Nickel in PDB 7w1f: Crystal Structure of the Dntp Triphosphohydrolase PA1124 From Pseudomonas Aeruginosa

All present enzymatic activity of Crystal Structure of the Dntp Triphosphohydrolase PA1124 From Pseudomonas Aeruginosa:
3.1.5.1;

The structure of Crystal Structure of the Dntp Triphosphohydrolase PA1124 From Pseudomonas Aeruginosa, PDB code: 7w1f was solved by H.B.Oh, W.S.Song, K.C.Lee, S.C.Park, S.I.Yoon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.66 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	88.077, 131.017, 136.462, 90, 90, 90
R / Rfree (%)	23 / 27.4

The binding sites of Nickel atom in the Crystal Structure of the Dntp Triphosphohydrolase PA1124 From Pseudomonas Aeruginosa (pdb code 7w1f). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of the Dntp Triphosphohydrolase PA1124 From Pseudomonas Aeruginosa, PDB code: 7w1f:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of the Dntp Triphosphohydrolase PA1124 From Pseudomonas Aeruginosa


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 the Dntp Triphosphohydrolase PA1124 From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni601 b:85.3 occ:1.00 OD1 A:ASP257 2.0 134.0 1.0 NE2 A:HIS74 2.1 98.0 1.0 NE2 A:HIS120 2.3 68.1 1.0 CE1 A:HIS74 2.9 90.3 1.0 CG A:ASP257 3.0 114.6 1.0 CE1 A:HIS120 3.2 68.0 1.0 CD2 A:HIS74 3.2 88.6 1.0 CD2 A:HIS120 3.3 69.2 1.0 OD2 A:ASP257 3.4 124.5 1.0 ND1 A:HIS74 4.1 88.9 1.0 OD2 A:ASP121 4.2 99.7 1.0 CG A:HIS74 4.2 84.5 1.0 ND1 A:HIS120 4.3 68.9 1.0 CG A:HIS120 4.4 69.7 1.0 CB A:ASP257 4.4 95.2 1.0 CG A:ASP121 4.6 92.5 1.0 OD1 A:ASP121 4.9 89.3 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of the Dntp Triphosphohydrolase PA1124 From Pseudomonas Aeruginosa


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 the Dntp Triphosphohydrolase PA1124 From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni601 b:94.1 occ:1.00 OD1 B:ASP257 1.9 163.9 1.0 NE2 B:HIS74 2.2 102.2 1.0 NE2 B:HIS120 2.4 94.8 1.0 CG B:ASP257 2.8 140.3 1.0 CE1 B:HIS120 2.9 100.4 1.0 OD2 B:ASP257 3.0 148.4 1.0 CD2 B:HIS74 3.1 100.5 1.0 CE1 B:HIS74 3.3 106.1 1.0 CD2 B:HIS120 3.5 96.1 1.0 ND1 B:HIS120 4.0 97.1 1.0 CB B:ASP257 4.2 116.8 1.0 OD2 B:ASP121 4.3 100.2 1.0 CG B:HIS74 4.3 97.0 1.0 ND1 B:HIS74 4.3 101.8 1.0 CG B:HIS120 4.3 89.3 1.0 CG B:ASP121 4.8 96.5 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of the Dntp Triphosphohydrolase PA1124 From Pseudomonas Aeruginosa


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 the Dntp Triphosphohydrolase PA1124 From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni601 b:105.3 occ:1.00 OD1 C:ASP257 2.0 167.5 1.0 NE2 C:HIS120 2.1 128.5 1.0 NE2 C:HIS74 2.1 129.0 1.0 CG C:ASP257 2.9 147.2 1.0 CE1 C:HIS120 3.0 119.3 1.0 OD2 C:ASP121 3.0 129.1 1.0 CE1 C:HIS74 3.1 121.7 1.0 CD2 C:HIS74 3.1 120.6 1.0 OD2 C:ASP257 3.2 156.2 1.0 CD2 C:HIS120 3.2 123.5 1.0 ND1 C:HIS120 4.1 120.8 1.0 CG C:ASP121 4.2 124.0 1.0 ND1 C:HIS74 4.2 121.4 1.0 CG C:HIS74 4.2 117.5 1.0 CG C:HIS120 4.2 121.0 1.0 CB C:ASP257 4.3 124.4 1.0 CD2 C:TYR261 4.5 123.1 1.0 NE2 C:GLN58 4.8 82.8 1.0 CE2 C:TYR261 4.8 121.9 1.0 CB C:ASP121 4.9 107.7 1.0 CG2 C:VAL78 5.0 90.6 1.0

H.B.Oh, K.C.Lee, S.C.Park, W.S.Song, S.I.Yoon. Structural Analysis of the Dntp Triphosphohydrolase PA1124 From Pseudomonas Aeruginosa. Biochem.Biophys.Res.Commun. V. 589 78 2022.
ISSN: ESSN 1090-2104
PubMed: 34894560
DOI: 10.1016/J.BBRC.2021.12.002