Atomistry » Iron » PDB 6f0b-6fl2 » 6f6k
Atomistry »
  Iron »
    PDB 6f0b-6fl2 »
      6f6k »

Iron in PDB 6f6k: R2-Like Ligand-Binding Oxidase V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

Enzymatic activity of R2-Like Ligand-Binding Oxidase V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor:
1.17.4.1;

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6k 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) 43.57 / 1.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 160.612, 55.655, 70.075, 90.00, 114.16, 90.00
R / Rfree (%) 19.8 / 26.3

Other elements in 6f6k:

The structure of R2-Like Ligand-Binding Oxidase V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the R2-Like Ligand-Binding Oxidase V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor (pdb code 6f6k). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the R2-Like Ligand-Binding Oxidase V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6k:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6f6k

Go back to Iron Binding Sites List in 6f6k
Iron binding site 1 out of 4 in the R2-Like Ligand-Binding Oxidase V72L Mutant with Anaerobically Reconstituted Mn/Fe 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 V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:25.7
occ:1.00
 ND1 A:HIS205 1.9 27.4 1.0
OE2 A:GLU102 2.0 29.0 1.0
OE1 A:GLU167 2.0 29.2 0.5
OE2 A:GLU167 2.0 24.0 0.5
OE2 A:GLU167 2.1 28.2 0.5
OE1 A:GLU202 2.1 36.2 1.0
OE2 A:GLU202 2.3 25.6 1.0
CD A:GLU167 2.3 25.1 0.5
CD A:GLU202 2.5 24.3 1.0
CE1 A:HIS205 2.7 31.1 1.0
HE1 A:HIS205 2.9 37.3 1.0
CD A:GLU102 3.0 29.8 1.0
CG A:HIS205 3.0 29.4 1.0
CD A:GLU167 3.1 27.7 0.5
HB3 A:HIS205 3.3 33.8 1.0
OE1 A:GLU102 3.3 23.3 1.0
HG2 A:GLU167 3.4 32.0 0.5
HB2 A:HIS205 3.5 33.8 1.0
CB A:HIS205 3.5 28.2 1.0
HZ A:PHE98 3.6 40.3 1.0
MN A:MN401 3.7 27.1 1.0
HE2 A:TYR162 3.7 32.4 1.0
HE2 A:PHE98 3.8 41.3 1.0
CZ A:PHE98 3.8 33.6 1.0
CG A:GLU167 3.8 26.6 0.5
CG A:GLU167 3.8 25.9 0.5
OE1 A:GLU167 3.9 23.5 0.5
CE2 A:PHE98 3.9 34.4 1.0
NE2 A:HIS205 3.9 22.8 1.0
CG A:GLU202 4.0 22.6 1.0
HG A:LEU72 4.0 40.4 1.0
HA A:GLU202 4.1 28.3 1.0
CD2 A:HIS205 4.1 22.5 1.0
O A:HOH549 4.2 36.5 1.0
HG3 A:GLU167 4.2 31.1 0.5
HG2 A:GLU167 4.2 31.1 0.5
HB3 A:GLU167 4.3 31.3 0.5
HE1 A:HIS105 4.3 42.5 1.0
HG2 A:GLU202 4.3 27.1 1.0
CG A:GLU102 4.4 30.3 1.0
O A:HOH514 4.4 36.6 1.0
HG3 A:GLU202 4.4 27.1 1.0
HB3 A:GLU167 4.5 31.2 0.5
HG2 A:GLU102 4.5 36.4 1.0
HG3 A:GLU167 4.5 32.0 0.5
CE1 A:PHE98 4.5 36.6 1.0
HD23 A:LEU72 4.6 40.1 1.0
CE2 A:TYR162 4.6 27.0 1.0
CD2 A:PHE98 4.7 29.5 1.0
HG3 A:GLU102 4.7 36.4 1.0
HE2 A:HIS205 4.7 27.4 1.0
CB A:GLU167 4.7 26.1 0.5
HB3 A:GLU202 4.8 31.8 1.0
OH A:TYR162 4.8 25.6 1.0
CB A:GLU202 4.8 26.5 1.0
CB A:GLU167 4.8 26.0 0.5
HD21 A:LEU72 4.8 40.1 1.0
HE1 A:PHE98 4.9 44.0 1.0
CA A:GLU202 4.9 23.6 1.0
CG A:LEU72 4.9 33.7 1.0
CE1 A:HIS105 4.9 35.4 1.0
HD2 A:HIS205 4.9 27.1 1.0

Iron binding site 2 out of 4 in 6f6k

Go back to Iron Binding Sites List in 6f6k
Iron binding site 2 out of 4 in the R2-Like Ligand-Binding Oxidase V72L Mutant with Anaerobically Reconstituted Mn/Fe 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 V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:65.1
occ:1.00
 O A:HOH560 2.0 46.1 1.0
NE2 A:HIS130 2.2 52.6 1.0
O A:HOH578 3.1 43.5 1.0
CE1 A:HIS130 3.1 36.8 1.0
CD2 A:HIS130 3.2 35.9 1.0
HE1 A:HIS130 3.2 44.1 1.0
HD2 A:HIS130 3.4 43.1 1.0
ND1 A:HIS130 4.2 44.0 1.0
CG A:HIS130 4.3 44.4 1.0
OD2 A:ASP129 4.4 43.6 1.0
HA3 A:GLY240 4.5 53.1 1.0
OD1 A:ASP129 4.7 51.9 1.0
HA2 A:GLY240 4.9 53.1 1.0
CG A:ASP129 5.0 51.7 1.0
HD1 A:HIS130 5.0 52.9 1.0

