Atomistry » Cobalt » PDB 6ega-6kfl » 6hx2
Atomistry »
  Cobalt »
    PDB 6ega-6kfl »
      6hx2 »

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

Protein crystallography data

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

Cobalt Binding Sites:

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 6hx2

Go back to Cobalt Binding Sites List in 6hx2
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 6hx2

Go back to Cobalt Binding Sites List in 6hx2
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 6hx2

Go back to Cobalt Binding Sites List in 6hx2
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 6hx2

Go back to Cobalt Binding Sites List in 6hx2
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 6hx2

Go back to Cobalt Binding Sites List in 6hx2
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 6hx2

Go back to Cobalt Binding Sites List in 6hx2
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 6hx2

Go back to Cobalt Binding Sites List in 6hx2
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 6hx2

Go back to Cobalt Binding Sites List in 6hx2
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 6hx2

Go back to Cobalt Binding Sites List in 6hx2
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 6hx2

Go back to Cobalt Binding Sites List in 6hx2
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

Reference:

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
Page generated: Sun Jul 13 20:57:58 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy