Calcium in PDB 6sdk: Crystal Structure of Bacterial Parb Dimer Bound to Cdp

The structure of Crystal Structure of Bacterial Parb Dimer Bound to Cdp, PDB code: 6sdk was solved by Y.M.Soh, J.Basquin, S.Gruber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.38 / 1.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.186, 104.501, 103.193, 90.00, 102.57, 90.00
R / Rfree (%)	18.4 / 21.3

The binding sites of Calcium atom in the Crystal Structure of Bacterial Parb Dimer Bound to Cdp (pdb code 6sdk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Bacterial Parb Dimer Bound to Cdp, PDB code: 6sdk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of Bacterial Parb Dimer Bound to Cdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Bacterial Parb Dimer Bound to Cdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:26.6 occ:1.00 O3B A:CDP301 2.2 24.6 1.0 OD1 A:ASN112 2.3 25.8 1.0 O1A A:CDP301 2.4 24.4 1.0 OE1 A:GLU111 2.5 30.7 1.0 O A:HOH499 2.6 29.4 1.0 O A:HOH413 2.6 32.2 1.0 O A:HOH436 2.6 33.5 1.0 HH12 A:ARG115 3.1 33.9 1.0 CG A:ASN112 3.3 26.8 1.0 PB A:CDP301 3.3 26.5 1.0 PA A:CDP301 3.4 25.3 1.0 HD21 A:ASN112 3.4 35.8 1.0 CD A:GLU111 3.6 34.0 1.0 HH21 A:ARG39 3.6 33.9 1.0 O3A A:CDP301 3.6 27.8 1.0 HH21 A:ARG80 3.6 29.6 1.0 ND2 A:ASN112 3.8 29.9 1.0 NH1 A:ARG115 3.8 28.2 1.0 O1B A:CDP301 3.8 27.5 1.0 HH22 A:ARG115 3.9 31.8 1.0 O5' A:CDP301 3.9 26.3 1.0 OE2 A:GLU111 3.9 30.0 1.0 HB1 A:ALA76 4.1 30.8 1.0 HH11 A:ARG115 4.2 33.9 1.0 NH2 A:ARG80 4.3 24.6 1.0 NH2 A:ARG39 4.3 28.3 1.0 HH22 A:ARG80 4.4 29.6 1.0 HA A:ASN112 4.4 28.1 1.0 HB3 A:GLU111 4.4 29.9 1.0 H A:GLY77 4.5 32.3 1.0 NH2 A:ARG115 4.5 26.5 1.0 HH22 A:ARG39 4.5 33.9 1.0 O A:HOH430 4.5 35.1 1.0 CZ A:ARG115 4.5 28.5 1.0 CB A:ASN112 4.6 28.0 1.0 HD22 A:ASN112 4.6 35.8 1.0 O2B A:CDP301 4.6 24.4 1.0 O2A A:CDP301 4.7 23.8 1.0 O A:HOH460 4.7 35.2 1.0 CA A:ASN112 4.8 23.4 1.0 CG A:GLU111 4.9 26.9 1.0 N A:ASN112 4.9 25.7 1.0 HB3 A:ASN112 4.9 33.5 1.0 HA A:ALA76 4.9 33.8 1.0 N A:GLY77 4.9 26.9 1.0 HA2 A:GLY77 5.0 33.7 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Bacterial Parb Dimer Bound to Cdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Bacterial Parb Dimer Bound to Cdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:33.5 occ:1.00 HE22 A:GLN37 2.4 37.8 1.0 H A:GLY77 2.5 32.3 1.0 H A:GLU78 2.5 30.8 1.0 HD22 A:ASN34 2.6 37.1 1.0 HA A:ALA76 2.9 33.8 1.0 NE2 A:GLN37 3.2 31.5 1.0 O A:HOH499 3.2 29.4 1.0 N A:GLY77 3.3 26.9 1.0 