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Iron in PDB 5a12: Crystal Structure of Chlorite Dismutase From Magnetospirillum Sp. in Complex with Azide

Enzymatic activity of Crystal Structure of Chlorite Dismutase From Magnetospirillum Sp. in Complex with Azide

All present enzymatic activity of Crystal Structure of Chlorite Dismutase From Magnetospirillum Sp. in Complex with Azide:
1.13.11.49;

Protein crystallography data

The structure of Crystal Structure of Chlorite Dismutase From Magnetospirillum Sp. in Complex with Azide, PDB code: 5a12 was solved by H.D.Correia, T.Santos-Silva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.44 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.234, 133.823, 77.622, 90.00, 113.03, 90.00
R / Rfree (%) 11.8 / 15.4

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Chlorite Dismutase From Magnetospirillum Sp. in Complex with Azide (pdb code 5a12). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of Chlorite Dismutase From Magnetospirillum Sp. in Complex with Azide, PDB code: 5a12:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 5a12

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Iron binding site 1 out of 5 in the Crystal Structure of Chlorite Dismutase From Magnetospirillum Sp. in Complex with Azide


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 Chlorite Dismutase From Magnetospirillum Sp. in Complex with Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe250

b:14.3
occ:1.00
FE A:HEM250 0.0 14.3 1.0
ND A:HEM250 1.9 13.7 1.0
NA A:HEM250 2.0 13.1 1.0
N1 A:AZI251 2.0 16.8 1.0
NC A:HEM250 2.1 12.7 1.0
NB A:HEM250 2.1 13.4 1.0
NE2 A:HIS170 2.2 14.3 1.0
N2 A:AZI251 2.9 18.1 1.0
C4D A:HEM250 3.0 13.5 1.0
C1D A:HEM250 3.0 12.4 1.0
C1A A:HEM250 3.0 13.6 1.0
CE1 A:HIS170 3.0 14.6 1.0
C4B A:HEM250 3.0 15.0 1.0
C1B A:HEM250 3.0 14.3 1.0
C1C A:HEM250 3.1 13.7 1.0
C4A A:HEM250 3.1 13.6 1.0
C4C A:HEM250 3.1 12.5 1.0
CD2 A:HIS170 3.2 14.9 1.0
CHA A:HEM250 3.4 14.2 1.0
CHD A:HEM250 3.4 13.3 1.0
CHB A:HEM250 3.4 15.8 1.0
CHC A:HEM250 3.4 14.0 1.0
N3 A:AZI251 4.1 19.8 1.0
ND1 A:HIS170 4.2 15.2 1.0
NE A:ARG183 4.2 15.8 1.0
C2A A:HEM250 4.2 14.5 1.0
C3A A:HEM250 4.2 13.6 1.0
C3D A:HEM250 4.2 13.8 1.0
C2D A:HEM250 4.3 13.0 1.0
C2B A:HEM250 4.3 15.4 1.0
C3C A:HEM250 4.3 14.8 1.0
C2C A:HEM250 4.3 14.0 1.0
C3B A:HEM250 4.3 16.1 1.0
CG A:HIS170 4.3 14.2 1.0
NH2 A:ARG183 4.4 17.8 1.0
CZ A:ARG183 4.8 16.3 1.0

Iron binding site 2 out of 5 in 5a12

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Iron binding site 2 out of 5 in the Crystal Structure of Chlorite Dismutase From Magnetospirillum Sp. in Complex with Azide


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 Chlorite Dismutase From Magnetospirillum Sp. in Complex with Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe250

