Cobalt in PDB 6hx2: The Structure of Dps From Listeria Innocua Soaked with Cobalt

The structure of The Structure of Dps From Listeria Innocua Soaked with Cobalt, PDB code: 6hx2 was solved by K.Zeth, M.Okuda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.05 / 1.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.581, 87.581, 277.363, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 17.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 45;

Binding sites:

The binding sites of Cobalt atom in the The Structure of Dps From Listeria Innocua Soaked with Cobalt (pdb code 6hx2). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 45 binding sites of Cobalt where determined in the The Structure of Dps From Listeria Innocua Soaked with Cobalt, PDB code: 6hx2:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 45 in the The Structure of Dps From Listeria Innocua Soaked with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of The Structure of Dps From Listeria Innocua Soaked with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co201 b:19.7 occ:0.82 OE2 A:GLU63 2.0 33.3 1.0 O A:HOH381 2.0 31.2 0.9 NE2 D:HIS32 2.1 21.7 1.0 O D:HOH322 2.1 34.7 1.0 OD2 A:ASP59 2.2 26.1 1.0 OD1 A:ASP59 2.3 26.3 1.0 CG A:ASP59 2.5 25.6 1.0 CD A:GLU63 3.0 26.1 1.0 CD2 D:HIS32 3.0 20.3 1.0 CE1 D:HIS32 3.1 22.9 1.0 HD2 D:HIS32 3.1 24.4 1.0 HE1 D:HIS32 3.3 27.4 1.0 OE1 A:GLU63 3.4 26.2 1.0 HE1 D:TRP33 3.6 26.1 1.0 O D:HOH356 3.8 36.5 1.0 CB A:ASP59 4.0 23.6 1.0 OD1 D:ASP48 4.0 28.1 1.0 HE1 D:HIS44 4.1 29.7 1.0 HG3 A:GLU63 4.1 28.0 1.0 CG A:GLU63 4.2 23.4 1.0 O A:HOH436 4.2 73.8 1.0 CG D:HIS32 4.2 20.9 1.0 ND1 D:HIS32 4.2 22.0 1.0 NE2 D:HIS44 4.3 24.5 1.0 O A:HOH315 4.3 42.9 1.0 HD1 D:TRP33 4.3 25.0 1.0 OD2 D:ASP48 4.3 31.4 1.0 NE1 D:TRP33 4.3 21.8 1.0 HB2 A:ASP59 4.4 28.4 1.0 HB3 A:ASP59 4.4 28.4 1.0 CE1 D:HIS44 4.4 24.7 1.0 O A:HOH471 4.5 91.4 1.0 HG2 A:GLU63 4.5 28.0 1.0 CG D:ASP48 4.6 27.7 1.0 O D:HOH376 4.6 42.4 1.0 CD1 D:TRP33 4.7 20.8 1.0 HH2 B:TRP145 4.8 28.3 1.0 HA A:ASP59 4.9 25.3 1.0 O A:ASP59 5.0 20.3 1.0 HD1 D:HIS32 5.0 26.4 1.0 CA A:ASP59 5.0 21.1 1.0

Cobalt binding site 2 out of 45 in the The Structure of Dps From Listeria Innocua Soaked with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of The Structure of Dps From Listeria Innocua Soaked with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co202 b:30.1 occ:0.72 O A:HOH428 2.0 33.7 0.9 O A:HOH439 2.1 29.3 1.0 CO A:CO208 2.1 44.7 0.5 O A:HOH337 2.1 32.6 1.0 O A:HOH446 2.2 34.9 0.9 ND1 A:HIS16 2.2 37.3 1.0 CE1 A:HIS16 3.1 36.4 1.0 O A:HOH466 3.1 67.9 1.0 HB2 A:HIS16 3.1 35.7 1.0 HE1 A:HIS16 3.2 43.6 1.0 CG A:HIS16 3.3 33.9 1.0 CB A:HIS16 3.7 29.8 1.0 O A:HOH464 3.9 51.0 1.0 O A:ASN82 4.0 32.2 1.0 O A:HOH361 4.2 29.0 1.0 HB3 A:ASN82 4.2 35.0 1.0 HA A:HIS16 4.2 30.0 1.0 NE2 A:HIS16 4.3 33.1 1.0 CD2 A:HIS16 4.4 32.9 1.0 HG2 A:GLU12 4.4 60.8 1.0 HB3 A:HIS16 4.5 35.7 1.0 OE2 A:GLU12 4.5 63.9 1.0 OD1 A:ASN82 4.5 32.1 1.0 CA A:HIS16 4.6 25.0 1.0 HA A:ASN82 4.6 36.2 1.0 O A:HOH440 4.8 57.3 1.0 CB A:ASN82 5.0 29.1 1.0 C A:ASN82 5.0 30.1 1.0

