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Iron in PDB 4hov: Dypb N246A in Complex with Manganese

Protein crystallography data

The structure of Dypb N246A in Complex with Manganese, PDB code: 4hov was solved by J.C.Grigg, R.Singh, L.D.Eltis, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.56 / 2.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 132.960, 132.960, 159.502, 90.00, 90.00, 120.00
R / Rfree (%) 16.7 / 19.5

Other elements in 4hov:

The structure of Dypb N246A in Complex with Manganese also contains other interesting chemical elements:

Manganese (Mn) 3 atoms
Chlorine (Cl) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Dypb N246A in Complex with Manganese (pdb code 4hov). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Dypb N246A in Complex with Manganese, PDB code: 4hov:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 4hov

Go back to Iron Binding Sites List in 4hov
Iron binding site 1 out of 3 in the Dypb N246A in Complex with Manganese


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dypb N246A in Complex with Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:26.3
occ:1.00
FE A:HEM401 0.0 26.3 1.0
ND A:HEM401 1.9 24.8 1.0
NA A:HEM401 2.0 24.6 1.0
NC A:HEM401 2.1 24.5 1.0
NE2 A:HIS226 2.1 24.4 1.0
NB A:HEM401 2.1 25.3 1.0
O A:HOH732 2.3 35.3 1.0
C1D A:HEM401 2.9 25.3 1.0
C4D A:HEM401 3.0 24.2 1.0
CE1 A:HIS226 3.0 26.2 1.0
C1A A:HEM401 3.0 25.0 1.0
C4B A:HEM401 3.0 26.1 1.0
C4A A:HEM401 3.0 25.3 1.0
C4C A:HEM401 3.1 25.3 1.0
C1B A:HEM401 3.1 24.7 1.0
C1C A:HEM401 3.1 25.9 1.0
CD2 A:HIS226 3.1 26.9 1.0
CHA A:HEM401 3.4 24.2 1.0
CHD A:HEM401 3.4 25.6 1.0
CHB A:HEM401 3.5 22.7 1.0
CHC A:HEM401 3.5 24.3 1.0
O A:HOH733 4.0 42.2 1.0
NH1 A:ARG244 4.1 25.6 1.0
ND1 A:HIS226 4.1 26.6 1.0
C2A A:HEM401 4.2 24.1 1.0
C2D A:HEM401 4.2 25.6 1.0
CG A:HIS226 4.2 27.4 1.0
C3D A:HEM401 4.2 26.9 1.0
C3A A:HEM401 4.2 24.7 1.0
C2B A:HEM401 4.3 25.6 1.0
C3C A:HEM401 4.3 24.5 1.0
C3B A:HEM401 4.3 27.0 1.0
C2C A:HEM401 4.3 24.9 1.0
OD1 A:ASN230 4.5 32.6 1.0
CD A:ARG244 4.7 27.4 1.0
CZ A:ARG244 4.9 26.6 1.0

Iron binding site 2 out of 3 in 4hov

Go back to Iron Binding Sites List in 4hov
Iron binding site 2 out of 3 in the Dypb N246A in Complex with Manganese


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dypb N246A in Complex with Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:28.6
occ:1.00
FE B:HEM401 0.0 28.6 1.0
ND B:HEM401 1.9 27.4 1.0
NA B:HEM401 2.0 25.6 1.0
NE2 B:HIS226 2.0 33.0 1.0
NB B:HEM401 2.1 27.2 1.0
NC B:HEM401 2.1 26.6 1.0
O B:HOH734 2.4 32.8 1.0
C1D B:HEM401 2.9 27.2 1.0
C4D B:HEM401 3.0 27.2 1.0
C1A B:HEM401 3.0 24.7 1.0
C4A B:HEM401 3.0 25.4 1.0
CE1 B:HIS226 3.0 29.7 1.0
CD2 B:HIS226 3.0 30.6 1.0
C1B B:HEM401 3.0 28.0 1.0
C4C B:HEM401 3.0 25.6 1.0
C4B B:HEM401 3.1 26.8 1.0
C1C B:HEM401 3.1 26.6 1.0
CHD B:HEM401 3.4 25.9 1.0
CHB B:HEM401 3.4 26.5 1.0
CHA B:HEM401 3.4 24.8 1.0
CHC B:HEM401 3.5 25.8 1.0
O B:HOH735 4.0 34.0 1.0
NH1 B:ARG244 4.1 28.0 1.0
ND1 B:HIS226 4.1 29.4 1.0
CG B:HIS226 4.2 30.4 1.0
C2D B:HEM401 4.2 27.2 1.0
C3A B:HEM401 4.2 25.8 1.0
C2A B:HEM401 4.2 25.1 1.0
C3D B:HEM401 4.2 27.2 1.0
C3C B:HEM401 4.3 26.1 1.0
C2B B:HEM401 4.3 27.9 1.0
C2C B:HEM401 4.3 26.7 1.0
C3B B:HEM401 4.3 28.2 1.0
ND2 B:ASN230 4.5 29.3 1.0
CD B:ARG244 4.7 26.8 1.0
CZ B:ARG244 4.9 30.4 1.0

Iron binding site 3 out of 3 in 4hov

Go back to Iron Binding Sites List in 4hov
Iron binding site 3 out of 3 in the Dypb N246A in Complex with Manganese


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dypb N246A in Complex with Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:30.2
occ:1.00
FE C:HEM401 0.0 30.2 1.0
ND C:HEM401 1.9 28.3 1.0
NA C:HEM401 2.0 28.8 1.0
NB C:HEM401 2.1 27.9 1.0
NC C:HEM401 2.1 29.5 1.0
NE2 C:HIS226 2.1 35.6 1.0
O C:HOH686 2.3 43.9 1.0
C1D C:HEM401 2.9 29.5 1.0
C4D C:HEM401 2.9 28.6 1.0
C1A C:HEM401 3.0 27.2 1.0
C4B C:HEM401 3.0 29.6 1.0
C4A C:HEM401 3.0 26.1 1.0
C1B C:HEM401 3.0 28.0 1.0
CD2 C:HIS226 3.0 34.3 1.0
C4C C:HEM401 3.1 28.6 1.0
C1C C:HEM401 3.1 29.0 1.0
CE1 C:HIS226 3.2 35.2 1.0
CHA C:HEM401 3.4 28.5 1.0
CHD C:HEM401 3.4 28.9 1.0
CHB C:HEM401 3.4 27.3 1.0
CHC C:HEM401 3.5 28.6 1.0
NH1 C:ARG244 4.1 29.1 1.0
O C:HOH687 4.2 52.5 1.0
C2D C:HEM401 4.2 29.1 1.0
C3D C:HEM401 4.2 28.5 1.0
CG C:HIS226 4.2 34.2 1.0
C2A C:HEM401 4.2 27.1 1.0
C3A C:HEM401 4.2 26.3 1.0
ND1 C:HIS226 4.2 34.5 1.0
C2B C:HEM401 4.2 26.5 1.0
C3B C:HEM401 4.3 27.0 1.0
C3C C:HEM401 4.3 30.4 1.0
C2C C:HEM401 4.3 30.5 1.0
OD1 C:ASN230 4.5 38.0 1.0
CD C:ARG244 4.7 32.3 1.0
CZ C:ARG244 4.9 30.9 1.0

Reference:

R.Singh, J.C.Grigg, W.Qin, J.F.Kadla, M.E.Murphy, L.D.Eltis. Improved Manganese-Oxidizing Activity of Dypb, A Peroxidase From A Lignolytic Bacterium. Acs Chem.Biol. V. 8 700 2013.
ISSN: ISSN 1554-8929
PubMed: 23305326
DOI: 10.1021/CB300608X
Page generated: Sun Dec 13 15:36:57 2020

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