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Iron in PDB 4myp: Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme

Protein crystallography data

The structure of Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme, PDB code: 4myp was solved by G.R.Malmirchegini, M.R.Sawaya, R.T.Clubb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.05 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 32.730, 67.690, 58.480, 90.00, 91.62, 90.00
R / Rfree (%) 19.5 / 22.5

Other elements in 4myp:

The structure of Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme (pdb code 4myp). 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 the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme, PDB code: 4myp:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 4myp

Go back to Iron Binding Sites List in 4myp
Iron binding site 1 out of 2 in the Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed 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 the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:32.7
occ:1.00
FE A:HEM401 0.0 32.7 1.0
NA A:HEM401 2.0 33.1 1.0
NB A:HEM401 2.0 33.2 1.0
NC A:HEM401 2.0 32.2 1.0
ND A:HEM401 2.0 31.9 1.0
OH A:TYR280 2.2 32.1 1.0
C1B A:HEM401 3.0 34.1 1.0
C4B A:HEM401 3.0 33.7 1.0
C4C A:HEM401 3.0 31.9 1.0
C1C A:HEM401 3.0 32.6 1.0
C1D A:HEM401 3.0 31.8 1.0
C4A A:HEM401 3.0 33.8 1.0
C1A A:HEM401 3.1 33.1 1.0
C4D A:HEM401 3.1 32.2 1.0
CZ A:TYR280 3.1 31.8 1.0
CHB A:HEM401 3.3 34.7 1.0
CHC A:HEM401 3.4 33.9 1.0
CHD A:HEM401 3.4 32.2 1.0
CHA A:HEM401 3.5 33.1 1.0
CE2 A:TYR280 3.6 30.0 1.0
C2B B:HEM401 3.8 37.4 1.0
C3B B:HEM401 4.0 37.1 1.0
CMB B:HEM401 4.0 40.1 1.0
CE1 A:TYR280 4.1 30.4 1.0
C2C A:HEM401 4.2 32.9 1.0
C2B A:HEM401 4.2 34.9 1.0
C3A A:HEM401 4.2 34.6 1.0
C3C A:HEM401 4.2 32.4 1.0
C3B A:HEM401 4.2 35.0 1.0
C2A A:HEM401 4.3 34.1 1.0
CAB B:HEM401 4.3 38.4 1.0
C2D A:HEM401 4.3 31.8 1.0
O1 A:GOL407 4.3 45.7 1.0
C3D A:HEM401 4.3 32.1 1.0
C1B B:HEM401 4.4 36.6 1.0
C4B B:HEM401 4.5 35.8 1.0
CBB B:HEM401 4.8 45.1 1.0
CE2 A:TYR289 4.8 38.8 1.0
NB B:HEM401 4.8 35.5 1.0
CD2 A:TYR280 4.9 29.3 1.0
C1 A:GOL407 5.0 48.9 1.0

Iron binding site 2 out of 2 in 4myp

Go back to Iron Binding Sites List in 4myp
Iron binding site 2 out of 2 in the Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed 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 the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:35.0
occ:1.00
FE B:HEM401 0.0 35.0 1.0
ND B:HEM401 2.0 34.3 1.0
NC B:HEM401 2.0 34.3 1.0
NA B:HEM401 2.0 35.9 1.0
NB B:HEM401 2.0 35.5 1.0
OH B:TYR280 2.4 39.9 1.0
C4C B:HEM401 2.9 34.0 1.0
C1D B:HEM401 2.9 34.1 1.0
C1C B:HEM401 3.0 34.5 1.0
C4D B:HEM401 3.0 34.8 1.0
C1B B:HEM401 3.0 36.6 1.0
C4B B:HEM401 3.0 35.8 1.0
C4A B:HEM401 3.0 36.8 1.0
C1A B:HEM401 3.0 36.1 1.0
CZ B:TYR280 3.2 40.4 1.0
CHD B:HEM401 3.3 34.3 1.0
CHC B:HEM401 3.4 35.8 1.0
CHB B:HEM401 3.4 37.5 1.0
CHA B:HEM401 3.5 36.0 1.0
CMA A:HEM401 3.5 36.7 1.0
C3A A:HEM401 3.7 34.6 1.0
CE1 B:TYR280 3.7 36.5 1.0
C2A A:HEM401 3.9 34.1 1.0
CE2 B:TYR280 4.0 34.5 1.0
O1 B:GOL406 4.2 70.5 1.0
C3C B:HEM401 4.2 34.3 1.0
C2C B:HEM401 4.2 34.7 1.0
CAA A:HEM401 4.2 35.8 1.0
C4A A:HEM401 4.3 33.8 1.0
C2D B:HEM401 4.3 34.3 1.0
C2A B:HEM401 4.3 37.5 1.0
C3A B:HEM401 4.3 37.9 1.0
C3D B:HEM401 4.3 34.7 1.0
C2B B:HEM401 4.3 37.4 1.0
C3B B:HEM401 4.3 37.1 1.0
C1 B:GOL406 4.5 72.7 1.0
C1A A:HEM401 4.7 33.1 1.0
CHB A:HEM401 4.7 34.7 1.0
CE1 B:TYR289 4.8 41.0 1.0
CD1 B:TYR280 4.9 35.3 1.0
NA A:HEM401 4.9 33.1 1.0

Reference:

G.R.Malmirchegini, S.Shnitkind, M.R.Sawaya, J.S.Rosinski, J.S.Olson, P.E.Klebba, R.T.Clubb. Novel Mechanism of Hemin Capture By HBP2, the Hemoglobin-Binding Hemophore From Listeria Monocytogenes J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
Page generated: Sun Dec 13 15:42:11 2020

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