Cobalt binding site 3 out of 45 in the The Structure of Dps From Listeria Innocua Soaked with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of The Structure of Dps From Listeria Innocua Soaked with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co203 b:20.1 occ:0.35 O A:HOH355 2.2 35.9 0.9 O A:HOH456 2.3 47.4 1.0 HG1 A:THR42 3.5 34.8 1.0 O A:HOH491 3.8 46.3 1.0 O A:HOH327 4.1 41.1 1.0 HG23 A:THR42 4.1 31.6 1.0 OG1 A:THR42 4.3 29.0 1.0 HA A:THR42 4.5 26.8 1.0 O A:HOH398 4.7 27.4 1.0 OE1 A:GLU45 4.9 59.5 1.0 CG2 A:THR42 4.9 26.4 1.0

Cobalt binding site 4 out of 45 in the The Structure of Dps From Listeria Innocua Soaked with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of The Structure of Dps From Listeria Innocua Soaked with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co204 b:43.8 occ:0.62 NE2 A:HIS38 2.2 58.1 1.0 CO A:CO210 2.3 73.1 0.4 O A:HOH469 2.4 31.4 0.5 CD2 A:HIS38 3.1 50.4 1.0 CE1 A:HIS38 3.2 61.6 1.0 HD2 A:HIS38 3.3 60.5 1.0 HE1 A:HIS38 3.4 74.0 1.0 ND1 A:HIS38 4.2 56.0 1.0 CG A:HIS38 4.2 46.4 1.0 HD1 A:HIS38 5.0 67.2 1.0

Cobalt binding site 5 out of 45 in the The Structure of Dps From Listeria Innocua Soaked with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of The Structure of Dps From Listeria Innocua Soaked with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co205 b:29.9 occ:0.29 OD2 A:ASP97 2.3 39.8 1.0 CG A:ASP97 3.3 36.2 1.0 OD1 A:ASP97 3.6 37.5 1.0 O A:HOH408 4.0 32.9 1.0 CB A:ASP97 4.6 31.2 1.0 HB2 A:ASP97 4.6 37.5 1.0

Cobalt binding site 6 out of 45 in the The Structure of Dps From Listeria Innocua Soaked with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of The Structure of Dps From Listeria Innocua Soaked with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co206 b:81.0 occ:0.66 O A:HOH436 2.1 73.8 1.0 O A:HOH471 2.3 91.4 1.0 OE1 A:GLU56 2.3 43.1 0.5 O A:HOH303 2.3 49.7 1.0 OE1 A:GLU56 2.4 43.0 0.5 O A:HOH462 2.4 59.3 1.0 OE2 A:GLU56 2.4 44.0 0.5 CD A:GLU56 2.7 40.4 0.5 O A:HOH315 3.0 42.9 1.0 CD A:GLU56 3.5 41.3 0.5 OD2 A:ASP59 4.0 26.1 1.0 OE2 A:GLU56 4.0 45.7 0.5 CG A:GLU56 4.2 31.0 0.5 OE2 A:GLU60 4.2 40.2 0.5 HB3 A:ASP59 4.3 28.4 1.0 O D:HOH322 4.4 34.7 1.0 HB3 A:GLU56 4.4 31.9 0.5 HA A:GLU56 4.5 28.2 0.5 HG2 A:GLU56 4.5 37.2 0.5 HG2 A:GLU60 4.5 38.0 0.5 HA A:GLU56 4.5 28.2 0.5 HG3 A:GLU60 4.6 38.0 0.5 CG A:GLU56 4.7 31.5 0.5 HG3 A:GLU56 4.7 37.2 0.5 HG3 A:GLU56 4.8 37.8 0.5 CG A:ASP59 4.9 25.6 1.0 O A:HOH381 4.9 31.2 0.9 HG2 A:GLU60 4.9 38.0 0.5 CB A:GLU56 5.0 26.6 0.5 HB2 A:GLU56 5.0 31.8 0.5

Cobalt binding site 7 out of 45 in the The Structure of Dps From Listeria Innocua Soaked with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of The Structure of Dps From Listeria Innocua Soaked with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co207 b:89.0 occ:0.90 O A:HOH435 2.4 42.8 1.0 O A:HOH449 3.0 46.9 1.0 HD1 A:HIS38 3.1 67.2 1.0 HB2 A:HIS38 3.8 43.1 1.0 ND1 A:HIS38 3.9 56.0 1.0 HB3 A:HIS38 4.3 43.1 1.0 CB A:HIS38 4.4 36.0 1.0 CG A:HIS38 4.6 46.4 1.0 HD21 A:ASN39 4.7 46.5 1.0 CE1 A:HIS38 4.9 61.6 1.0

Cobalt binding site 8 out of 45 in the The Structure of Dps From Listeria Innocua Soaked with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of The Structure of Dps From Listeria Innocua Soaked with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co208 b:44.7 occ:0.48 CO A:CO202 2.1 30.1 0.7 O A:HOH466 2.2 67.9 1.0 O A:HOH428 2.8 33.7 0.9 O A:HOH337 2.9 32.6 1.0 O A:HOH439 2.9 29.3 1.0 O A:HOH446 3.0 34.9 0.9 OE2 A:GLU12 3.6 63.9 1.0 O A:HOH440 3.9 57.3 1.0 OD1 A:ASN82 4.1 32.1 1.0 O A:HOH361 4.4 29.0 1.0 ND1 A:HIS16 4.4 37.3 1.0 HG2 A:GLU12 4.4 60.8 1.0 HG3 A:GLU12 4.5 60.8 1.0 CD A:GLU12 4.5 62.8 1.0 CG A:GLU12 4.7 50.7 1.0 HB2 A:HIS16 4.8 35.7 1.0 HE1 A:HIS16 4.9 43.6 1.0 HA A:ASN82 5.0 36.2 1.0

Cobalt binding site 9 out of 45 in the The Structure of Dps From Listeria Innocua Soaked with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of The Structure of Dps From Listeria Innocua Soaked with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co209 b:99.1 occ:0.82 O A:HOH429 1.7 0.7 1.0 CO B:CO208 2.2 69.4 0.6 CO F:CO203 2.5 63.9 0.2 OD1 A:ASP131 2.7 51.7 1.0 OD2 A:ASP131 2.8 52.7 1.0 O A:HOH389 2.8 43.5 1.0 CG A:ASP131 3.1 45.9 1.0 O B:HOH367 3.2 52.0 1.0 O F:HOH332 3.7 57.1 1.0 O B:HOH377 3.7 44.8 1.0 OD1 F:ASP131 3.8 40.7 1.0 HB2 A:ALA135 3.9 29.7 1.0 O A:HOH460 4.3 50.1 1.0 OD1 B:ASP131 4.3 53.1 1.0 OD2 F:ASP131 4.4 44.9 1.0 O A:ASP131 4.4 24.6 1.0 O A:HOH307 4.4 56.3 1.0 O A:HOH309 4.4 84.2 1.0 CG F:ASP131 4.5 38.4 1.0 CB A:ASP131 4.6 31.3 1.0 O F:HOH311 4.7 53.0 1.0 CB A:ALA135 4.9 24.8 1.0 C A:ASP131 4.9 24.2 1.0

Cobalt binding site 10 out of 45 in the The Structure of Dps From Listeria Innocua Soaked with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of The Structure of Dps From Listeria Innocua Soaked with Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co210 b:73.1 occ:0.39 CO A:CO204 2.3 43.8 0.6 NE2 A:HIS38 2.7 58.1 1.0 HE1 A:HIS38 2.7 74.0 1.0 CE1 A:HIS38 3.0 61.6 1.0 O A:HOH469 3.7 31.4 0.5 CD2 A:HIS38 4.0 50.4 1.0 ND1 A:HIS38 4.3 56.0 1.0 HD2 A:HIS38 4.4 60.5 1.0 CG A:HIS38 4.8 46.4 1.0 HD1 A:HIS38 4.9 67.2 1.0

K.Zeth, E.Sancho-Vaello, M.Okuda. Metal Positions and Translocation Pathways of the Dodecameric Ferritin-Like Protein Dps. Inorg.Chem. V. 58 11351 2019.
ISSN: ISSN 0020-1669
PubMed: 31433627
DOI: 10.1021/ACS.INORGCHEM.9B00301