Iron in PDB 1veq: Mycobacterium Smegmatis Dps Hexagonal Form

The structure of Mycobacterium Smegmatis Dps Hexagonal Form, PDB code: 1veq was solved by S.Roy, S.Gupta, S.Das, K.Sekar, D.Chatterji, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.89 / 3.98
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	194.667, 194.667, 120.612, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 24.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Mycobacterium Smegmatis Dps Hexagonal Form (pdb code 1veq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Mycobacterium Smegmatis Dps Hexagonal Form, PDB code: 1veq:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the Mycobacterium Smegmatis Dps Hexagonal Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Mycobacterium Smegmatis Dps Hexagonal Form within 5.0Å range: probe atom residue distance (Å) B Occ J:Fe201 b:4.3 occ:0.60 OE2 J:GLU70 2.1 41.6 1.0 NE2 A:HIS39 2.2 43.4 1.0 OD2 J:ASP66 2.5 41.4 1.0 OD1 J:ASP66 2.6 41.4 1.0 CD J:GLU70 2.8 41.6 1.0 CG J:ASP66 2.9 41.4 1.0 CE1 A:HIS39 3.0 43.4 1.0 OE1 J:GLU70 3.2 41.6 1.0 CD2 A:HIS39 3.4 43.4 1.0 NE2 A:HIS51 3.8 36.5 1.0 CE1 A:HIS51 3.9 36.5 1.0 CG J:GLU70 4.0 41.6 1.0 OD2 A:ASP55 4.0 47.1 1.0 NZ A:LYS36 4.2 35.5 1.0 ND1 A:HIS39 4.2 43.4 1.0 CG A:HIS39 4.4 43.4 1.0 CB J:ASP66 4.4 41.4 1.0 CG A:ASP55 4.8 47.1 1.0 OD1 A:ASP55 4.9 47.1 1.0 CD2 A:HIS51 4.9 36.5 1.0

Iron binding site 2 out of 12 in the Mycobacterium Smegmatis Dps Hexagonal Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Mycobacterium Smegmatis Dps Hexagonal Form within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe202 b:22.0 occ:0.60 OE2 E:GLU70 2.2 45.6 1.0 OD1 E:ASP66 2.3 48.1 1.0 NE2 B:HIS39 2.3 53.0 1.0 OD2 E:ASP66 2.4 48.1 1.0 CG E:ASP66 2.7 48.1 1.0 CD E:GLU70 2.8 45.6 1.0 OE1 E:GLU70 3.1 45.6 1.0 CE1 B:HIS39 3.2 53.0 1.0 CD2 B:HIS39 3.4 53.0 1.0 CG E:GLU70 3.9 45.6 1.0 OD2 B:ASP55 4.0 32.2 1.0 NE2 B:HIS51 4.0 15.0 1.0 NZ B:LYS36 4.0 48.6 1.0 CE1 B:HIS51 4.1 15.0 1.0 CB E:ASP66 4.2 48.1 1.0 ND1 B:HIS39 4.4 53.0 1.0 CG B:HIS39 4.5 53.0 1.0 OD1 B:ASP55 4.8 32.2 1.0 CG B:ASP55 4.8 32.2 1.0

Iron binding site 3 out of 12 in the Mycobacterium Smegmatis Dps Hexagonal Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Mycobacterium Smegmatis Dps Hexagonal Form within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe203 b:6.2 occ:0.60 NE2 C:HIS39 2.2 38.4 1.0 OE2 I:GLU70 2.3 31.5 1.0 OD2 I:ASP66 2.5 40.9 1.0 OD1 I:ASP66 2.5 40.9 1.0 CG I:ASP66 2.8 40.9 1.0 CD I:GLU70 3.0 31.5 1.0 CE1 C:HIS39 3.1 38.4 1.0 OE1 I:GLU70 3.3 31.5 1.0 CD2 C:HIS39 3.4 38.4 1.0 OD2 C:ASP55 3.7 41.9 1.0 NZ C:LYS36 3.9 11.7 1.0 NE2 C:HIS51 4.1 27.0 1.0 CG I:GLU70 4.1 31.5 1.0 CE1 C:HIS51 4.2 27.0 1.0 ND1 C:HIS39 4.3 38.4 1.0 CB I:ASP66 4.3 40.9 1.0 CG C:HIS39 4.4 38.4 1.0 OD1 C:ASP55 4.5 41.9 1.0 CG C:ASP55 4.5 41.9 1.0