O A:HOH430 3.3 35.1 1.0 HB3 A:GLU78 3.3 35.7 1.0 HG22 A:ILE74 3.3 31.6 1.0 HB2 A:GLU78 3.3 35.7 1.0 N A:GLU78 3.4 25.7 1.0 ND2 A:ASN34 3.5 30.9 1.0 HE21 A:GLN37 3.6 37.8 1.0 HB2 A:ASN34 3.6 41.3 1.0 CB A:GLU78 3.7 29.7 1.0 CA A:ALA76 3.7 28.1 1.0 HD21 A:ASN34 3.9 37.1 1.0 C A:ALA76 3.9 29.5 1.0 HG21 A:ILE74 4.0 31.6 1.0 O1B A:CDP301 4.0 27.5 1.0 CG2 A:ILE74 4.0 26.4 1.0 O A:HOH436 4.1 33.5 1.0 CD A:GLN37 4.1 32.8 1.0 O A:VAL75 4.1 27.2 1.0 OE1 A:GLN37 4.2 33.4 1.0 CA A:GLU78 4.2 27.7 1.0 CA A:GLY77 4.3 28.1 1.0 C A:GLY77 4.3 24.2 1.0 CB A:ASN34 4.3 34.4 1.0 HB3 A:ASN34 4.3 41.3 1.0 N A:ALA76 4.3 26.5 1.0 O A:HOH460 4.3 35.2 1.0 C A:VAL75 4.4 28.1 1.0 CG A:ASN34 4.4 35.4 1.0 HG23 A:ILE74 4.4 31.6 1.0 HD21 A:ASN112 4.6 35.8 1.0 HD2 A:PRO38 4.6 35.6 1.0 HA A:GLU78 4.7 33.3 1.0 HA2 A:GLY77 4.7 33.7 1.0 H A:ARG79 4.8 29.1 1.0 HB1 A:ALA76 4.9 30.8 1.0 O3B A:CDP301 4.9 24.6 1.0 CB A:ALA76 4.9 25.6 1.0 H A:ALA76 4.9 31.8 1.0 HA A:GLN37 4.9 35.3 1.0 HA3 A:GLY77 5.0 33.7 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of Bacterial Parb Dimer Bound to Cdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Bacterial Parb Dimer Bound to Cdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:24.2 occ:1.00 OD1 B:ASN112 2.2 22.0 1.0 O2B B:CDP301 2.3 20.8 1.0 O2A B:CDP301 2.4 22.1 1.0 O B:HOH475 2.4 27.2 1.0 OE1 B:GLU111 2.4 27.7 1.0 O B:HOH411 2.7 24.8 1.0 O B:HOH408 2.7 38.0 1.0 HH12 B:ARG115 3.1 31.4 1.0 CG B:ASN112 3.3 28.3 1.0 PB B:CDP301 3.3 22.6 1.0 HD21 B:ASN112 3.4 33.4 1.0 PA B:CDP301 3.4 22.6 1.0 CD B:GLU111 3.5 30.8 1.0 O3A B:CDP301 3.6 21.8 1.0 HH21 B:ARG80 3.6 27.1 1.0 ND2 B:ASN112 3.7 27.8 1.0 NH1 B:ARG115 3.8 26.2 1.0 O3B B:CDP301 3.8 19.3 1.0 OE2 B:GLU111 3.9 35.8 1.0 HH21 B:ARG39 3.9 37.4 1.0 O5' B:CDP301 3.9 22.8 1.0 HH22 B:ARG115 4.0 33.9 1.0 HH11 B:ARG115 4.2 31.4 1.0 HB1 B:ALA76 4.3 33.6 1.0 NH2 B:ARG80 4.3 22.6 1.0 HA B:ASN112 4.3 24.9 1.0 HH22 B:ARG80 4.4 27.1 1.0 HB3 B:GLU111 4.5 31.1 1.0 O B:HOH421 4.5 29.5 1.0 CB B:ASN112 4.5 22.4 1.0 HD22 B:ASN112 4.5 33.4 1.0 NH2 B:ARG115 4.6 28.3 1.0 CZ B:ARG115 4.6 26.9 1.0 H B:GLY77 4.6 25.9 1.0 NH2 B:ARG39 4.6 31.1 1.0 O1B B:CDP301 4.7 20.9 1.0 HH22 B:ARG39 4.7 37.4 1.0 O B:HOH444 4.7 31.1 1.0 HD2 B:ARG39 4.7 47.2 1.0 HA B:ALA76 4.8 30.7 1.0 CA B:ASN112 4.8 20.8 1.0 O1A B:CDP301 4.8 22.2 1.0 HB3 B:ASN112 4.8 26.9 1.0 CG B:GLU111 4.8 32.8 1.0 N B:ASN112 4.9 25.1 1.0 N B:GLY77 5.0 21.6 1.0 C B:GLU111 5.0 24.7 1.0 HA2 B:GLY77 5.0 27.6 