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Iron in PDB 3h8t: Structure of Porphyromonas Gingivalis Heme-Binding Protein Hmuy in Complex with Heme

Protein crystallography data

The structure of Structure of Porphyromonas Gingivalis Heme-Binding Protein Hmuy in Complex with Heme, PDB code: 3h8t was solved by H.Wojtowicz, T.Guevara, C.Tallant, M.Olczak, A.Sroka, J.Potempa, M.Sola, T.Olczak, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.60 / 1.80
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.740, 93.740, 113.730, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 18.7

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Porphyromonas Gingivalis Heme-Binding Protein Hmuy in Complex with Heme (pdb code 3h8t). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of Porphyromonas Gingivalis Heme-Binding Protein Hmuy in Complex with Heme, PDB code: 3h8t:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3h8t

Go back to Iron Binding Sites List in 3h8t
Iron binding site 1 out of 2 in the Structure of Porphyromonas Gingivalis Heme-Binding Protein Hmuy in Complex with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Porphyromonas Gingivalis Heme-Binding Protein Hmuy in Complex with Heme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:7.2
occ:1.00
FE A:HEM301 0.0 7.2 1.0
NE2 A:HIS134 2.0 7.0 1.0
NB A:HEM301 2.0 6.0 1.0
NA A:HEM301 2.0 6.8 1.0
NC A:HEM301 2.0 6.0 1.0
ND A:HEM301 2.1 7.2 1.0
NE2 A:HIS166 2.1 8.7 1.0
CD2 A:HIS134 3.0 6.2 1.0
C1B A:HEM301 3.0 6.6 1.0
CE1 A:HIS166 3.0 7.4 1.0
C4C A:HEM301 3.0 7.7 1.0
C1D A:HEM301 3.0 8.1 1.0
CE1 A:HIS134 3.0 8.4 1.0
C4A A:HEM301 3.0 7.3 1.0
CD2 A:HIS166 3.1 7.0 1.0
C1A A:HEM301 3.1 6.9 1.0
C4B A:HEM301 3.1 6.3 1.0
C4D A:HEM301 3.1 6.7 1.0
C1C A:HEM301 3.1 5.7 1.0
CHD A:HEM301 3.4 7.2 1.0
CHB A:HEM301 3.4 6.3 1.0
CHA A:HEM301 3.4 6.4 1.0
CHC A:HEM301 3.5 5.1 1.0
ND1 A:HIS134 4.1 7.6 1.0
ND1 A:HIS166 4.1 7.5 1.0
CG A:HIS134 4.2 7.7 1.0
CG A:HIS166 4.2 7.3 1.0
C2B A:HEM301 4.3 4.8 1.0
C3C A:HEM301 4.3 7.1 1.0
C3A A:HEM301 4.3 7.2 1.0
C3B A:HEM301 4.3 6.5 1.0
C2D A:HEM301 4.3 6.8 1.0
C2A A:HEM301 4.3 6.4 1.0
C3D A:HEM301 4.3 6.6 1.0
C2C A:HEM301 4.3 6.8 1.0
O A:HOH900 4.8 6.7 1.0

Iron binding site 2 out of 2 in 3h8t

Go back to Iron Binding Sites List in 3h8t
Iron binding site 2 out of 2 in the Structure of Porphyromonas Gingivalis Heme-Binding Protein Hmuy in Complex with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Porphyromonas Gingivalis Heme-Binding Protein Hmuy in Complex with Heme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:6.9
occ:1.00
FE B:HEM301 0.0 6.9 1.0
ND B:HEM301 2.0 6.6 1.0
NB B:HEM301 2.0 6.3 1.0
NA B:HEM301 2.0 5.6 1.0
NE2 B:HIS134 2.1 8.8 1.0
NE2 B:HIS166 2.1 6.2 1.0
NC B:HEM301 2.1 5.4 1.0
C1D B:HEM301 3.0 6.8 1.0
CE1 B:HIS166 3.0 7.9 1.0
CD2 B:HIS134 3.0 8.0 1.0
C4A B:HEM301 3.0 6.5 1.0
CE1 B:HIS134 3.0 7.4 1.0
C1B B:HEM301 3.1 5.8 1.0
C1A B:HEM301 3.1 6.3 1.0
C4D B:HEM301 3.1 6.0 1.0
CD2 B:HIS166 3.1 6.6 1.0
C4C B:HEM301 3.1 7.4 1.0
C4B B:HEM301 3.1 6.0 1.0
C1C B:HEM301 3.1 5.0 1.0
CHD B:HEM301 3.4 6.4 1.0
CHB B:HEM301 3.4 4.5 1.0
CHA B:HEM301 3.4 5.2 1.0
CHC B:HEM301 3.4 4.3 1.0
ND1 B:HIS166 4.1 6.7 1.0
ND1 B:HIS134 4.2 8.6 1.0
CG B:HIS134 4.2 8.5 1.0
CG B:HIS166 4.2 5.9 1.0
C3A B:HEM301 4.3 5.2 1.0
C2D B:HEM301 4.3 7.2 1.0
C2A B:HEM301 4.3 4.5 1.0
C2B B:HEM301 4.3 5.2 1.0
C3D B:HEM301 4.3 6.9 1.0
C3C B:HEM301 4.3 6.9 1.0
C3B B:HEM301 4.3 5.7 1.0
C2C B:HEM301 4.3 3.3 1.0
O B:HOH572 4.8 7.0 1.0

Reference:

H.Wojtowicz, T.Guevara, C.Tallant, M.Olczak, A.Sroka, J.Potempa, M.Sola, T.Olczak, F.X.Gomis-Ruth. Unique Structure and Stability of Hmuy, A Novel Heme-Binding Protein of Porphyromonas Gingivalis Plos Pathog. V. 5 00419 2009.
ISSN: ISSN 1553-7366
PubMed: 19424422
DOI: 10.1371/JOURNAL.PPAT.1000419
Page generated: Sun Dec 13 15:07:26 2020

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