Iron binding site 4 out of 12 in the Mycobacterium Smegmatis Dps Hexagonal Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Mycobacterium Smegmatis Dps Hexagonal Form within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe204 b:34.3 occ:0.60 NE2 D:HIS39 2.2 47.3 1.0 OE2 G:GLU70 2.3 19.4 1.0 OD2 G:ASP66 2.4 62.0 1.0 OD1 G:ASP66 2.5 62.0 1.0 CG G:ASP66 2.7 62.0 1.0 CD G:GLU70 3.0 19.4 1.0 CE1 D:HIS39 3.0 47.3 1.0 OE1 G:GLU70 3.3 19.4 1.0 CD2 D:HIS39 3.4 47.3 1.0 OD2 D:ASP55 3.8 68.2 1.0 NE2 D:HIS51 4.0 46.4 1.0 NZ D:LYS36 4.0 22.0 1.0 CE1 D:HIS51 4.1 46.4 1.0 CG G:GLU70 4.1 19.4 1.0 ND1 D:HIS39 4.2 47.3 1.0 CB G:ASP66 4.2 62.0 1.0 CG D:HIS39 4.4 47.3 1.0 CG D:ASP55 4.6 68.2 1.0 OD1 D:ASP55 4.6 68.2 1.0

Iron binding site 5 out of 12 in the Mycobacterium Smegmatis Dps Hexagonal Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Mycobacterium Smegmatis Dps Hexagonal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe205 b:21.6 occ:0.60 OD1 B:ASP66 2.2 49.5 1.0 OE2 B:GLU70 2.3 28.5 1.0 NE2 E:HIS39 2.4 41.5 1.0 OD2 B:ASP66 2.4 49.5 1.0 CG B:ASP66 2.6 49.5 1.0 CD B:GLU70 2.8 28.5 1.0 OE1 B:GLU70 3.1 28.5 1.0 CE1 E:HIS39 3.3 41.5 1.0 CD2 E:HIS39 3.5 41.5 1.0 OD2 E:ASP55 3.9 73.7 1.0 CG B:GLU70 4.0 28.5 1.0 NZ E:LYS36 4.0 80.2 1.0 NE2 E:HIS51 4.1 30.5 1.0 CB B:ASP66 4.2 49.5 1.0 CE1 E:HIS51 4.2 30.5 1.0 ND1 E:HIS39 4.4 41.5 1.0 CG E:HIS39 4.6 41.5 1.0 OD1 E:ASP55 4.8 73.7 1.0 CG E:ASP55 4.8 73.7 1.0

Iron binding site 6 out of 12 in the Mycobacterium Smegmatis Dps Hexagonal Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Mycobacterium Smegmatis Dps Hexagonal Form within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe206 b:1.8 occ:0.60 OE2 L:GLU70 2.2 35.8 1.0 OD1 L:ASP66 2.3 35.7 1.0 NE2 F:HIS39 2.4 33.7 1.0 OD2 L:ASP66 2.4 35.7 1.0 CG L:ASP66 2.7 35.7 1.0 CD L:GLU70 2.8 35.8 1.0 OE1 L:GLU70 3.1 35.8 1.0 CE1 F:HIS39 3.2 33.7 1.0 CD2 F:HIS39 3.4 33.7 1.0 OD2 F:ASP55 3.9 25.9 1.0 CG L:GLU70 4.0 35.8 1.0 NZ F:LYS36 4.0 33.8 1.0 NE2 F:HIS51 4.1 41.6 1.0 CB L:ASP66 4.2 35.7 1.0 CE1 F:HIS51 4.2 41.6 1.0 ND1 F:HIS39 4.4 33.7 1.0 CG F:HIS39 4.5 33.7 1.0 OD1 F:ASP55 4.7 25.9 1.0 CG F:ASP55 4.7 25.9 1.0

Iron binding site 7 out of 12 in the Mycobacterium Smegmatis Dps Hexagonal Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Mycobacterium Smegmatis Dps Hexagonal Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe207 b:40.5 occ:0.60 OD1 D:ASP66 2.1 76.4 1.0 OE2 D:GLU70 2.3 59.4 1.0 OD2 D:ASP66 2.4 76.4 1.0 CG D:ASP66 2.5 76.4 1.0 NE2 G:HIS39 2.7 64.8 1.0 CD D:GLU70 2.8 59.4 1.0 OE1 D:GLU70 2.9 59.4 1.0 CE1 G:HIS39 3.5 64.8 1.0 CD2 G:HIS39 3.7 64.8 1.0 CG D:GLU70 3.9 59.4 1.0 CB D:ASP66 4.0 76.4 1.0 OD2 G:ASP55 4.1 19.4 1.0 NE2 G:HIS51 4.2 49.0 1.0 NZ G:LYS36 4.2 0.2 1.0 CE1 G:HIS51 4.3 49.0 1.0 ND1 G:HIS39 4.7 64.8 1.0 CG G:HIS39 4.8 64.8 1.0 OD1 G:ASP55 4.9 19.4 1.0 CG G:ASP55 5.0 19.4 1.0

Iron binding site 8 out of 12 in the Mycobacterium Smegmatis Dps Hexagonal Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Mycobacterium Smegmatis Dps Hexagonal Form within 5.0Å range: probe atom residue distance (Å) B Occ K:Fe208 b:5.5 occ:0.60 OE2 K:GLU70 2.1 28.7 1.0 OD1 K:ASP66 2.2 12.2 1.0 OD2 K:ASP66 2.3 12.2 1.0 NE2 H:HIS39 2.3 59.5 1.0 CG K:ASP66 2.5 12.2 1.0 CD K:GLU70 2.7 28.7 1.0 OE1 K:GLU70 3.1 28.7 1.0 CE1 H:HIS39 3.2 59.5 1.0 CD2 H:HIS39 3.3 59.5 1.0 CG K:GLU70 3.8 28.7 1.0 NZ H:LYS36 3.9 57.1 1.0 OD2 H:ASP55 4.0 47.7 1.0 CB K:ASP66 4.1 12.2 1.0 NE2 H:HIS51 4.1 31.2 1.0 CE1 H:HIS51 4.1 31.2 1.0 ND1 H:HIS39 4.4 59.5 1.0 CG H:HIS39 4.5 59.5 1.0 OD1 H:ASP55 4.7 47.7 1.0 CG H:ASP55 4.8 47.7 1.0

Iron binding site 9 out of 12 in the Mycobacterium Smegmatis Dps Hexagonal Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Mycobacterium Smegmatis Dps Hexagonal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe209 b:4.3 occ:0.60 OE2 C:GLU70 2.2 16.8 1.0 OD1 C:ASP66 2.3 46.8 1.0 NE2 I:HIS39 2.3 61.8 1.0 OD2 C:ASP66 2.4 46.8 1.0 CG C:ASP66 2.6 46.8 1.0 CD C:GLU70 2.8 16.8 1.0 OE1 C:GLU70 3.2 16.8 1.0 CE1 I:HIS39 3.2 61.8 1.0 CD2 I:HIS39 3.4 61.8 1.0 NZ I:LYS36 3.9 57.2 1.0 OD2 I:ASP55 3.9 52.1 1.0 CG C:GLU70 3.9 16.8 1.0 NE2 I:HIS51 4.1 21.4 1.0 CB C:ASP66 4.2 46.8 1.0 CE1 I:HIS51 4.2 21.4 1.0 ND1 I:HIS39 4.4 61.8 1.0 CG I:HIS39 4.5 61.8 1.0 OD1 I:ASP55 4.7 52.1 1.0 CG I:ASP55 4.7 52.1 1.0

Iron binding site 10 out of 12 in the Mycobacterium Smegmatis Dps Hexagonal Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Mycobacterium Smegmatis Dps Hexagonal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe210 b:7.4 occ:0.60 OE2 A:GLU70 2.1 25.0 1.0 OD1 A:ASP66 2.3 19.2 1.0 OD2 A:ASP66 2.4 19.2 1.0 NE2 J:HIS39 2.4 43.6 1.0 CG A:ASP66 2.7 19.2 1.0 CD A:GLU70 2.8 25.0 1.0 OE1 A:GLU70 3.1 25.0 1.0 CE1 J:HIS39 3.3 43.6 1.0 CD2 J:HIS39 3.5 43.6 1.0 CG A:GLU70 3.9 25.0 1.0 NE2 J:HIS51 4.0 14.4 1.0 OD2 J:ASP55 4.0 40.1 1.0 CE1 J:HIS51 4.1 14.4 1.0 NZ J:LYS36 4.2 46.0 1.0 CB A:ASP66 4.2 19.2 1.0 ND1 J:HIS39 4.4 43.6 1.0 CG J:HIS39 4.6 43.6 1.0 CG J:ASP55 4.9 40.1 1.0 OD1 J:ASP55 4.9 40.1 1.0

S.Roy, S.Gupta, S.Das, K.Sekar, D.Chatterji, M.Vijayan. X-Ray Analysis of Mycobacterium Smegmatis Dps and A Comparative Study Involving Other Dps and Dps-Like Molecules J.Mol.Biol. V. 339 1103 2004.
ISSN: ISSN 0022-2836
PubMed: 15178251
DOI: 10.1016/J.JMB.2004.04.042