Atomistry » Iron » PDB 5da5-5eaw » 5dco
Atomistry »
  Iron »
    PDB 5da5-5eaw »
      5dco »

Iron in PDB 5dco: R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Diiron Cofactor (Short Soak)

Enzymatic activity of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Diiron Cofactor (Short Soak)

All present enzymatic activity of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Diiron Cofactor (Short Soak):
1.17.4.1;

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Diiron Cofactor (Short Soak), PDB code: 5dco 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) 48.22 / 2.33
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 55.629, 96.695, 128.342, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 22.6

Iron Binding Sites:

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

Iron binding site 1 out of 2 in 5dco

Go back to Iron Binding Sites List in 5dco
Iron binding site 1 out of 2 in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Diiron Cofactor (Short Soak)


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 Aerobically Reconstituted Diiron Cofactor (Short Soak) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:41.3
occ:1.00
O1 A:PLM403 1.9 46.1 1.0
OE2 A:GLU102 2.2 36.5 1.0
OE2 A:GLU69 2.2 47.2 1.0
O A:HOH507 2.2 43.3 1.0
ND1 A:HIS105 2.3 37.3 1.0
O A:HOH506 2.5 39.4 1.0
C1 A:PLM403 2.7 43.2 1.0
O2 A:PLM403 3.1 44.1 1.0
CD A:GLU69 3.1 40.6 1.0
CE1 A:HIS105 3.1 35.2 1.0
HE1 A:HIS105 3.2 42.2 1.0
CD A:GLU102 3.2 37.6 1.0
OE1 A:GLU69 3.3 51.1 1.0
CG A:HIS105 3.3 41.1 1.0
FE A:FE402 3.5 40.9 1.0
HB2 A:HIS105 3.5 49.9 1.0
HB3 A:HIS105 3.6 49.9 1.0
OE1 A:GLU102 3.6 44.6 1.0
CB A:HIS105 3.7 41.5 1.0
HA A:GLU102 3.8 36.6 1.0
OE1 A:GLU202 3.9 49.6 1.0
HG21 A:VAL72 3.9 59.9 1.0
HG A:LEU198 4.0 43.6 1.0
HE1 A:HIS205 4.1 45.0 1.0
C2 A:PLM403 4.1 39.4 1.0
H31 A:PLM403 4.2 49.2 1.0
HA A:GLU69 4.2 43.9 1.0
H32 A:PLM403 4.3 49.2 1.0
NE2 A:HIS105 4.3 33.9 1.0
OH A:TYR175 4.4 52.5 1.0
CD2 A:HIS105 4.4 43.3 1.0
HH A:TYR175 4.4 63.0 1.0
CG A:GLU69 4.5 42.2 1.0
HB3 A:GLU69 4.5 51.3 1.0
C3 A:PLM403 4.5 41.0 1.0
CG A:GLU102 4.6 39.0 1.0
H22 A:PLM403 4.7 47.3 1.0
OE2 A:GLU202 4.7 42.5 1.0
CA A:GLU102 4.7 30.5 1.0
CD A:GLU202 4.7 43.5 1.0
HB3 A:GLU102 4.7 37.9 1.0
CG2 A:VAL72 4.7 49.9 1.0
CE1 A:HIS205 4.7 37.5 1.0
HG23 A:VAL72 4.8 59.9 1.0
ND1 A:HIS205 4.8 43.0 1.0
CB A:GLU69 4.8 42.7 1.0
H21 A:PLM403 4.8 47.3 1.0
HG3 A:GLU69 4.9 50.7 1.0
CB A:GLU102 4.9 31.5 1.0
CG A:LEU198 4.9 36.3 1.0
HD23 A:LEU198 4.9 45.8 1.0
HG22 A:VAL72 4.9 59.9 1.0
CA A:GLU69 5.0 36.6 1.0

Iron binding site 2 out of 2 in 5dco

Go back to Iron Binding Sites List in 5dco
Iron binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Diiron Cofactor (Short Soak)


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 Aerobically Reconstituted Diiron Cofactor (Short Soak) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:40.9
occ:1.00
O2 A:PLM403 2.0 44.1 1.0
OE2 A:GLU167 2.0 29.7 1.0
O A:HOH507 2.0 43.3 1.0
ND1 A:HIS205 2.2 43.0 1.0
OE1 A:GLU102 2.2 44.6 1.0
OE2 A:GLU202 2.3 42.5 1.0
HG2 A:GLU167 2.8 38.6 1.0
CD A:GLU167 3.0 32.8 1.0
CE1 A:HIS205 3.0 37.5 1.0
C1 A:PLM403 3.1 43.2 1.0
HE1 A:HIS205 3.1 45.0 1.0
CD A:GLU102 3.1 37.6 1.0
CD A:GLU202 3.2 43.5 1.0
CG A:HIS205 3.2 34.6 1.0
OE2 A:GLU102 3.4 36.5 1.0
CG A:GLU167 3.4 32.2 1.0
OE1 A:GLU202 3.5 49.6 1.0
HB3 A:HIS205 3.5 30.0 1.0
FE A:FE401 3.5 41.3 1.0
HB2 A:HIS205 3.5 30.0 1.0
CB A:HIS205 3.7 25.0 1.0
HE2 A:PHE98 3.7 45.6 1.0
O1 A:PLM403 3.7 46.1 1.0
HE2 A:TYR162 3.9 52.9 1.0
HA A:GLU202 4.0 43.1 1.0
HG3 A:GLU167 4.0 38.6 1.0
OE1 A:GLU167 4.0 29.5 1.0
CE2 A:PHE98 4.1 38.0 1.0
HZ A:PHE98 4.2 37.2 1.0
NE2 A:HIS205 4.2 32.1 1.0
HG21 A:VAL72 4.2 59.9 1.0
HB3 A:GLU167 4.3 37.7 1.0
HE1 A:HIS105 4.3 42.2 1.0
CD2 A:HIS205 4.3 35.9 1.0
H22 A:PLM403 4.3 47.3 1.0
C2 A:PLM403 4.3 39.4 1.0
CZ A:PHE98 4.4 31.0 1.0
CB A:GLU167 4.5 31.4 1.0
CG A:GLU102 4.5 39.0 1.0
CG A:GLU202 4.6 38.5 1.0
H21 A:PLM403 4.6 47.3 1.0
HG2 A:GLU102 4.7 46.8 1.0
HG3 A:GLU202 4.7 46.2 1.0
HG3 A:GLU102 4.8 46.8 1.0
CE2 A:TYR162 4.8 44.1 1.0
CA A:GLU202 4.9 35.9 1.0
CE1 A:HIS105 4.9 35.2 1.0
HG11 A:VAL72 4.9 59.1 1.0
ND1 A:HIS105 4.9 37.3 1.0
HE2 A:HIS205 4.9 38.5 1.0
O A:HOH506 4.9 39.4 1.0
HH A:TYR175 5.0 63.0 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: Sun Dec 13 15:59:20 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy