Iron in PDB 3qvd: Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point.

The structure of Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point., PDB code: 3qvd was solved by B.D.Dillard, J.M.Demick, M.W.W.Adams, W.N.Lanzilotta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.73 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.589, 104.458, 104.512, 90.00, 90.51, 90.00
R / Rfree (%)	21.1 / 23.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iron atom in the Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point. (pdb code 3qvd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point., PDB code: 3qvd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in the Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe172 b:34.7 occ:1.00 SG A:CYS157 2.3 33.1 1.0 SG A:CYS142 2.3 34.5 1.0 SG A:CYS160 2.3 38.9 1.0 SG A:CYS145 2.3 35.0 1.0 CB A:CYS157 3.1 34.7 1.0 CB A:CYS142 3.2 34.4 1.0 CB A:CYS145 3.5 35.1 1.0 CB A:CYS160 3.5 35.3 1.0 N A:CYS160 3.8 34.5 1.0 N A:CYS145 3.8 32.7 1.0 CA A:CYS160 4.2 35.8 1.0 CA A:CYS145 4.2 32.3 1.0 CB A:TYR147 4.2 33.6 1.0 CB A:ILE144 4.3 36.1 1.0 CB A:VAL159 4.6 37.1 1.0 CA A:CYS157 4.6 33.9 1.0 CB A:ALA162 4.6 38.6 1.0 CA A:CYS142 4.7 34.9 1.0 C A:ILE144 4.7 34.4 1.0 N A:GLY161 4.8 36.6 1.0 N A:TYR147 4.8 32.7 1.0 C A:CYS160 4.8 38.0 1.0 C A:VAL159 4.8 35.5 1.0 C A:CYS145 4.8 33.2 1.0 N A:ALA162 4.9 37.6 1.0 N A:GLY146 4.9 32.6 1.0 CA A:ILE144 4.9 34.6 1.0 CG2 A:ILE144 5.0 34.0 1.0

Iron binding site 2 out of 28 in the Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe173 b:35.7 occ:1.00 OE2 B:GLU52 2.1 31.6 1.0 OE2 A:GLU114 2.1 30.9 1.0 OE1 A:GLU80 2.1 29.9 1.0 ND1 A:HIS117 2.3 29.4 1.0 OE2 A:GLU80 2.4 28.9 1.0 O1 A:PEO1 2.4 44.4 1.0 CD A:GLU80 2.6 30.3 1.0 CD B:GLU52 2.9 32.0 1.0 OE1 B:GLU52 3.1 32.3 1.0 O2 A:PEO1 3.1 42.6 1.0 CE1 A:HIS117 3.2 31.4 1.0 CD A:GLU114 3.2 32.7 1.0 CG A:HIS117 3.3 29.9 1.0 FE B:FE2173 3.7 36.6 1.0 CB A:HIS117 3.7 31.1 1.0 OE1 A:GLU114 3.8 34.2 1.0 CG A:GLU80 4.1 30.2 1.0 CA A:GLU114 4.1 34.1 1.0 OE2 A:GLU83 4.2 45.5 1.0 CG A:GLU114 4.3 34.5 1.0 CB A:GLU114 4.3 34.9 1.0 NE2 A:HIS117 4.3 31.3 1.0 CG B:GLU52 4.4 30.5 1.0 CD2 A:HIS117 4.4 32.5 1.0 CG2 B:ILE48 4.5 24.6 1.0 CE1 B:TYR26 4.6 35.1 1.0 OH B:TYR26 4.6 34.9 1.0 N A:GLU114 4.8 33.5 1.0 CB A:GLU80 5.0 32.1 1.0

