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Iron in PDB 4xbv: R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor

Enzymatic activity of R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor:
1.17.4.1;

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor, PDB code: 4xbv was solved by J.J.Griese, M.Hogbom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.62 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 128.584, 98.077, 55.987, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.9

Iron Binding Sites:

The binding sites of Iron atom in the R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor (pdb code 4xbv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor, PDB code: 4xbv:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4xbv

Go back to Iron Binding Sites List in 4xbv
Iron binding site 1 out of 6 in the R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:20.8
occ:1.00
 O2 A:PLM404 1.8 37.5 1.0
O A:HOH546 1.9 32.9 1.0
OE1 A:GLU102 2.0 21.4 1.0
ND1 A:HIS105 2.1 19.8 1.0
OE1 A:GLU69 2.1 21.2 1.0
OE2 A:GLU202 2.3 22.3 1.0
C1 A:PLM404 2.8 34.7 1.0
CE1 A:HIS105 2.9 20.3 1.0
HE1 A:HIS105 3.0 24.4 1.0
CD A:GLU102 3.1 22.7 1.0
CD A:GLU69 3.1 30.6 1.0
CG A:HIS105 3.2 19.0 1.0
CD A:GLU202 3.3 27.2 1.0
OE2 A:GLU69 3.4 31.7 1.0
O1 A:PLM404 3.4 26.7 1.0
HB2 A:HIS105 3.5 27.4 1.0
HA A:GLU102 3.5 20.4 1.0
OE2 A:GLU102 3.5 23.7 1.0
FE A:FE2402 3.6 24.7 1.0
HB3 A:HIS105 3.6 27.4 1.0
CB A:HIS105 3.7 22.9 1.0
HG21 A:VAL72 3.8 21.4 1.0
HG A:LEU198 3.9 35.5 1.0
HE1 A:HIS205 4.0 22.9 1.0
HD21 A:LEU198 4.1 43.5 1.0
HG2 A:GLU202 4.1 37.0 1.0
NE2 A:HIS105 4.1 19.1 1.0
HG3 A:GLU202 4.1 37.0 1.0
CG A:GLU202 4.2 30.8 1.0
OE1 A:GLU202 4.2 28.1 1.0
H31 A:PLM404 4.2 38.1 1.0
C2 A:PLM404 4.2 39.4 1.0
H32 A:PLM404 4.2 38.1 1.0
CD2 A:HIS105 4.3 20.3 1.0
HD11 A:LEU198 4.3 29.8 1.0
HG23 A:VAL72 4.3 21.4 1.0
CG A:GLU102 4.4 18.5 1.0
HA A:GLU69 4.4 26.1 1.0
CA A:GLU102 4.4 17.0 1.0
CG2 A:VAL72 4.5 17.8 1.0
CG A:GLU69 4.5 22.4 1.0
C3 A:PLM404 4.5 31.8 1.0
HB3 A:GLU102 4.6 20.4 1.0
CG A:LEU198 4.6 29.6 1.0
HB3 A:GLU69 4.7 24.8 1.0
CE1 A:HIS205 4.7 19.1 1.0
HG22 A:VAL72 4.7 21.4 1.0
CB A:GLU102 4.7 17.0 1.0
CD2 A:LEU198 4.7 36.3 1.0
HG3 A:GLU69 4.8 26.9 1.0
ND1 A:HIS205 4.8 22.5 1.0
H22 A:PLM404 4.8 47.3 1.0
HE2 A:HIS105 4.9 22.9 1.0
OH A:TYR175 4.9 53.6 1.0
H21 A:PLM404 4.9 47.3 1.0
HD23 A:LEU198 4.9 43.5 1.0
CD1 A:LEU198 4.9 24.9 1.0
HG2 A:GLU102 4.9 22.2 1.0
HH A:TYR175 5.0 64.3 1.0
HG3 A:GLU102 5.0 22.2 1.0
CB A:GLU69 5.0 20.7 1.0

Iron binding site 2 out of 6 in 4xbv

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Iron binding site 2 out of 6 in the R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:24.7
occ:1.00
 OE2 A:GLU167 1.9 26.7 1.0
O1 A:PLM404 1.9 26.7 1.0
OE2 A:GLU102 2.0 23.7 1.0
ND1 A:HIS205 2.0 22.5 1.0
OE1 A:GLU202 2.2 28.1 1.0
OE2 A:GLU202 2.3 22.3 1.0
CD A:GLU202 2.5 27.2 1.0
CE1 A:HIS205 2.9 19.1 1.0
CD A:GLU102 3.0 22.7 1.0
HE1 A:HIS205 3.0 22.9 1.0
C1 A:PLM404 3.0 34.7 1.0
CD A:GLU167 3.0 29.2 1.0
CG A:HIS205 3.1 18.8 1.0
OE1 A:GLU102 3.3 21.4 1.0
HB3 A:HIS205 3.4 26.7 1.0
HB2 A:HIS205 3.4 26.7 1.0
O2 A:PLM404 3.5 37.5 1.0
CB A:HIS205 3.6 22.2 1.0
HG2 A:GLU167 3.6 37.9 1.0
FE A:FE2401 3.6 20.8 1.0
HE2 A:PHE98 3.8 25.7 1.0
OE1 A:GLU167 3.9 39.1 1.0
CG A:GLU167 3.9 31.6 1.0
HA A:GLU202 3.9 27.9 1.0
HE2 A:TYR162 3.9 31.4 1.0
CE2 A:PHE98 4.0 21.4 1.0
CG A:GLU202 4.0 30.8 1.0
HZ A:PHE98 4.0 27.7 1.0
NE2 A:HIS205 4.0 24.3 1.0
CZ A:PHE98 4.2 23.1 1.0
CD2 A:HIS205 4.2 22.0 1.0
O A:HOH546 4.2 32.9 1.0
HE1 A:HIS105 4.3 24.4 1.0
CG A:GLU102 4.3 18.5 1.0
HG21 A:VAL72 4.3 21.4 1.0
HB3 A:GLU167 4.3 25.1 1.0
HG2 A:GLU102 4.3 22.2 1.0
HG2 A:GLU202 4.4 37.0 1.0
HG3 A:GLU202 4.5 37.0 1.0
C2 A:PLM404 4.5 39.4 1.0
HG3 A:GLU102 4.5 22.2 1.0
O A:HOH590 4.5 36.5 1.0
HB3 A:GLU202 4.6 28.6 1.0
HG3 A:GLU167 4.6 37.9 1.0
H22 A:PLM404 4.6 47.3 1.0
CB A:GLU202 4.7 23.9 1.0
CB A:GLU167 4.7 20.9 1.0
CA A:GLU202 4.8 23.2 1.0
CD2 A:PHE98 4.8 22.0 1.0
H21 A:PLM404 4.8 47.3 1.0
HE2 A:HIS205 4.8 29.1 1.0
CE2 A:TYR162 4.8 26.1 1.0
CE1 A:HIS105 4.9 20.3 1.0
ND1 A:HIS105 4.9 19.8 1.0
HG23 A:VAL72 5.0 21.4 1.0
CE1 A:PHE98 5.0 20.7 1.0

Iron binding site 3 out of 6 in 4xbv

Go back to Iron Binding Sites List in 4xbv
Iron binding site 3 out of 6 in the R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:45.6
occ:0.77
 O A:HOH595 2.1 43.0 1.0
O A:HOH594 2.1 42.1 1.0
O A:HOH582 2.2 46.8 1.0
NE2 A:HIS130 2.2 34.0 1.0
CE1 A:HIS130 3.2 38.1 1.0
CD2 A:HIS130 3.2 35.6 1.0
HE1 A:HIS130 3.3 45.8 1.0
HD2 A:HIS130 3.3 42.7 1.0
OD2 A:ASP129 4.2 44.3 1.0
O A:HOH589 4.2 37.6 1.0
ND1 A:HIS130 4.3 32.1 1.0
CG A:HIS130 4.3 29.6 1.0
OD1 A:ASP129 4.5 39.6 1.0
HA3 A:GLY240 4.7 37.3 1.0
CG A:ASP129 4.8 41.6 1.0
O A:HOH559 4.9 39.0 1.0
O A:HOH579 4.9 40.9 1.0
HA2 A:GLY240 5.0 37.3 1.0