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of Bacterial Parb Dimer Bound to Cdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Bacterial Parb Dimer Bound to Cdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:29.4 occ:1.00 HE22 B:GLN37 2.4 33.0 1.0 H B:GLY77 2.5 25.9 1.0 H B:GLU78 2.5 28.3 1.0 HD22 B:ASN34 2.6 31.6 1.0 HA B:ALA76 3.0 30.7 1.0 O B:HOH421 3.2 29.5 1.0 NE2 B:GLN37 3.2 27.5 1.0 O B:HOH475 3.2 27.2 1.0 N B:GLY77 3.2 21.6 1.0 HG22 B:ILE74 3.3 33.2 1.0 N B:GLU78 3.4 23.6 1.0 HB3 B:GLU78 3.4 35.5 1.0 HB2 B:GLU78 3.4 35.5 1.0 ND2 B:ASN34 3.4 26.3 1.0 HE21 B:GLN37 3.7 33.0 1.0 HB2 B:ASN34 3.7 31.7 1.0 CB B:GLU78 3.8 29.5 1.0 CA B:ALA76 3.8 25.6 1.0 HD21 B:ASN34 3.8 31.6 1.0 HG21 B:ILE74 3.9 33.2 1.0 O B:HOH411 4.0 24.8 1.0 C B:ALA76 4.0 24.9 1.0 O3B B:CDP301 4.0 19.3 1.0 CG2 B:ILE74 4.0 27.7 1.0 O B:VAL75 4.1 24.0 1.0 CD B:GLN37 4.1 32.0 1.0 OE1 B:GLN37 4.1 27.9 1.0 CA B:GLU78 4.2 25.3 1.0 CA B:GLY77 4.2 23.0 1.0 O B:HOH444 4.3 31.1 1.0 C B:GLY77 4.3 27.9 1.0 CB B:ASN34 4.3 26.4 1.0 N B:ALA76 4.3 22.0 1.0 HB3 B:ASN34 4.3 31.7 1.0 C B:VAL75 4.4 25.3 1.0 CG B:ASN34 4.4 25.9 1.0 HG23 B:ILE74 4.5 33.2 1.0 HD2 B:PRO38 4.5 32.0 1.0 HD21 B:ASN112 4.6 33.4 1.0 HA2 B:GLY77 4.6 27.6 1.0 HA B:GLU78 4.7 30.3 1.0 HA B:GLN37 4.8 28.7 1.0 H B:ARG79 4.8 26.0 1.0 O2B B:CDP301 4.9 20.8 1.0 H B:ALA76 4.9 26.4 1.0 HD2 B:ARG39 4.9 47.2 1.0 HA3 B:GLY77 5.0 27.6 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of Bacterial Parb Dimer Bound to Cdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Bacterial Parb Dimer Bound to Cdp within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:24.2 occ:1.00 HD21 C:ASN112 1.6 23.5 1.0 O2B C:CDP301 2.3 21.1 1.0 ND2 C:ASN112 2.3 19.6 1.0 O2A C:CDP301 2.4 19.9 1.0 O C:HOH427 2.4 25.4 1.0 O C:HOH477 2.4 26.1 1.0 OE1 C:GLU111 2.4 26.7 1.0 HD22 C:ASN112 2.6 23.5 1.0 O C:HOH417 2.7 29.8 1.0 HH12 C:ARG115 3.1 34.4 1.0 PB C:CDP301 3.3 22.2 1.0 CG C:ASN112 3.4 28.6 1.0 PA C:CDP301 3.4 21.8 1.0 CD C:GLU111 3.5 30.0 1.0 HH21 C:ARG39 3.5 30.1 1.0 HH21 C:ARG80 3.6 27.1 1.0 O3A C:CDP301 3.6 21.8 1.0 OD1 C:ASN112 3.8 32.9 1.0 NH1 C:ARG115 3.8 28.6 1.0 OE2 C:GLU111 3.9 34.0 1.0 O5' C:CDP301 3.9 23.4 1.0 O1B C:CDP301 3.9 20.8 1.0 HH22 C:ARG115 4.0 30.7 1.0 HH11 C:ARG115 4.2 34.4 1.0 NH2 C:ARG39 4.3 25.1 1.0 HB1 C:ALA76 4.3 29.5 1.0 NH2 C:ARG80 4.3 22.6 1.0 HA C:ASN112 4.3 26.4 1.0 HH22 C:ARG39 4.3 30.1 1.0 HH22 C:ARG80 4.4 27.1 1.0 HB3 C:GLU111 4.5 32.6 1.0 NH2 C:ARG115 4.5 25.6 