Iron binding site 3 out of 28 in the Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe174 b:34.4 occ:0.55 OE1 B:GLU114 2.0 38.2 1.0 OE2 A:GLU52 2.1 33.4 1.0 FE A:FE175 2.1 34.1 0.5 ND1 A:HIS55 2.2 32.3 1.0 OE2 A:GLU19 2.3 38.8 1.0 OE1 A:GLU19 2.4 33.9 1.0 CD A:GLU19 2.6 37.0 1.0 CD B:GLU114 2.9 35.0 1.0 CE1 A:HIS55 3.0 32.9 1.0 OE2 B:GLU114 3.1 30.6 1.0 CD A:GLU52 3.2 32.4 1.0 CG A:HIS55 3.3 32.6 1.0 O B:HOH204 3.5 39.2 1.0 CB A:HIS55 3.7 30.3 1.0 FE B:FE2174 3.7 33.6 1.0 OE1 A:GLU52 3.7 34.1 1.0 CA A:GLU52 4.1 31.1 1.0 CG A:GLU19 4.2 33.8 1.0 NE2 A:HIS55 4.2 34.7 1.0 OE1 B:GLU83 4.2 43.5 1.0 CG A:GLU52 4.3 31.2 1.0 CG B:GLU114 4.3 32.1 1.0 CB A:GLU52 4.3 28.7 1.0 CD2 A:HIS55 4.3 32.3 1.0 CB B:ALA110 4.6 35.2 1.0 OH B:TYR88 4.6 31.0 1.0 CE2 B:TYR88 4.8 30.5 1.0 CB A:GLU19 4.9 33.2 1.0 OE2 B:GLU83 4.9 47.3 1.0 N A:GLU52 4.9 29.1 1.0 O A:ALA51 4.9 30.4 1.0 CE1 B:HIS117 5.0 30.1 1.0 CD B:GLU83 5.0 42.9 1.0

Iron binding site 4 out of 28 in the Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe175 b:34.1 occ:0.45 O B:HOH204 2.0 39.2 1.0 FE A:FE2174 2.1 34.4 0.6 OE1 B:GLU83 2.7 43.5 1.0 OE2 A:GLU19 2.8 38.8 1.0 OE1 B:GLU114 2.9 38.2 1.0 OE1 A:GLU19 2.9 33.9 1.0 CD A:GLU19 3.1 37.0 1.0 OE2 A:GLU52 3.1 33.4 1.0 OE2 B:GLU83 3.1 47.3 1.0 CD B:GLU83 3.3 42.9 1.0 CD A:GLU52 3.4 32.4 1.0 CD B:GLU114 3.4 35.0 1.0 FE B:FE2174 3.5 33.6 1.0 OE1 A:GLU52 3.5 34.1 1.0 OE2 B:GLU114 3.6 30.6 1.0 CB A:ALA22 4.1 30.6 1.0 CG A:GLU19 4.3 33.8 1.0 ND1 A:HIS55 4.3 32.3 1.0 CG A:GLU52 4.4 31.2 1.0 CA A:GLU19 4.5 33.1 1.0 CG B:GLU114 4.6 32.1 1.0 OE2 B:GLU80 4.6 37.3 1.0 CB A:GLU52 4.7 28.7 1.0 CG B:GLU83 4.8 39.4 1.0 OE1 B:GLU80 4.8 37.8 1.0 O B:HOH198 4.8 51.1 1.0 CB A:GLU19 4.8 33.2 1.0 CE2 B:TYR88 4.9 30.5 1.0 OH B:TYR88 4.9 31.0 1.0

Iron binding site 5 out of 28 in the Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe172 b:33.9 occ:1.00 SG B:CYS142 2.3 33.5 1.0 SG B:CYS157 2.3 34.2 1.0 SG B:CYS160 2.3 34.4 1.0 SG B:CYS145 2.3 33.1 1.0 CB B:CYS157 3.2 37.0 1.0 CB B:CYS142 3.2 34.4 1.0 CB B:CYS160 3.4 34.7 1.0 CB B:CYS145 3.6 32.9 1.0 N B:CYS145 3.8 31.8 1.0 N B:CYS160 3.8 33.9 1.0 CA B:CYS160 4.2 34.4 1.0 CB B:TYR147 4.2 37.9 1.0 CA B:CYS145 4.2 31.2 1.0 CB B:ILE144 4.3 35.4 1.0 CB B:ALA162 4.4 38.1 1.0 CA B:CYS157 4.6 35.9 1.0 CA B:CYS142 4.7 34.0 1.0 N B:TYR147 4.7 34.5 1.0 C B:ILE144 4.7 33.6 1.0 CB B:VAL159 4.7 33.4 1.0 C B:CYS145 4.8 31.4 1.0 N B:ALA162 4.8 35.1 1.0 C B:CYS160 4.8 34.1 1.0 N B:GLY146 4.8 30.3 1.0 N B:GLY161 4.9 34.6 1.0 C B:VAL159 4.9 34.0 1.0 CA B:ILE144 4.9 35.1 1.0 CG2 B:ILE144 4.9 36.4 1.0 N B:ILE144 5.0 36.0 1.0