Iron binding site 3 out of 4 in 6f6k

Go back to Iron Binding Sites List in 6f6k
Iron binding site 3 out of 4 in the R2-Like Ligand-Binding Oxidase V72L Mutant with Anaerobically Reconstituted Mn/Fe 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 V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:30.6
occ:1.00
 OE2 B:GLU102 1.9 27.8 1.0
OE1 B:GLU167 2.0 26.6 0.5
OE2 B:GLU167 2.0 27.7 0.5
OE2 B:GLU167 2.1 29.4 0.5
OE1 B:GLU202 2.2 43.4 1.0
ND1 B:HIS205 2.2 29.6 1.0
CD B:GLU167 2.3 24.2 0.5
OE2 B:GLU202 2.4 39.5 1.0
CD B:GLU202 2.6 36.7 1.0
CD B:GLU102 2.9 25.2 1.0
CD B:GLU167 2.9 26.4 0.5
CE1 B:HIS205 3.1 30.3 1.0
CG B:HIS205 3.2 18.8 1.0
HG2 B:GLU167 3.2 36.4 0.5
HB3 B:HIS205 3.2 35.2 1.0
HE1 B:HIS205 3.3 36.3 1.0
OE1 B:GLU102 3.3 29.3 1.0
HB2 B:HIS205 3.5 35.2 1.0
CB B:HIS205 3.5 29.3 1.0
CG B:GLU167 3.6 30.4 0.5
HE2 B:PHE98 3.6 29.1 1.0
MN B:MN401 3.7 28.6 1.0
HE2 B:TYR162 3.8 23.0 1.0
OE1 B:GLU167 3.8 23.6 0.5
CG B:GLU167 3.8 30.7 0.5
HG B:LEU72 3.8 45.5 1.0
HZ B:PHE98 3.8 36.8 1.0
CE2 B:PHE98 3.9 24.3 1.0
CZ B:PHE98 4.0 30.7 1.0
HA B:GLU202 4.1 37.3 1.0
CG B:GLU202 4.1 39.6 1.0
HB3 B:GLU167 4.1 30.3 0.5
HG3 B:GLU167 4.2 36.8 0.5
O B:HOH521 4.2 36.6 1.0
HG2 B:GLU167 4.2 36.8 0.5
HG3 B:GLU167 4.3 36.4 0.5
NE2 B:HIS205 4.3 25.3 1.0
CG B:GLU102 4.3 20.9 1.0
CD2 B:HIS205 4.3 34.7 1.0
HE1 B:HIS105 4.3 44.0 1.0
HB3 B:GLU167 4.4 30.3 0.5
HG2 B:GLU102 4.4 25.1 1.0
HG3 B:GLU202 4.5 47.5 1.0
HG3 B:GLU102 4.5 25.1 1.0
CB B:GLU167 4.6 25.3 0.5
HG2 B:GLU202 4.6 47.5 1.0
O B:HOH559 4.6 35.8 1.0
CE2 B:TYR162 4.6 19.1 1.0
CB B:GLU167 4.6 25.3 0.5
HB3 B:GLU202 4.7 35.1 1.0
CD2 B:PHE98 4.7 31.1 1.0
HD23 B:LEU72 4.7 51.5 1.0
CG B:LEU72 4.7 37.9 1.0
HB3 B:LEU72 4.8 44.1 1.0
CB B:GLU202 4.8 29.2 1.0
CE1 B:PHE98 4.8 33.4 1.0
CA B:GLU202 4.9 31.1 1.0
CE1 B:HIS105 4.9 36.7 1.0
ND1 B:HIS105 4.9 24.8 1.0
HD2 B:PHE98 5.0 37.4 1.0
OH B:TYR162 5.0 26.0 1.0

Iron binding site 4 out of 4 in 6f6k

Go back to Iron Binding Sites List in 6f6k
Iron binding site 4 out of 4 in the R2-Like Ligand-Binding Oxidase V72L Mutant with Anaerobically Reconstituted Mn/Fe 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 V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:61.9
occ:0.91
 NE2 B:HIS130 2.2 56.6 1.0
O B:HOH522 2.2 47.3 1.0
O B:HOH533 2.2 51.9 1.0
CE1 B:HIS130 2.9 47.0 1.0
HE1 B:HIS130 2.9 56.4 1.0
O B:HOH573 3.0 50.7 1.0
CD2 B:HIS130 3.3 48.0 1.0
HD2 B:HIS130 3.6 57.6 1.0
ND1 B:HIS130 4.1 54.8 1.0
CG B:HIS130 4.3 48.6 1.0
OD2 B:ASP129 4.4 59.1 1.0
OD1 B:ASP129 4.6 53.5 1.0
HA3 B:GLY240 4.7 54.6 1.0
O B:HOH516 4.7 43.2 1.0
O B:HOH531 4.7 46.5 1.0
HD1 B:HIS130 4.8 65.8 1.0
HA2 B:GLY240 4.9 54.6 1.0
CG B:ASP129 5.0 58.6 1.0

Reference:

J.J.Griese, R.M.M.Branca, V.Srinivas, M.Hogbom. Ether Cross-Link Formation in the R2-Like Ligand-Binding Oxidase. J. Biol. Inorg. Chem. V. 23 879 2018.
ISSN: ESSN 1432-1327
PubMed: 29946980
DOI: 10.1007/S00775-018-1583-3
Page generated: Tue Aug 6 18:04:46 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy