1 61.3 1.0
CHD G:HEM301 3.4 55.7 1.0
CHA G:HEM301 3.4 61.1 1.0
CHB G:HEM301 3.5 62.3 1.0
CHC G:HEM301 3.5 55.7 1.0
CD2 G:HIS81 3.9 47.5 1.0
C3C G:HEM301 4.3 50.7 1.0
C2C G:HEM301 4.3 50.5 1.0
C2A G:HEM301 4.3 66.5 1.0
C3A G:HEM301 4.3 67.0 1.0
C2D G:HEM301 4.3 59.0 1.0
CG G:HIS81 4.3 44.0 1.0
C2B G:HEM301 4.3 59.3 1.0
C3B G:HEM301 4.3 54.2 1.0
C3D G:HEM301 4.3 60.3 1.0
CB G:HIS81 4.4 39.7 1.0
NH1 G:ARG40 4.5 61.9 1.0
NE2 G:HIS81 4.7 45.3 1.0

Iron binding site 5 out of 8 in 4y1q

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Iron binding site 5 out of 8 in the Crystal Structure of Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis


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 Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe301

b:89.1
occ:1.00
FE I:HEM301 0.0 89.1 1.0
NA I:HEM301 2.0 68.2 1.0
NC I:HEM301 2.1 68.0 1.0
NB I:HEM301 2.1 62.6 1.0
ND I:HEM301 2.1 68.7 1.0
C4C I:HEM301 3.1 59.3 1.0
C1A I:HEM301 3.1 63.5 1.0
C1C I:HEM301 3.1 62.6 1.0
C4A I:HEM301 3.1 66.5 1.0
C1D I:HEM301 3.1 59.5 1.0
C1B I:HEM301 3.1 61.0 1.0
C4B I:HEM301 3.1 60.6 1.0
C4D I:HEM301 3.1 63.9 1.0
CHA I:HEM301 3.4 61.8 1.0
CHD I:HEM301 3.4 56.9 1.0
CHC I:HEM301 3.4 58.0 1.0
CHB I:HEM301 3.5 60.8 1.0
CD2 I:HIS81 4.0 49.0 1.0
C3C I:HEM301 4.3 56.3 1.0
C2C I:HEM301 4.3 54.6 1.0
C2A I:HEM301 4.3 63.5 1.0
C3A I:HEM301 4.3 67.5 1.0
C2B I:HEM301 4.3 59.6 1.0
C3B I:HEM301 4.3 55.4 1.0
C2D I:HEM301 4.3 58.1 1.0
C3D I:HEM301 4.3 64.8 1.0
CG I:HIS81 4.4 47.3 1.0
CB I:HIS81 4.4 43.5 1.0
NE2 I:HIS81 4.9 50.4 1.0

Iron binding site 6 out of 8 in 4y1q

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Iron binding site 6 out of 8 in the Crystal Structure of Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis


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 Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Fe301

b:90.9
occ:1.00
FE K:HEM301 0.0 90.9 1.0
NC K:HEM301 2.1 60.4 1.0
NA K:HEM301 2.1 69.3 1.0
NB K:HEM301 2.1 62.3 1.0
ND K:HEM301 2.1 66.3 1.0
C4C K:HEM301 3.1 55.2 1.0
C1A K:HEM301 3.1 65.0 1.0
C1D K:HEM301 3.1 58.2 1.0
C1C K:HEM301 3.1 58.8 1.0
C4A K:HEM301 3.1 65.2 1.0
C4D K:HEM301 3.1 63.8 1.0
C1B K:HEM301 3.1 60.1 1.0
C4B K:HEM301 3.1 56.8 1.0
CHA K:HEM301 3.4 60.7 1.0
CHD K:HEM301 3.4 53.9 1.0
CHC K:HEM301 3.5 57.0 1.0
CHB K:HEM301 3.5 57.2 1.0
CD2 K:HIS81 4.2 46.5 1.0
C2D K:HEM301 4.3 58.3 1.0
C3C K:HEM301 4.3 54.4 1.0
C2A K:HEM301 4.3 65.4 1.0
C2C K:HEM301 4.3 51.3 1.0
C3A K:HEM301 4.3 68.3 1.0
C3D K:HEM301 4.3 65.7 1.0
C2B K:HEM301 4.3 59.5 1.0
C3B K:HEM301 4.3 53.6 1.0
NH1 K:ARG40 4.6 65.3 1.0
CG K:HIS81 4.6 43.8 1.0
CB K:HIS81 4.6 41.1 1.0
CD K:ARG40 4.9 54.5 1.0