Iron binding site 4 out of 6 in 4xbv

Go back to Iron Binding Sites List in 4xbv
Iron binding site 4 out of 6 in the R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:24.9
occ:1.00
 O2 B:PLM404 1.9 32.2 1.0
ND1 B:HIS205 1.9 20.3 1.0
OE2 B:GLU167 2.0 28.9 1.0
OE2 B:GLU102 2.0 25.6 1.0
OE1 B:GLU202 2.2 23.8 1.0
OE2 B:GLU202 2.3 23.7 1.0
CD B:GLU202 2.6 29.9 1.0
CE1 B:HIS205 2.8 24.2 1.0
HE1 B:HIS205 2.8 29.0 1.0
C1 B:PLM404 3.0 38.8 1.0
CD B:GLU102 3.0 17.0 1.0
CD B:GLU167 3.1 31.4 1.0
CG B:HIS205 3.1 18.0 1.0
OE1 B:GLU102 3.3 18.8 1.0
O1 B:PLM404 3.4 41.0 1.0
HB3 B:HIS205 3.5 26.9 1.0
HB2 B:HIS205 3.5 26.9 1.0
HG2 B:GLU167 3.6 35.9 1.0
FE B:FE2402 3.6 20.7 1.0
CB B:HIS205 3.6 22.4 1.0
HE2 B:PHE98 3.8 27.9 1.0
CG B:GLU167 3.9 29.9 1.0
NE2 B:HIS205 3.9 20.4 1.0
OE1 B:GLU167 4.0 38.9 1.0
CE2 B:PHE98 4.0 23.3 1.0
HA B:GLU202 4.0 24.2 1.0
HZ B:PHE98 4.0 27.9 1.0
HE2 B:TYR162 4.0 27.4 1.0
CG B:GLU202 4.1 26.2 1.0
CD2 B:HIS205 4.1 17.7 1.0
CZ B:PHE98 4.2 23.3 1.0
HE1 B:HIS105 4.2 23.9 1.0
HG21 B:VAL72 4.2 24.8 1.0
HB3 B:GLU167 4.3 28.9 1.0
CG B:GLU102 4.3 17.5 1.0
HG2 B:GLU102 4.4 21.0 1.0
HG2 B:GLU202 4.5 31.5 1.0
C2 B:PLM404 4.5 39.5 1.0
HG3 B:GLU202 4.5 31.5 1.0
HG3 B:GLU102 4.5 21.0 1.0
H21 B:PLM404 4.6 47.4 1.0
HB3 B:GLU202 4.6 33.3 1.0
HG3 B:GLU167 4.7 35.9 1.0
O B:HOH599 4.7 33.2 1.0
HE2 B:HIS205 4.7 24.4 1.0
H22 B:PLM404 4.7 47.4 1.0
CB B:GLU167 4.7 24.1 1.0
CB B:GLU202 4.8 27.8 1.0
CD2 B:PHE98 4.8 20.4 1.0
CA B:GLU202 4.9 20.1 1.0
CE1 B:HIS105 4.9 19.9 1.0
ND1 B:HIS105 4.9 19.9 1.0
CE2 B:TYR162 4.9 22.9 1.0
HB B:VAL72 5.0 29.8 1.0

