Nickel in PDB 5b7z: Crystal Structure of Hyperthermophilic Thermotoga Maritima L-Ketose-3- Epimerase with NI2+

The structure of Crystal Structure of Hyperthermophilic Thermotoga Maritima L-Ketose-3- Epimerase with NI2+, PDB code: 5b7z was solved by T.P.Cao, S.M.Shin, D.W.Lee, S.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.51 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.225, 55.220, 58.693, 107.16, 102.23, 92.35
R / Rfree (%)	17.2 / 19.7

The binding sites of Nickel atom in the Crystal Structure of Hyperthermophilic Thermotoga Maritima L-Ketose-3- Epimerase with NI2+ (pdb code 5b7z). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Hyperthermophilic Thermotoga Maritima L-Ketose-3- Epimerase with NI2+, PDB code: 5b7z:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Hyperthermophilic Thermotoga Maritima L-Ketose-3- Epimerase with NI2+


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 Hyperthermophilic Thermotoga Maritima L-Ketose-3- Epimerase with NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni305 b:10.8 occ:1.00 ND1 A:HIS208 2.0 8.7 1.0 OD2 A:ASP182 2.0 11.4 1.0 OE2 A:GLU149 2.0 9.2 1.0 OE2 A:GLU243 2.1 11.0 1.0 O A:HOH429 2.3 15.4 1.0 CE1 A:HIS208 2.9 11.4 1.0 CD A:GLU149 3.0 9.5 1.0 CG A:HIS208 3.0 9.9 1.0 CD A:GLU243 3.0 13.4 1.0 CG A:ASP182 3.1 9.4 1.0 OE1 A:GLU149 3.3 10.5 1.0 OE1 A:GLU243 3.3 14.7 1.0 CB A:HIS208 3.4 10.4 1.0 CB A:ASP182 3.5 9.4 1.0 O A:HOH568 3.9 13.6 1.0 NH2 A:ARG214 4.0 13.5 1.0 NE2 A:HIS208 4.1 10.4 1.0 CD2 A:HIS208 4.1 9.9 1.0 OD1 A:ASP182 4.2 9.9 1.0 O A:HOH554 4.2 12.5 1.0 CD2 A:HIS185 4.3 8.9 1.0 CG A:GLU149 4.3 7.9 1.0 CG A:GLU243 4.4 12.6 1.0 NE2 A:HIS185 4.6 10.6 1.0 CB A:GLU243 4.7 9.7 1.0 CA A:ASP182 4.8 9.4 1.0 O A:HOH658 4.9 30.4 1.0 CA A:HIS208 4.9 9.6 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Hyperthermophilic Thermotoga Maritima L-Ketose-3- Epimerase with NI2+


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 Hyperthermophilic Thermotoga Maritima L-Ketose-3- Epimerase with NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni302 b:12.3 occ:1.00 OD2 B:ASP182 2.0 11.8 1.0 OE2 B:GLU149 2.0 11.4 1.0 ND1 B:HIS208 2.0 10.6 1.0 OE2 B:GLU243 2.1 13.2 1.0 O B:HOH418 2.3 16.4 1.0 CD B:GLU149 3.0 11.1 1.0 CD B:GLU243 3.0 14.2 1.0 CE1 B:HIS208 3.0 12.7 1.0 CG B:HIS208 3.0 9.7 1.0 CG B:ASP182 3.1 10.9 1.0 OE1 B:GLU149 3.3 10.7 1.0 OE1 B:GLU243 3.3 14.7 1.0 CB B:HIS208 3.4 10.7 1.0 CB B:ASP182 3.5 9.6 1.0 O B:HOH536 3.9 14.2 1.0 NH2 B:ARG214 4.0 14.0 1.0 NE2 B:HIS208 4.1 11.7 1.0 CD2 B:HIS208 4.2 11.7 1.0 OD1 B:ASP182 4.2 11.3 1.0 O B:HOH561 4.2 14.0 1.0 CG B:GLU149 4.3 9.1 1.0 CD2 B:HIS185 4.3 10.3 1.0 CG B:GLU243 4.3 12.4 1.0 NE2 B:HIS185 4.5 10.6 1.0 CB B:GLU243 4.6 12.1 1.0 CA B:ASP182 4.8 10.3 1.0 CA B:HIS208 4.9 11.7 1.0

S.M.Shin, T.P.Cao, J.M.Choi, S.B.Kim, S.J.Lee, S.H.Lee, D.W.Lee. TM0416, A Hyperthermophilic Promiscuous Nonphosphorylated Sugar Isomerase, Catalyzes Various C5AND C6EPIMERIZATION Reactions Appl. Environ. Microbiol. V. 83 2017.
ISSN: ESSN 1098-5336
PubMed: 28258150
DOI: 10.1128/AEM.03291-16