Iron in PDB 2yjk: Structure of Dps From Microbacterium Arborescens in the High Iron Form

The structure of Structure of Dps From Microbacterium Arborescens in the High Iron Form, PDB code: 2yjk was solved by K.Zeth, R.Buecheler, W.Boland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.98 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.580, 92.050, 128.580, 90.00, 96.04, 90.00
R / Rfree (%)	16.992 / 21.65

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Iron atom in the Structure of Dps From Microbacterium Arborescens in the High Iron Form (pdb code 2yjk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 17 binding sites of Iron where determined in the Structure of Dps From Microbacterium Arborescens in the High Iron Form, PDB code: 2yjk:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 17 in the Structure of Dps From Microbacterium Arborescens in the High Iron Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Dps From Microbacterium Arborescens in the High Iron Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1159 b:42.5 occ:1.00 FE A:OFE1159 0.0 42.5 1.0 NE2 B:HIS40 2.4 27.4 1.0 OE2 A:GLU71 2.4 42.3 1.0 OD1 A:ASP67 2.5 42.2 1.0 OD2 A:ASP67 2.5 41.4 1.0 O A:OFE1159 2.5 24.1 0.5 O A:HOH2027 2.6 47.4 1.0 CG A:ASP67 2.8 35.4 1.0 CD A:GLU71 3.1 38.0 1.0 CE1 B:HIS40 3.4 27.0 1.0 CD2 B:HIS40 3.4 22.8 1.0 OE1 A:GLU71 3.4 40.8 1.0 OD2 B:ASP56 3.9 41.6 1.0 NZ B:LYS37 4.1 31.0 1.0 NE1 B:TRP41 4.1 24.4 1.0 CE1 B:HIS52 4.3 32.2 1.0 CG A:GLU71 4.3 32.2 1.0 NE2 B:HIS52 4.3 34.0 1.0 CB A:ASP67 4.4 26.6 1.0 CD1 B:TRP41 4.4 23.2 1.0 ND1 B:HIS40 4.5 24.0 1.0 CG B:HIS40 4.5 25.1 1.0 CG B:ASP56 4.6 36.8 1.0 OD1 B:ASP56 4.8 40.6 1.0

Iron binding site 2 out of 17 in the Structure of Dps From Microbacterium Arborescens in the High Iron Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Dps From Microbacterium Arborescens in the High Iron Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1159 b:38.7 occ:1.00 FE B:OFE1159 0.0 38.7 1.0 OE2 B:GLU71 2.2 36.0 1.0 O B:OFE1159 2.2 42.0 1.0 NE2 A:HIS40 2.3 26.6 1.0 OD1 B:ASP67 2.4 33.3 1.0 OD2 B:ASP67 2.6 36.0 1.0 CG B:ASP67 2.8 31.1 1.0 CD B:GLU71 3.0 30.9 1.0 CE1 A:HIS40 3.2 29.5 1.0 CD2 A:HIS40 3.3 24.1 1.0 OE1 B:GLU71 3.4 34.8 1.0 NZ A:LYS37 4.1 31.7 1.0 OD2 A:ASP56 4.1 40.5 1.0 NE1 A:TRP41 4.2 23.3 1.0 CG B:GLU71 4.2 27.2 1.0 NE2 A:HIS52 4.2 26.9 1.0 CE1 A:HIS52 4.3 27.4 1.0 CB B:ASP67 4.4 22.6 1.0 ND1 A:HIS40 4.4 26.8 1.0 CG A:HIS40 4.4 26.3 1.0 CD1 A:TRP41 4.5 18.4 1.0 CG A:ASP56 4.7 34.6 1.0 OD1 A:ASP56 4.8 39.4 1.0 O A:HOH2013 5.0 46.6 1.0

Iron binding site 3 out of 17 in the Structure of Dps From Microbacterium Arborescens in the High Iron Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Dps From Microbacterium Arborescens in the High Iron Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1160 b:15.6 occ:0.20 O B:HOH2051 1.9 20.5 1.0 O D:HOH2055 1.9 21.4 1.0 O D:HOH2059 1.9 25.5 1.0 O B:HOH2047 1.9 27.5 1.0 O L:HOH2053 2.1 23.0 1.0 O L:HOH2050 2.1 26.4 1.0 O B:HOH2050 3.9 18.2 1.0 OE1 D:GLN135 4.0 29.3 1.0 OE1 L:GLN135 4.0 28.0 1.0 OE1 B:GLN135 4.0 25.7 1.0 O D:HOH2058 4.0 17.6 1.0 O B:HOH2045 4.1 29.1 1.0 O L:HOH2052 4.1 15.8 1.0 O L:HOH2049 4.1 24.0 1.0 O D:HOH2054 4.2 28.3 1.0 O B:HOH2052 4.4 33.5 1.0 O D:HOH2060 4.6 29.4 1.0 CD1 B:LEU132 4.9 25.9 1.0 FE L:FE1160 4.9 5.1 0.2 CD1 L:LEU132 5.0 28.6 1.0