Iron binding site 5 out of 6 in 4xbv

Go back to Iron Binding Sites List in 4xbv
Iron binding site 5 out of 6 in the R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:20.7
occ:1.00
 O1 B:PLM404 1.8 41.0 1.0
OE1 B:GLU102 2.0 18.8 1.0
ND1 B:HIS105 2.1 19.9 1.0
OE1 B:GLU69 2.1 20.0 1.0
O B:HOH599 2.3 33.2 1.0
OE2 B:GLU202 2.3 23.7 1.0
C1 B:PLM404 2.9 38.8 1.0
CE1 B:HIS105 2.9 19.9 1.0
HE1 B:HIS105 3.0 23.9 1.0
CD B:GLU69 3.0 26.6 1.0
CD B:GLU102 3.2 17.0 1.0
CG B:HIS105 3.2 20.0 1.0
OE2 B:GLU69 3.3 30.8 1.0
CD B:GLU202 3.4 29.9 1.0
O2 B:PLM404 3.5 32.2 1.0
HB2 B:HIS105 3.5 27.8 1.0
OE2 B:GLU102 3.6 25.6 1.0
FE B:FE2401 3.6 24.9 1.0
HB3 B:HIS105 3.6 27.8 1.0
HA B:GLU102 3.6 20.1 1.0
CB B:HIS105 3.7 23.2 1.0
HG21 B:VAL72 3.8 24.8 1.0
HG B:LEU198 3.9 37.5 1.0
HE1 B:HIS205 4.0 29.0 1.0
NE2 B:HIS105 4.1 21.9 1.0
HG3 B:GLU202 4.1 31.5 1.0
H31 B:PLM404 4.1 40.3 1.0
C2 B:PLM404 4.2 39.5 1.0
OE1 B:GLU202 4.2 23.8 1.0
CG B:GLU202 4.2 26.2 1.0
HG2 B:GLU202 4.2 31.5 1.0
HD11 B:LEU198 4.2 33.6 1.0
CD2 B:HIS105 4.3 24.0 1.0
HD21 B:LEU198 4.3 35.7 1.0
HA B:GLU69 4.4 25.6 1.0
CG B:GLU69 4.4 21.2 1.0
H22 B:PLM404 4.5 47.4 1.0
CG B:GLU102 4.5 17.5 1.0
CA B:GLU102 4.5 16.7 1.0
HG23 B:VAL72 4.5 24.8 1.0
CG2 B:VAL72 4.6 20.6 1.0
CE1 B:HIS205 4.6 24.2 1.0
C3 B:PLM404 4.6 33.6 1.0
HB3 B:GLU69 4.6 25.1 1.0
CG B:LEU198 4.6 31.3 1.0
OH B:TYR175 4.7 49.4 1.0
H32 B:PLM404 4.7 40.3 1.0
HB3 B:GLU102 4.7 19.9 1.0
HG3 B:GLU69 4.8 25.5 1.0
ND1 B:HIS205 4.8 20.3 1.0
HG22 B:VAL72 4.8 24.8 1.0
HH B:TYR175 4.8 59.2 1.0
CB B:GLU102 4.8 16.6 1.0
CD1 B:LEU198 4.8 28.0 1.0
HE2 B:HIS105 4.9 26.2 1.0
CD2 B:LEU198 4.9 29.8 1.0
CB B:GLU69 5.0 20.9 1.0

Iron binding site 6 out of 6 in 4xbv

Go back to Iron Binding Sites List in 4xbv
Iron binding site 6 out of 6 in the R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Diiron Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:53.5
occ:0.77
 O B:HOH581 1.9 48.6 1.0
O B:HOH578 2.1 47.0 1.0
O B:HOH592 2.2 56.1 1.0
NE2 B:HIS130 2.3 42.8 1.0
CD2 B:HIS130 3.1 39.4 1.0
HD2 B:HIS130 3.2 47.3 1.0
CE1 B:HIS130 3.3 41.7 1.0
O B:HOH590 3.5 47.2 1.0
HE1 B:HIS130 3.6 50.1 1.0
CG B:HIS130 4.3 38.1 1.0
ND1 B:HIS130 4.4 43.4 1.0
OD2 B:ASP129 4.4 54.1 1.0
OD1 B:ASP129 4.5 45.4 1.0
HA3 B:GLY240 4.7 42.0 1.0
O B:HOH548 4.8 43.0 1.0
O B:HOH587 4.8 46.5 1.0
CG B:ASP129 4.9 50.6 1.0
HA2 B:GLY240 5.0 42.0 1.0

Reference:

J.J.Griese, R.Kositzki, P.Schrapers, R.M.Branca, A.Nordstrom, J.Lehtio, M.Haumann, M.Hogbom. Structural Basis For Oxygen Activation at A Heterodinuclear Manganese/Iron Cofactor. J.Biol.Chem. V. 290 25254 2015.
ISSN: ESSN 1083-351X
PubMed: 26324712
DOI: 10.1074/JBC.M115.675223
Page generated: Mon Aug 5 15:27:25 2024

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