Nickel in PDB 6h4c: A Polyamorous Repressor: Deciphering the Evolutionary Strategy Used By the Phage-Inducible Chromosomal Islands to Spread in Nature.

The structure of A Polyamorous Repressor: Deciphering the Evolutionary Strategy Used By the Phage-Inducible Chromosomal Islands to Spread in Nature., PDB code: 6h4c was solved by J.R.Ciges-Tomas, C.Alite, J.Z.Bowring, J.Donderis, J.R.Penades, A.Marina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.93 / 2.52
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	144.490, 144.490, 149.420, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 24.2

The structure of A Polyamorous Repressor: Deciphering the Evolutionary Strategy Used By the Phage-Inducible Chromosomal Islands to Spread in Nature. also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Nickel atom in the A Polyamorous Repressor: Deciphering the Evolutionary Strategy Used By the Phage-Inducible Chromosomal Islands to Spread in Nature. (pdb code 6h4c). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the A Polyamorous Repressor: Deciphering the Evolutionary Strategy Used By the Phage-Inducible Chromosomal Islands to Spread in Nature., PDB code: 6h4c:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in the A Polyamorous Repressor: Deciphering the Evolutionary Strategy Used By the Phage-Inducible Chromosomal Islands to Spread in Nature.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of A Polyamorous Repressor: Deciphering the Evolutionary Strategy Used By the Phage-Inducible Chromosomal Islands to Spread in Nature. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:0.2 occ:1.00 CB A:LYS46 4.3 50.0 1.0 C F:GLY109 4.4 46.9 1.0 CA F:GLY109 4.5 47.4 1.0 OD1 F:ASP110 4.6 56.9 1.0 O F:GLY109 4.6 47.4 1.0 N F:ASP110 4.6 42.6 1.0 CB A:ASN87 4.7 45.8 1.0 O A:ASN87 4.8 40.2 1.0 CG A:ASN87 4.8 51.6 1.0 CA A:LYS46 4.9 50.4 1.0 CD2 F:TYR113 4.9 40.8 1.0 ND2 A:ASN87 4.9 52.3 1.0 CG1 A:VAL44 5.0 37.0 1.0

Nickel binding site 2 out of 5 in the A Polyamorous Repressor: Deciphering the Evolutionary Strategy Used By the Phage-Inducible Chromosomal Islands to Spread in Nature.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of A Polyamorous Repressor: Deciphering the Evolutionary Strategy Used By the Phage-Inducible Chromosomal Islands to Spread in Nature. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:0.0 occ:1.00 OD1 B:ASP110 4.1 56.4 1.0 C B:GLY109 4.3 49.6 1.0 O B:HOH312 4.3 68.7 1.0 N B:ASP110 4.5 49.8 1.0 O B:GLY109 4.5 48.6 1.0 CA B:GLY109 4.5 47.4 1.0 CB C:LYS46 4.8 52.2 1.0 CD2 B:TYR113 5.0 42.6 1.0 CA B:ASP110 5.0 48.9 1.0 CG1 C:VAL44 5.0 38.9 1.0

Nickel binding site 3 out of 5 in the A Polyamorous Repressor: Deciphering the Evolutionary Strategy Used By the Phage-Inducible Chromosomal Islands to Spread in Nature.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of A Polyamorous Repressor: Deciphering the Evolutionary Strategy Used By the Phage-Inducible Chromosomal Islands to Spread in Nature. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni204 b:0.0 occ:1.00 O C:HOH334 3.2 58.1 1.0 NE C:ARG121 3.5 57.5 1.0 NH2 C:ARG121 3.7 55.9 1.0 CZ C:ARG121 4.1 57.2 1.0 CG1 C:VAL36 4.3 48.5 1.0 CB C:VAL36 4.5 43.2 1.0 CD C:ARG121 4.5 55.4 1.0

Nickel binding site 4 out of 5 in the A Polyamorous Repressor: Deciphering the Evolutionary Strategy Used By the Phage-Inducible Chromosomal Islands to Spread in Nature.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of A Polyamorous Repressor: Deciphering the Evolutionary Strategy Used By the Phage-Inducible Chromosomal Islands to Spread in Nature. within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni203 b:0.1 occ:1.00 CZ E:PHE108 4.3 63.1 1.0 CE2 E:PHE108 4.4 61.0 1.0 CD2 E:HIS72 4.5 49.2 1.0 CE1 E:PHE108 4.6 61.4 1.0 CE2 E:TYR123 4.6 65.1 1.0 NE2 E:HIS72 4.6 51.6 1.0 OH E:TYR123 4.8 64.4 1.0 C1 E:PEG202 4.9 81.1 1.0 CD2 E:PHE108 4.9 59.8 1.0 OH E:TYR126 5.0 45.2 1.0

Nickel binding site 5 out of 5 in the A Polyamorous Repressor: Deciphering the Evolutionary Strategy Used By the Phage-Inducible Chromosomal Islands to Spread in Nature.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of A Polyamorous Repressor: Deciphering the Evolutionary Strategy Used By the Phage-Inducible Chromosomal Islands to Spread in Nature. within 5.0Å range: probe atom residue distance (Å) B Occ H:Ni202 b:0.5 occ:1.00 O H:HOH307 2.4 82.0 1.0 OD1 H:ASP95 3.6 77.3 1.0 CG H:ASP95 4.4 67.0 1.0 CD2 H:TYR98 4.4 60.0 1.0 O H:HOH306 4.6 73.6 1.0 CE2 H:TYR98 4.8 59.0 1.0 CD H:PRO68 4.9 66.6 1.0 O H:GLY66 4.9 74.0 1.0 OD2 H:ASP95 4.9 65.5 1.0 CG1 H:ILE67 5.0 66.2 1.0

J.Rafael Ciges-Tomas, C.Alite, S.Humphrey, J.Donderis, J.Bowring, X.Salvatella, J.R.Penades, A.Marina. The Structure of A Polygamous Repressor Reveals How Phage-Inducible Chromosomal Islands Spread in Nature. Nat Commun V. 10 3676 2019.
ISSN: ESSN 2041-1723
PubMed: 31417084
DOI: 10.1038/S41467-019-11504-2