1.0 H C:GLY77 4.5 29.6 1.0 CZ C:ARG115 4.5 27.8 1.0 O C:HOH431 4.5 32.5 1.0 CB C:ASN112 4.6 20.7 1.0 O3B C:CDP301 4.6 20.9 1.0 O C:HOH460 4.8 29.5 1.0 O1A C:CDP301 4.8 21.3 1.0 CA C:ASN112 4.8 22.0 1.0 CG C:GLU111 4.8 26.3 1.0 HA C:ALA76 4.8 26.4 1.0 HB3 C:ASN112 4.9 24.8 1.0 N C:ASN112 4.9 21.7 1.0 N C:GLY77 5.0 24.7 1.0 HA2 C:GLY77 5.0 28.1 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of Bacterial Parb Dimer Bound to Cdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Bacterial Parb Dimer Bound to Cdp within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:27.9 occ:1.00 HE22 C:GLN37 2.5 34.3 1.0 H C:GLY77 2.5 29.6 1.0 H C:GLU78 2.5 27.1 1.0 HD22 C:ASN34 2.6 30.6 1.0 HA C:ALA76 3.0 26.4 1.0 HB2 C:GLU78 3.2 31.0 1.0 NE2 C:GLN37 3.3 28.6 1.0 N C:GLY77 3.3 24.7 1.0 O C:HOH477 3.3 26.1 1.0 O C:HOH431 3.3 32.5 1.0 N C:GLU78 3.4 22.5 1.0 HG22 C:ILE74 3.4 28.3 1.0 ND2 C:ASN34 3.4 25.5 1.0 HB2 C:ASN34 3.5 32.2 1.0 HE21 C:GLN37 3.6 34.3 1.0 HB3 C:GLU78 3.7 31.0 1.0 CA C:ALA76 3.8 22.0 1.0 CB C:GLU78 3.8 25.8 1.0 O C:HOH448 3.8 32.0 1.0 HD21 C:ASN34 3.9 30.6 1.0 O1B C:CDP301 3.9 20.8 1.0 C C:ALA76 4.0 23.6 1.0 O C:HOH427 4.0 25.4 1.0 HG21 C:ILE74 4.1 28.3 1.0 HB3 C:ASN34 4.1 32.2 1.0 CB C:ASN34 4.1 26.9 1.0 O C:VAL75 4.2 28.5 1.0 CG2 C:ILE74 4.2 23.6 1.0 CD C:GLN37 4.2 29.0 1.0 CA C:GLU78 4.2 26.2 1.0 CA C:GLY77 4.2 23.4 1.0 C C:GLY77 4.3 24.8 1.0 OE1 C:GLN37 4.3 28.3 1.0 CG C:ASN34 4.3 25.5 1.0 N C:ALA76 4.3 24.1 1.0 O C:HOH460 4.3 29.5 1.0 C C:VAL75 4.4 26.3 1.0 HG23 C:ILE74 4.6 28.3 1.0 HD2 C:PRO38 4.6 34.3 1.0 HA2 C:GLY77 4.6 28.1 1.0 HA C:GLU78 4.8 31.4 1.0 H C:ARG79 4.8 23.6 1.0 O2B C:CDP301 4.9 21.1 1.0 H C:ALA76 4.9 28.9 1.0 HA C:GLN37 4.9 31.5 1.0 OE2 C:GLU78 4.9 30.6 1.0 PB C:CDP301 5.0 22.2 1.0 HB1 C:ALA76 5.0 29.5 1.0 HA3 C:GLY77 5.0 28.1 1.0 CB C:ALA76 5.0 24.6 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of Bacterial Parb Dimer Bound to Cdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Bacterial Parb Dimer Bound to Cdp within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:26.5 occ:1.00 HD21 D:ASN112 1.6 29.3 1.0 ND2 D:ASN112 2.3 24.4 1.0 O1A D:CDP301 2.3 21.3 1.0 O1B D:CDP301 2.3 29.4 1.0 OE1 D:GLU111 2.4 29.1 1.0 HD22 D:ASN112 2.5 29.3 1.0 O D:HOH402 2.5 30.0 1.0 O D:HOH464 2.5 28.4 1.0 O D:HOH453 2.7 28.9 1.0 HH12 D:ARG115 3.1 33.2 1.0 PA D:CDP301 3.3 26.5 1.0 CD D:GLU111 3.4 29.6 1.0 PB D:CDP301 3.4 27.1 1.0 CG D:ASN112 3.4 27.4 1.0 HH21 D:ARG39 3.5 37.8 1.0 