Iron binding site 4 out of 17 in the Structure of Dps From Microbacterium Arborescens in the High Iron Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Dps From Microbacterium Arborescens in the High Iron Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1159 b:41.4 occ:1.00 FE C:OFE1159 0.0 41.4 1.0 O C:OFE1159 2.2 15.9 0.5 OE2 C:GLU71 2.2 43.4 1.0 NE2 I:HIS40 2.4 30.7 1.0 OD2 C:ASP67 2.6 42.0 1.0 O C:HOH2024 2.6 29.8 1.0 CD C:GLU71 3.0 39.0 1.0 CE1 I:HIS40 3.4 24.5 1.0 OE1 C:GLU71 3.4 38.8 1.0 CD2 I:HIS40 3.5 24.7 1.0 CG C:ASP67 3.7 40.5 1.0 OD2 I:ASP56 4.0 43.4 1.0 NZ I:LYS37 4.1 30.1 1.0 CE1 I:HIS52 4.2 33.2 1.0 NE2 I:HIS52 4.2 34.5 1.0 CG C:GLU71 4.3 31.8 1.0 NE1 I:TRP41 4.3 23.1 1.0 CB C:ASP67 4.3 27.4 1.0 ND1 I:HIS40 4.5 27.0 1.0 OD1 I:ASP56 4.5 42.0 1.0 CG I:ASP56 4.6 37.5 1.0 CG I:HIS40 4.6 26.0 1.0 CD1 I:TRP41 4.7 23.6 1.0 OD1 C:ASP67 4.8 42.8 1.0

Iron binding site 5 out of 17 in the Structure of Dps From Microbacterium Arborescens in the High Iron Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Dps From Microbacterium Arborescens in the High Iron Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1160 b:19.7 occ:0.20 OD2 A:ASP128 4.1 44.1 1.0 OD1 A:ASP128 4.2 38.9 1.0 OD1 C:ASP128 4.2 45.9 1.0 OD1 E:ASP128 4.2 44.6 1.0 OD2 E:ASP128 4.3 49.9 1.0 OD2 C:ASP128 4.4 52.1 1.0 CG A:ASP128 4.6 43.2 1.0 CG E:ASP128 4.7 48.6 1.0 CG C:ASP128 4.7 46.6 1.0

Iron binding site 6 out of 17 in the Structure of Dps From Microbacterium Arborescens in the High Iron Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Dps From Microbacterium Arborescens in the High Iron Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1159 b:41.3 occ:1.00 FE D:OFE1159 0.0 41.3 1.0 O D:OFE1159 2.2 19.0 0.5 OE2 D:GLU71 2.3 38.6 1.0 NE2 J:HIS40 2.3 24.9 1.0 OD1 D:ASP67 2.3 21.1 0.5 OD2 D:ASP67 2.5 23.4 0.5 CG D:ASP67 2.8 22.4 0.5 O D:HOH2026 2.8 36.1 1.0 CD D:GLU71 3.0 34.9 1.0 CD2 J:HIS40 3.2 24.2 1.0 CE1 J:HIS40 3.4 23.7 1.0 OE1 D:GLU71 3.4 37.6 1.0 OD2 J:ASP56 3.9 41.5 1.0 NE1 J:TRP41 4.1 23.0 1.0 NZ J:LYS37 4.1 31.9 1.0 CG D:GLU71 4.2 29.9 1.0 CB D:ASP67 4.3 21.3 0.5 NE2 J:HIS52 4.4 29.6 1.0 CB D:ASP67 4.4 22.9 0.5 CG J:HIS40 4.4 25.9 1.0 CE1 J:HIS52 4.4 28.4 1.0 OD2 D:ASP67 4.4 33.1 0.5 CD1 J:TRP41 4.4 22.7 1.0 ND1 J:HIS40 4.5 25.7 1.0 CG D:ASP67 4.5 26.2 0.5 OD1 J:ASP56 4.5 38.4 1.0 CG J:ASP56 4.6 37.3 1.0

Iron binding site 7 out of 17 in the Structure of Dps From Microbacterium Arborescens in the High Iron Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Dps From Microbacterium Arborescens in the High Iron Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1160 b:14.2 occ:0.20 O K:HOH2047 1.6 28.3 1.0 O I:HOH2036 1.7 24.3 1.0 O K:HOH2046 1.9 24.4 1.0 O G:HOH2081 1.9 29.9 1.0 O G:HOH2080 2.0 40.4 1.0 O I:HOH2037 2.1 25.7 1.0 O G:HOH2085 4.0 38.5 1.0 OD1 G:ASP128 4.0 38.3 1.0 OD1 K:ASP128 4.1 44.6 1.0 OD2 G:ASP128 4.2 42.6 1.0 OD1 I:ASP128 4.3 40.9 1.0 OD2 K:ASP128 4.4 49.1 1.0 OD2 I:ASP128 4.5 47.8 1.0 CG G:ASP128 4.6 38.1 1.0 CG K:ASP128 4.7 45.5 1.0 CG I:ASP128 4.8 42.8 1.0

