Nickel in PDB 6mrj: Crystal Structure of H.Pylori Nikr in Complex with Dna

The structure of Crystal Structure of H.Pylori Nikr in Complex with Dna, PDB code: 6mrj was solved by E.Pozharski, V.De Serrano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.47 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.370, 94.180, 204.060, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 24.1

The structure of Crystal Structure of H.Pylori Nikr in Complex with Dna also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of H.Pylori Nikr in Complex with Dna (pdb code 6mrj). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of H.Pylori Nikr in Complex with Dna, PDB code: 6mrj:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of H.Pylori Nikr in Complex with Dna


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of H.Pylori Nikr in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:63.7 occ:1.00 NE2 A:HIS99 2.0 64.6 1.0 NE2 D:HIS88 2.1 61.7 1.0 ND1 A:HIS101 2.1 54.5 1.0 SG A:CYS107 2.3 69.7 1.0 CE1 A:HIS99 3.0 64.0 1.0 CE1 D:HIS88 3.0 61.5 1.0 CE1 A:HIS101 3.0 53.8 1.0 CD2 D:HIS88 3.1 62.1 1.0 CD2 A:HIS99 3.1 65.0 1.0 CG A:HIS101 3.1 53.4 1.0 CA A:HIS101 3.4 51.9 1.0 CB A:HIS101 3.5 51.0 1.0 CB A:CYS107 3.5 66.0 1.0 CG1 D:ILE84 3.8 73.6 1.0 CD1 D:ILE84 3.8 82.9 1.0 N A:HIS101 4.0 53.3 1.0 CA A:CYS107 4.0 65.8 1.0 O A:ILE100 4.1 57.5 1.0 ND1 A:HIS99 4.1 64.2 1.0 ND1 D:HIS88 4.2 62.5 1.0 NE2 A:HIS101 4.2 54.4 1.0 CG A:HIS99 4.2 62.6 1.0 CG D:HIS88 4.2 60.9 1.0 CD2 A:HIS101 4.2 54.8 1.0 C A:ILE100 4.3 58.3 1.0 O A:ASN106 4.5 68.6 1.0 C A:HIS101 4.7 59.8 1.0 N A:CYS107 4.9 66.0 1.0 CB A:HIS74 4.9 67.8 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of H.Pylori Nikr in Complex with Dna


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of H.Pylori Nikr in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni203 b:86.5 occ:1.00 NE2 D:HIS99 2.0 80.2 1.0 ND1 D:HIS101 2.0 88.2 1.0 NE2 A:HIS88 2.1 99.9 1.0 SG D:CYS107 2.2 91.9 1.0 CG D:HIS101 3.0 86.3 1.0 CE1 D:HIS99 3.0 80.1 1.0 CE1 D:HIS101 3.0 87.7 1.0 CD2 D:HIS99 3.0 80.0 1.0 CD2 A:HIS88 3.1 0.1 1.0 CE1 A:HIS88 3.1 99.6 1.0 CA D:HIS101 3.2 81.7 1.0 CB D:HIS101 3.3 82.7 1.0 CB D:CYS107 3.4 87.5 1.0 CG2 A:ILE84 3.5 92.1 1.0 N D:HIS101 3.8 81.0 1.0 O D:ILE100 3.9 81.2 1.0 CA D:CYS107 4.0 86.2 1.0 NE2 D:HIS101 4.1 87.9 1.0 CD2 D:HIS101 4.1 88.0 1.0 C D:ILE100 4.1 82.0 1.0 ND1 D:HIS99 4.2 80.3 1.0 CG D:HIS99 4.2 77.8 1.0 CG A:HIS88 4.2 98.7 1.0 ND1 A:HIS88 4.3 0.3 1.0 O D:ASN106 4.4 92.6 1.0 C D:HIS101 4.6 88.2 1.0 N D:CYS107 4.9 87.4 1.0 N D:MET102 4.9 86.3 1.0 CB A:ILE84 5.0 91.5 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of H.Pylori Nikr in Complex with Dna


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of H.Pylori Nikr in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:88.1 occ:1.00 ND1 B:HIS101 2.0 80.6 1.0 NE2 B:HIS99 2.0 70.7 1.0 SG B:CYS107 2.3 78.5 1.0 NE2 C:HIS88 2.3 0.2 1.0 CE1 B:HIS101 2.9 80.1 1.0 CE1 B:HIS99 3.0 70.2 1.0 CG B:HIS101 3.0 78.4 1.0 CD2 B:HIS99 3.0 70.7 1.0 CE1 C:HIS88 3.3 99.8 1.0 CD2 C:HIS88 3.3 0.5 1.0 CA B:HIS101 3.3 73.0 1.0 CB B:HIS101 3.4 74.1 1.0 CB B:CYS107 3.5 74.5 1.0 CD1 C:ILE84 3.6 91.8 1.0 CG1 C:ILE84 3.7 90.7 1.0 N B:HIS101 3.9 71.0 1.0 O B:ILE100 4.0 66.3 1.0 CA B:CYS107 4.1 74.3 1.0 NE2 B:HIS101 4.1 80.5 1.0 CD2 B:HIS101 4.1 80.6 1.0 ND1 B:HIS99 4.1 70.2 1.0 CG B:HIS99 4.1 68.1 1.0 C B:ILE100 4.2 69.0 1.0 ND1 C:HIS88 4.4 0.5 1.0 CG C:HIS88 4.4 99.0 1.0 O B:ASN106 4.5 81.9 1.0 C B:HIS101 4.7 82.5 1.0 N B:CYS107 4.9 76.2 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of H.Pylori Nikr in Complex with Dna


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of H.Pylori Nikr in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni202 b:62.5 occ:1.00 ND1 C:HIS101 2.0 55.3 1.0 NE2 B:HIS88 2.1 63.1 1.0 NE2 C:HIS99 2.2 48.3 1.0 SG C:CYS107 2.2 62.3 1.0 CD2 B:HIS88 2.9 63.8 1.0 CE1 C:HIS101 3.0 55.3 1.0 CG C:HIS101 3.0 53.5 1.0 CE1 B:HIS88 3.2 62.9 1.0 CE1 C:HIS99 3.2 48.4 1.0 CD2 C:HIS99 3.2 49.2 1.0 CA C:HIS101 3.3 51.0 1.0 CB C:HIS101 3.3 50.6 1.0 CG2 B:ILE84 3.4 70.3 1.0 CB C:CYS107 3.6 58.9 1.0 N C:HIS101 4.0 49.7 1.0 O C:ILE100 4.1 50.8 1.0 NE2 C:HIS101 4.1 55.7 1.0 CA C:CYS107 4.1 59.0 1.0 CD2 C:HIS101 4.1 55.7 1.0 CG B:HIS88 4.1 63.0 1.0 ND1 B:HIS88 4.2 64.0 1.0 C C:ILE100 4.3 51.3 1.0 ND1 C:HIS99 4.3 50.7 1.0 CG C:HIS99 4.3 49.9 1.0 O C:ASN106 4.4 65.2 1.0 C C:HIS101 4.6 59.6 1.0 O C:HOH302 4.7 69.9 1.0 CB B:ILE84 4.8 70.9 1.0 N C:CYS107 4.9 60.0 1.0 CD1 B:ILE84 4.9 79.0 1.0 N C:MET102 4.9 58.0 1.0

E.Pozharski, V.De Serrano. Crystal Structure of H.Pylori Nikr in Complex with Dna To Be Published.