HH21 D:ARG80 3.7 31.1 1.0 OE2 D:GLU111 3.7 30.5 1.0 O3A D:CDP301 3.7 24.9 1.0 HH22 D:ARG115 3.8 30.7 1.0 NH1 D:ARG115 3.8 27.7 1.0 O2B D:CDP301 3.9 25.9 1.0 OD1 D:ASN112 3.9 31.6 1.0 O5' D:CDP301 3.9 26.8 1.0 HB1 D:ALA76 4.2 32.1 1.0 HH11 D:ARG115 4.3 33.2 1.0 NH2 D:ARG39 4.3 31.5 1.0 HA D:ASN112 4.3 30.2 1.0 NH2 D:ARG80 4.3 25.9 1.0 NH2 D:ARG115 4.4 25.6 1.0 HH22 D:ARG80 4.4 31.1 1.0 HB3 D:GLU111 4.5 29.7 1.0 O D:HOH456 4.5 36.0 1.0 HH22 D:ARG39 4.5 37.8 1.0 CZ D:ARG115 4.5 28.9 1.0 H D:GLY77 4.5 32.0 1.0 CB D:ASN112 4.6 24.4 1.0 O2A D:CDP301 4.7 25.0 1.0 O D:HOH486 4.7 33.2 1.0 O3B D:CDP301 4.8 25.1 1.0 CG D:GLU111 4.8 30.5 1.0 CA D:ASN112 4.8 25.2 1.0 HB3 D:ASN112 4.8 29.4 1.0 HA D:ALA76 4.9 33.2 1.0 H5'1 D:CDP301 5.0 31.1 1.0 N D:ASN112 5.0 24.8 1.0 C5' D:CDP301 5.0 25.9 1.0 N D:GLY77 5.0 26.6 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of Bacterial Parb Dimer Bound to Cdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Bacterial Parb Dimer Bound to Cdp within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:35.2 occ:1.00 HD22 D:ASN34 2.5 41.2 1.0 HE22 D:GLN37 2.5 41.5 1.0 H D:GLY77 2.6 32.0 1.0 H D:GLU78 2.6 32.4 1.0 HA D:ALA76 3.0 33.2 1.0 O D:HOH456 3.2 36.0 1.0 O D:HOH464 3.2 28.4 1.0 HB2 D:GLU78 3.3 43.6 1.0 ND2 D:ASN34 3.3 34.3 1.0 NE2 D:GLN37 3.3 34.6 1.0 N D:GLY77 3.3 26.6 1.0 HG22 D:ILE74 3.4 36.9 1.0 HB3 D:GLU78 3.4 43.6 1.0 N D:GLU78 3.4 27.0 1.0 HB2 D:ASN34 3.5 43.5 1.0 HE21 D:GLN37 3.7 41.5 1.0 CB D:GLU78 3.7 36.4 1.0 HD21 D:ASN34 3.7 41.2 1.0 CA D:ALA76 3.8 27.7 1.0 HG21 D:ILE74 3.9 36.9 1.0 O D:VAL75 4.0 28.7 1.0 C D:ALA76 4.0 27.4 1.0 O2B D:CDP301 4.0 25.9 1.0 O D:HOH453 4.0 28.9 1.0 CG2 D:ILE74 4.1 30.8 1.0 CB D:ASN34 4.2 36.3 1.0 CA D:GLU78 4.2 30.9 1.0 CG D:ASN34 4.2 38.2 1.0 HB3 D:ASN34 4.3 43.5 1.0 CD D:GLN37 4.3 37.8 1.0 CA D:GLY77 4.3 27.6 1.0 O D:HOH486 4.3 33.2 1.0 C D:GLY77 4.3 29.0 1.0 C D:VAL75 4.4 29.9 1.0 OE1 D:GLN37 4.4 34.5 1.0 N D:ALA76 4.4 32.4 1.0 HG23 D:ILE74 4.6 36.9 1.0 HD2 D:PRO38 4.6 40.9 1.0 HA2 D:GLY77 4.7 33.1 1.0 HA D:GLU78 4.7 37.0 1.0 H D:ARG79 4.8 33.7 1.0 O1B D:CDP301 4.9 29.4 1.0 OE1 D:GLU78 4.9 40.6 1.0 HB1 D:ALA76 4.9 32.1 1.0 CB D:ALA76 5.0 26.8 1.0 HA D:GLN37 5.0 38.7 1.0

Y.M.Soh, I.F.Davidson, S.Zamuner, J.Basquin, F.P.Bock, M.Taschner, J.W.Veening, P.De Los Rios, J.M.Peters, S.Gruber. Self-Organization Ofparscentromeres By the Parb Ctp Hydrolase. Science 2019.
ISSN: ESSN 1095-9203
PubMed: 31649139
DOI: 10.1126/SCIENCE.AAY3965