Iron binding site 8 out of 17 in the Structure of Dps From Microbacterium Arborescens in the High Iron Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Dps From Microbacterium Arborescens in the High Iron Form within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe1159 b:41.1 occ:1.00 FE E:OFE1159 0.0 41.1 1.0 OE2 E:GLU71 2.2 40.6 1.0 OD1 E:ASP67 2.4 43.1 1.0 NE2 F:HIS40 2.4 24.0 1.0 O E:OFE1159 2.5 19.1 0.5 O E:HOH2029 2.6 31.5 1.0 CD E:GLU71 3.1 37.3 1.0 CD2 F:HIS40 3.3 25.3 1.0 OE1 E:GLU71 3.4 39.4 1.0 CE1 F:HIS40 3.4 30.0 1.0 CG E:ASP67 3.5 40.9 1.0 OD2 F:ASP56 4.0 41.4 1.0 NE1 F:TRP41 4.1 24.2 1.0 NZ F:LYS37 4.2 31.7 1.0 NE2 F:HIS52 4.2 31.6 1.0 CB E:ASP67 4.3 29.5 1.0 CD1 F:TRP41 4.3 26.2 1.0 CG E:GLU71 4.4 30.8 1.0 CE1 F:HIS52 4.4 32.4 1.0 OD2 E:ASP67 4.4 49.8 1.0 CG F:HIS40 4.5 26.4 1.0 ND1 F:HIS40 4.5 28.0 1.0 OD1 F:ASP56 4.6 35.9 1.0 CG F:ASP56 4.6 35.8 1.0

Iron binding site 9 out of 17 in the Structure of Dps From Microbacterium Arborescens in the High Iron Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of Dps From Microbacterium Arborescens in the High Iron Form within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe1159 b:35.7 occ:1.00 FE F:OFE1159 0.0 35.7 1.0 OE2 F:GLU71 2.1 38.5 1.0 NE2 E:HIS40 2.4 22.8 1.0 O E:HOH2012 2.4 36.2 1.0 O F:OFE1159 2.5 27.2 0.5 OD2 F:ASP67 2.5 33.5 1.0 OD1 F:ASP67 2.5 32.8 1.0 CG F:ASP67 2.8 30.2 1.0 CD F:GLU71 2.9 35.7 1.0 CD2 E:HIS40 3.2 21.5 1.0 CE1 E:HIS40 3.4 25.3 1.0 OE1 F:GLU71 3.4 37.6 1.0 CG F:GLU71 4.1 28.6 1.0 NE1 E:TRP41 4.1 18.6 1.0 OD2 E:ASP56 4.2 41.4 1.0 NE2 E:HIS52 4.2 30.4 1.0 NZ E:LYS37 4.2 30.7 1.0 CE1 E:HIS52 4.3 28.1 1.0 CB F:ASP67 4.4 23.6 1.0 CD1 E:TRP41 4.4 20.1 1.0 CG E:HIS40 4.4 23.8 1.0 ND1 E:HIS40 4.5 23.4 1.0 CG E:ASP56 4.8 35.0 1.0 OD1 E:ASP56 4.8 39.9 1.0 O E:HOH2013 4.8 44.9 1.0

Iron binding site 10 out of 17 in the Structure of Dps From Microbacterium Arborescens in the High Iron Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of Dps From Microbacterium Arborescens in the High Iron Form within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe1159 b:34.5 occ:1.00 FE G:OFE1159 0.0 34.5 1.0 O G:OFE1159 2.2 17.9 0.5 NE2 H:HIS40 2.2 23.1 1.0 OE2 G:GLU71 2.3 37.2 1.0 OD2 G:ASP67 2.4 34.1 1.0 O G:HOH2040 2.5 33.6 1.0 OD1 G:ASP67 2.5 35.9 1.0 CG G:ASP67 2.8 28.5 1.0 CD G:GLU71 3.1 34.2 1.0 CD2 H:HIS40 3.2 21.7 1.0 CE1 H:HIS40 3.2 25.1 1.0 OE1 G:GLU71 3.5 34.3 1.0 NZ H:LYS37 3.9 28.1 1.0 OD2 H:ASP56 4.0 37.0 1.0 NE1 H:TRP41 4.2 19.6 1.0 NE2 H:HIS52 4.2 28.1 1.0 CG G:GLU71 4.3 24.2 1.0 CE1 H:HIS52 4.3 25.0 1.0 ND1 H:HIS40 4.3 21.9 1.0 CB G:ASP67 4.3 20.5 1.0 CG H:HIS40 4.4 20.3 1.0 CD1 H:TRP41 4.5 19.3 1.0 OD1 H:ASP56 4.5 35.8 1.0 CG H:ASP56 4.6 30.8 1.0 O G:HOH2035 4.9 46.5 1.0

J.Pesek, R.Buecheler, R.Albrecht, W.Boland, K.Zeth. Structure and Mechanism of Iron Translocation By A Dps Protein From Microbacterium Arborescens. J.Biol.Chem. V. 286 34872 2011.
ISSN: ISSN 0021-9258
PubMed: 21768097
DOI: 10.1074/JBC.M111.246108