Iron binding site 6 out of 28 in the Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe173 b:36.6 occ:1.00 OE1 A:GLU114 2.0 34.2 1.0 OE1 B:GLU52 2.1 32.3 1.0 O2 A:PEO1 2.2 42.6 1.0 OE1 B:GLU19 2.2 32.8 1.0 ND1 B:HIS55 2.3 34.1 1.0 OE2 B:GLU19 2.4 30.9 1.0 CD B:GLU19 2.6 32.2 1.0 CD A:GLU114 2.8 32.7 1.0 OE2 A:GLU114 3.0 30.9 1.0 CD B:GLU52 3.2 32.0 1.0 CE1 B:HIS55 3.2 34.8 1.0 O1 A:PEO1 3.4 44.4 1.0 CG B:HIS55 3.4 32.6 1.0 FE A:FE2173 3.7 35.7 1.0 OE2 B:GLU52 3.7 31.6 1.0 CB B:HIS55 3.8 31.6 1.0 OE2 A:GLU83 4.1 45.5 1.0 CG B:GLU19 4.1 31.0 1.0 CA B:GLU52 4.1 31.4 1.0 CG A:GLU114 4.3 34.5 1.0 CG B:GLU52 4.3 30.5 1.0 CB B:GLU52 4.3 30.4 1.0 NE2 B:HIS55 4.3 35.6 1.0 CD2 B:HIS55 4.5 35.3 1.0 CB A:ALA110 4.6 34.7 1.0 OH A:TYR88 4.7 32.3 1.0 CE2 A:TYR88 4.8 32.7 1.0 CB B:GLU19 4.9 32.2 1.0 N B:GLU52 4.9 30.8 1.0 CE1 A:HIS117 4.9 31.4 1.0 O A:ALA110 4.9 36.6 1.0 O B:ALA51 5.0 29.2 1.0 ND1 A:HIS117 5.0 29.4 1.0

Iron binding site 7 out of 28 in the Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe174 b:33.6 occ:1.00 OE2 B:GLU114 2.1 30.6 1.0 OE2 B:GLU80 2.1 37.3 1.0 OE1 A:GLU52 2.1 34.1 1.0 ND1 B:HIS117 2.3 30.8 1.0 O B:HOH204 2.3 39.2 1.0 OE1 B:GLU80 2.3 37.8 1.0 CD B:GLU80 2.5 36.6 1.0 CD A:GLU52 3.0 32.4 1.0 CD B:GLU114 3.1 35.0 1.0 CE1 B:HIS117 3.1 30.1 1.0 OE2 A:GLU52 3.2 33.4 1.0 CG B:HIS117 3.3 30.7 1.0 FE A:FE175 3.5 34.1 0.5 CB B:HIS117 3.7 31.2 1.0 FE A:FE2174 3.7 34.4 0.6 OE1 B:GLU114 3.7 38.2 1.0 CG B:GLU80 4.0 36.5 1.0 CA B:GLU114 4.0 34.3 1.0 OE1 B:GLU83 4.1 43.5 1.0 CG B:GLU114 4.2 32.1 1.0 CB B:GLU114 4.2 34.3 1.0 NE2 B:HIS117 4.3 30.9 1.0 CG2 A:ILE48 4.4 30.7 1.0 CD2 B:HIS117 4.4 30.1 1.0 CG A:GLU52 4.4 31.2 1.0 OH A:TYR26 4.5 37.6 1.0 CE1 A:TYR26 4.6 36.1 1.0 N B:GLU114 4.7 33.6 1.0 CE1 A:HIS55 4.9 32.9 1.0 CB B:GLU80 4.9 36.0 1.0

Iron binding site 8 out of 28 in the Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point. within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe173 b:33.9 occ:1.00 SG C:CYS157 2.3 32.7 1.0 SG C:CYS145 2.3 33.4 1.0 SG C:CYS142 2.3 35.5 1.0 SG C:CYS160 2.3 38.3 1.0 CB C:CYS157 3.2 34.4 1.0 CB C:CYS142 3.3 32.1 1.0 CB C:CYS160 3.5 36.5 1.0 CB C:CYS145 3.5 34.9 1.0 N C:CYS160 3.8 37.0 1.0 N C:CYS145 3.8 31.9 1.0 CA C:CYS160 4.2 37.8 1.0 CA C:CYS145 4.2 32.7 1.0 CB C:TYR147 4.3 32.1 1.0 CB C:ILE144 4.3 37.3 1.0 CB C:VAL159 4.6 37.4 1.0 CB C:ALA162 4.6 37.0 1.0 CA C:CYS157 4.6 33.9 1.0 CA C:CYS142 4.7 33.2 1.0 C C:ILE144 4.7 33.5 1.0 N C:TYR147 4.8 32.9 1.0 C C:VAL159 4.8 36.5 1.0 C C:CYS160 4.8 39.1 1.0 N C:GLY161 4.8 38.9 1.0 N C:ALA162 4.9 38.0 1.0 C C:CYS145 4.9 32.5 1.0 CA C:ILE144 4.9 34.6 1.0 N C:GLY146 4.9 32.4 1.0 N C:ILE144 5.0 34.3 1.0 CG2 C:ILE144 5.0 37.1 1.0