b:15.2
occ:1.00
FE B:HEM250 0.0 15.2 1.0
ND B:HEM250 1.9 14.8 1.0
NA B:HEM250 2.0 14.2 1.0
N3 B:AZI251 2.1 18.1 1.0
NB B:HEM250 2.1 14.2 1.0
NC B:HEM250 2.1 14.3 1.0
NE2 B:HIS170 2.1 14.2 1.0
C4D B:HEM250 3.0 15.0 1.0
C1D B:HEM250 3.0 14.7 1.0
N2 B:AZI251 3.0 19.0 1.0
CE1 B:HIS170 3.0 15.2 1.0
C4B B:HEM250 3.0 15.0 1.0
C1A B:HEM250 3.0 14.5 1.0
C1B B:HEM250 3.0 14.9 1.0
C4A B:HEM250 3.0 15.3 1.0
C4C B:HEM250 3.1 15.2 1.0
C1C B:HEM250 3.1 14.9 1.0
CD2 B:HIS170 3.2 15.4 1.0
CHD B:HEM250 3.4 14.3 1.0
CHA B:HEM250 3.4 14.6 1.0
CHB B:HEM250 3.4 14.9 1.0
CHC B:HEM250 3.4 14.8 1.0
N1 B:AZI251 4.1 20.9 1.0
ND1 B:HIS170 4.1 15.4 1.0
NE B:ARG183 4.2 17.4 1.0
C2B B:HEM250 4.2 15.9 1.0
C3D B:HEM250 4.2 14.6 1.0
C2A B:HEM250 4.2 14.8 1.0
C3A B:HEM250 4.3 15.6 1.0
C2D B:HEM250 4.3 14.0 1.0
C3B B:HEM250 4.3 17.0 1.0
C2C B:HEM250 4.3 15.2 1.0
C3C B:HEM250 4.3 15.3 1.0
CG B:HIS170 4.3 15.1 1.0
NH2 B:ARG183 4.4 19.3 1.0
CZ B:ARG183 4.8 18.9 1.0

Iron binding site 3 out of 5 in 5a12

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Iron binding site 3 out of 5 in the Crystal Structure of Chlorite Dismutase From Magnetospirillum Sp. in Complex with Azide


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 Chlorite Dismutase From Magnetospirillum Sp. in Complex with Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe250

b:15.2
occ:1.00
FE C:HEM250 0.0 15.2 1.0
ND C:HEM250 1.9 14.9 1.0
NA C:HEM250 2.0 15.1 1.0
N3 C:AZI251 2.0 18.4 1.0
NB C:HEM250 2.1 14.5 1.0
NC C:HEM250 2.1 13.6 1.0
NE2 C:HIS170 2.1 14.6 1.0
C1D C:HEM250 3.0 14.7 1.0
C4D C:HEM250 3.0 13.5 1.0
N2 C:AZI251 3.0 17.7 1.0
C1A C:HEM250 3.0 15.8 1.0
C1B C:HEM250 3.0 15.0 1.0
C4B C:HEM250 3.0 14.8 1.0
CE1 C:HIS170 3.0 14.2 1.0
C4C C:HEM250 3.0 14.4 1.0
C4A C:HEM250 3.1 15.5 1.0
C1C C:HEM250 3.1 14.1 1.0
CD2 C:HIS170 3.2 15.4 1.0
CHD C:HEM250 3.4 14.1 1.0
CHA C:HEM250 3.4 15.0 1.0
CHC C:HEM250 3.4 14.0 1.0
CHB C:HEM250 3.4 14.8 1.0
N1 C:AZI251 4.1 20.8 1.0
ND1 C:HIS170 4.2 15.6 1.0
NE C:ARG183 4.2 18.7 1.0
C2D C:HEM250 4.2 13.5 1.0
C3D C:HEM250 4.2 14.2 1.0
C2A C:HEM250 4.2 15.6 1.0
C2B C:HEM250 4.3 15.6 1.0
C3A C:HEM250 4.3 16.2 1.0
C2C C:HEM250 4.3 13.8 1.0
C3C C:HEM250 4.3 15.4 1.0
CG C:HIS170 4.3 15.1 1.0
C3B C:HEM250 4.3 15.7 1.0
NH2 C:ARG183 4.4 19.6 1.0
CZ C:ARG183 4.8 19.6 1.0

Iron binding site 4 out of 5 in 5a12

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Iron binding site 4 out of 5 in the Crystal Structure of Chlorite Dismutase From Magnetospirillum Sp. in Complex with Azide


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 Chlorite Dismutase From Magnetospirillum Sp. in Complex with Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe250

b:16.1
occ:1.00
FE D:HEM250 0.0 16.1 1.0
ND D:HEM250 1.9 15.2 1.0
N3 D:AZI251 2.0 18.9 1.0
NA D:HEM250 2.0 14.9 1.0
NB D:HEM250 2.1 15.9 1.0
NC D:HEM250 2.1 13.7 1.0
NE2 D:HIS170 2.2 16.0 1.0
N2 D:AZI251 3.0 19.4 1.0
C1D D:HEM250 3.0 15.1 1.0
C4D D:HEM250 3.0 15.4 1.0
C1B D:HEM250 3.0 16.2 1.0
C4B D:HEM250 3.0 16.5 1.0
CE1 D:HIS170 3.0 15.4 1.0
C4C D:HEM250 3.0 15.2 1.0
C1A D:HEM250 3.0 15.8 1.0
C4A D:HEM250 3.1 16.4 1.0
C1C D:HEM250 3.1 15.1 1.0
CD2 D:HIS170 3.2 15.3 1.0
CHD D:HEM250 3.4 14.9 1.0
CHA D:HEM250 3.4 15.2 1.0
CHC D:HEM250 3.4 15.7 1.0
CHB D:HEM250 3.4 16.4 1.0
N1 D:AZI251 4.1 22.4 1.0
NE D:ARG183 4.2 17.8 1.0
ND1 D:HIS170 4.2 16.6 1.0
C3D D:HEM250 4.2 15.7 1.0
C2D D:HEM250 4.2 14.5 1.0
C3C D:HEM250 4.3 16.2 1.0
C2B D:HEM250 4.3 17.1 1.0
C3A D:HEM250 4.3 16.3 1.0
C2C D:HEM250 4.3 15.2 1.0
C2A D:HEM250 4.3 17.0 1.0
C3B D:HEM250 4.3 17.4 1.0
CG D:HIS170 4.3 16.8 1.0
NH2 D:ARG183 4.4 18.6 1.0
CZ D:ARG183 4.7 19.6 1.0

Iron binding site 5 out of 5 in 5a12

Go back to Iron Binding Sites List in 5a12
Iron binding site 5 out of 5 in the Crystal Structure of Chlorite Dismutase From Magnetospirillum Sp. in Complex with Azide


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 Chlorite Dismutase From Magnetospirillum Sp. in Complex with Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe250

b:13.8
occ:1.00
FE E:HEM250 0.0 13.8 1.0
N3 E:AZI251 1.9 17.0 1.0
ND E:HEM250 1.9 13.4 1.0
NA E:HEM250 2.0 13.5 1.0
NB E:HEM250 2.0 12.6 1.0
NC E:HEM250 2.1 13.3 1.0
NE2 E:HIS170 2.2 13.5 1.0
N2 E:AZI251 2.9 19.2 1.0
C4D E:HEM250 3.0 13.5 1.0
C1D E:HEM250 3.0 14.1 1.0
C1A E:HEM250 3.0 14.5 1.0
C4A E:HEM250 3.0 14.8 1.0
C4B E:HEM250 3.0 13.1 1.0
C1B E:HEM250 3.0 14.2 1.0
C4C E:HEM250 3.1 13.3 1.0
C1C E:HEM250 3.1 12.5 1.0
CE1 E:HIS170 3.1 14.9 1.0
CD2 E:HIS170 3.2 13.8 1.0
CHA E:HEM250 3.4 13.7 1.0
CHC E:HEM250 3.4 12.9 1.0
CHD E:HEM250 3.4 13.5 1.0
CHB E:HEM250 3.4 14.0 1.0
N1 E:AZI251 4.0 21.0 1.0
NE E:ARG183 4.2 15.8 1.0
ND1 E:HIS170 4.2 14.7 1.0
C2A E:HEM250 4.2 14.8 1.0
C3A E:HEM250 4.2 14.4 1.0
C2B E:HEM250 4.3 14.6 1.0
C3D E:HEM250 4.3 13.4 1.0
C2D E:HEM250 4.3 13.7 1.0
C2C E:HEM250 4.3 12.6 1.0
C3C E:HEM250 4.3 13.6 1.0
C3B E:HEM250 4.3 14.3 1.0
CG E:HIS170 4.3 14.5 1.0
NH2 E:ARG183 4.4 15.2 1.0
CZ E:ARG183 4.8 14.0 1.0

Reference:

A.De Schutter, H.Correia, D.M.Freire, M.G.Rivas, A.C.Rizzi, T.Santos-Silva, P.J.Gonzalez, S.Van Doorslaer. Ligand Binding to Chlorite Dismutase From Magnetospirillum Sp. J.Phys.Chem.B V. 119 13859 2015.
ISSN: ISSN 1089-5647
PubMed: 26287794
DOI: 10.1021/ACS.JPCB.5B04141
Page generated: Mon Aug 5 18:42:36 2024

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