Iron binding site 7 out of 8 in 4y1q

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Iron binding site 7 out of 8 in the Crystal Structure of Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis


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 Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe301

b:81.8
occ:1.00
FE M:HEM301 0.0 81.8 1.0
NA M:HEM301 2.1 69.2 1.0
NC M:HEM301 2.1 65.0 1.0
NB M:HEM301 2.1 61.0 1.0
ND M:HEM301 2.1 63.0 1.0
C4C M:HEM301 3.0 55.0 1.0
C1A M:HEM301 3.1 63.4 1.0
C1C M:HEM301 3.1 60.9 1.0
C4A M:HEM301 3.1 64.9 1.0
C1D M:HEM301 3.1 54.8 1.0
C1B M:HEM301 3.1 61.5 1.0
C4B M:HEM301 3.1 57.5 1.0
C4D M:HEM301 3.1 58.0 1.0
CHD M:HEM301 3.4 52.7 1.0
CHA M:HEM301 3.4 57.2 1.0
CHC M:HEM301 3.4 55.1 1.0
CHB M:HEM301 3.5 60.0 1.0
CD2 M:HIS81 3.9 45.7 1.0
C3C M:HEM301 4.2 51.6 1.0
C2C M:HEM301 4.3 55.1 1.0
C2A M:HEM301 4.3 63.5 1.0
C3A M:HEM301 4.3 66.1 1.0
C2B M:HEM301 4.3 56.1 1.0
C3B M:HEM301 4.3 53.8 1.0
C2D M:HEM301 4.3 52.9 1.0
C3D M:HEM301 4.3 58.4 1.0
CG M:HIS81 4.4 41.9 1.0
CB M:HIS81 4.5 38.6 1.0
NE2 M:HIS81 4.8 46.3 1.0
CD M:ARG40 4.9 59.1 1.0

Iron binding site 8 out of 8 in 4y1q

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Iron binding site 8 out of 8 in the Crystal Structure of Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis


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 Hasa Mutant Y75A Monomer From Yersinia Pseudotuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe301

b:0.0
occ:1.00
FE O:HEM301 0.0 0.0 1.0
NC O:HEM301 2.0 62.0 1.0
NA O:HEM301 2.0 74.9 1.0
NB O:HEM301 2.1 62.2 1.0
ND O:HEM301 2.1 70.5 1.0
C4C O:HEM301 3.1 58.3 1.0
C1A O:HEM301 3.1 71.5 1.0
C1C O:HEM301 3.1 61.0 1.0
C1B O:HEM301 3.1 63.7 1.0
C4A O:HEM301 3.1 71.8 1.0
C1D O:HEM301 3.1 58.1 1.0
C4B O:HEM301 3.1 61.0 1.0
C4D O:HEM301 3.1 64.4 1.0
CHA O:HEM301 3.4 66.1 1.0
CHD O:HEM301 3.4 55.6 1.0
CHB O:HEM301 3.4 64.7 1.0
CHC O:HEM301 3.4 58.8 1.0
CD2 O:HIS81 4.0 52.3 1.0
C3C O:HEM301 4.3 54.6 1.0
C2C O:HEM301 4.3 56.3 1.0
C2A O:HEM301 4.3 70.9 1.0
C2B O:HEM301 4.3 60.6 1.0
C3A O:HEM301 4.3 76.1 1.0
C3B O:HEM301 4.3 56.8 1.0
C2D O:HEM301 4.3 60.1 1.0
C3D O:HEM301 4.3 62.7 1.0
CG O:HIS81 4.4 46.7 1.0
CB O:HIS81 4.4 39.7 1.0
NE2 O:HIS81 4.9 53.2 1.0

Reference:

M.Kanadani, T.Sato, T.Hino, S.Nagano, S.Ozaki. The Crystal Structure of Heme Acquisition System A From Yersinia Pseudotuberculosis (Hasaypt): Roles of the Axial Ligand TYR75 and Two Distal Arginines in Heme Binding J.Inorg.Biochem. V. 151 26 2015.
ISSN: ISSN 0162-0134
PubMed: 26210321
DOI: 10.1016/J.JINORGBIO.2015.07.007
Page generated: Mon Aug 5 16:05:19 2024

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