Iron binding site 9 out of 28 in the Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point. within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe174 b:29.2 occ:0.56 OE2 C:GLU52 2.1 32.5 1.0 OE2 C:GLU19 2.2 31.9 1.0 OE1 D:GLU114 2.2 36.2 1.0 ND1 C:HIS55 2.2 28.3 1.0 FE D:FE175 2.3 38.0 0.4 OE1 C:GLU19 2.3 32.1 1.0 CD C:GLU19 2.5 29.9 1.0 CD D:GLU114 3.0 37.8 1.0 OE2 D:GLU114 3.1 35.5 1.0 CE1 C:HIS55 3.1 28.1 1.0 CD C:GLU52 3.2 33.0 1.0 CG C:HIS55 3.3 29.5 1.0 O D:HOH197 3.3 58.0 0.7 CB C:HIS55 3.7 30.0 1.0 FE D:FE2174 3.8 34.3 1.0 OE1 C:GLU52 3.8 32.4 1.0 CG C:GLU19 4.0 28.2 1.0 OE1 D:GLU83 4.1 44.2 1.0 CA C:GLU52 4.1 31.8 1.0 NE2 C:HIS55 4.3 32.8 1.0 CG C:GLU52 4.3 29.8 1.0 CB C:GLU52 4.3 31.0 1.0 CD2 C:HIS55 4.4 29.7 1.0 CG D:GLU114 4.4 35.5 1.0 CB D:ALA110 4.6 34.5 1.0 OH D:TYR88 4.6 31.4 1.0 CE2 D:TYR88 4.8 32.1 1.0 OE2 D:GLU83 4.8 45.4 1.0 CB C:GLU19 4.8 28.7 1.0 CD D:GLU83 4.8 42.5 1.0 N C:GLU52 4.9 31.2 1.0

Iron binding site 10 out of 28 in the Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Exposure of Rubrerythrin From Pyrococcus Furiosus to Peroxide, Fifteen Second Time Point. within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe175 b:34.6 occ:1.00 OE2 D:GLU52 2.0 33.0 1.0 OE2 C:GLU114 2.2 33.5 1.0 OE2 C:GLU80 2.2 30.8 1.0 OE1 C:GLU80 2.3 32.0 1.0 ND1 C:HIS117 2.3 28.7 1.0 O1 C:PEO172 2.5 46.4 1.0 CD C:GLU80 2.6 32.1 1.0 CD D:GLU52 2.9 33.3 1.0 O2 C:PEO172 3.0 43.1 1.0 OE1 D:GLU52 3.1 32.9 1.0 CD C:GLU114 3.2 35.4 1.0 CE1 C:HIS117 3.3 30.2 1.0 CG C:HIS117 3.4 29.1 1.0 CB C:HIS117 3.7 30.5 1.0 FE D:FE2173 3.7 34.8 1.0 OE1 C:GLU114 3.9 34.4 1.0 CA C:GLU114 4.1 36.0 1.0 CG C:GLU80 4.1 31.4 1.0 OE2 C:GLU83 4.3 44.2 1.0 CB C:GLU114 4.3 37.0 1.0 CG C:GLU114 4.3 36.0 1.0 CG D:GLU52 4.4 31.1 1.0 NE2 C:HIS117 4.4 30.1 1.0 CG2 D:ILE48 4.4 28.3 1.0 CD2 C:HIS117 4.5 29.0 1.0 CE1 D:TYR26 4.6 30.8 1.0 OH D:TYR26 4.6 29.7 1.0 N C:GLU114 4.8 35.6 1.0 CB C:GLU80 4.9 29.9 1.0

B.D.Dillard, J.M.Demick, M.W.Adams, W.N.Lanzilotta. A Cryo-Crystallographic Time Course For Peroxide Reduction By Rubrerythrin From Pyrococcus Furiosus. J.Biol.Inorg.Chem. V. 16 949 2011.
ISSN: ISSN 0949-8257
PubMed: 21647777
DOI: 10.1007/S00775-011-0795-6