Nickel in PDB 2afb: Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution

The structure of Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution, PDB code: 2afb was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.63 / 2.05
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	120.993, 120.993, 260.300, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 23

The structure of Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Nickel atom in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution (pdb code 2afb). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution, PDB code: 2afb:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution


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 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni340 b:32.2 occ:1.00 ND1 A:HIS67 2.1 22.7 1.0 O A:HOH346 2.2 9.7 1.0 O B:HOH345 2.3 19.3 1.0 O A:HOH345 2.6 20.5 1.0 CE1 A:HIS67 2.9 21.5 1.0 CG A:HIS67 3.2 25.9 1.0 CB A:HIS67 3.6 25.1 1.0 O A:HOH516 3.9 49.0 1.0 NE2 A:HIS67 4.1 31.8 1.0 CA A:HIS67 4.1 25.7 1.0 O B:HOH446 4.1 38.6 1.0 CD2 A:HIS67 4.2 26.6 1.0 CD A:LYS70 4.5 35.6 1.0 NZ A:LYS70 4.9 42.0 1.0 OG1 A:THR30 4.9 32.7 1.0 CE1 A:PHE71 5.0 28.3 1.0

Nickel binding site 2 out of 6 in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution


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 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni341 b:17.1 occ:0.33 NE2 A:HIS271 2.1 23.1 1.0 O A:HOH347 2.2 15.1 0.3 CE1 A:HIS271 3.0 32.5 1.0 CD2 A:HIS271 3.1 26.1 1.0 ND1 A:HIS271 4.1 22.3 1.0 CG A:HIS271 4.2 28.3 1.0 CG2 A:VAL249 4.7 29.9 1.0

Nickel binding site 3 out of 6 in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution


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 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni342 b:42.8 occ:1.00 OD2 A:ASP48 2.1 34.1 1.0 ND1 A:HIS0 2.2 48.9 1.0 O A:HOH348 2.4 29.7 1.0 O A:HOH349 2.5 30.2 1.0 CG A:ASP48 2.9 30.1 1.0 CG A:HIS0 3.1 40.9 1.0 OD1 A:ASP48 3.1 23.3 1.0 CB A:HIS0 3.2 33.3 1.0 CE1 A:HIS0 3.3 51.1 1.0 O A:HOH486 3.9 36.9 1.0 CA A:HIS0 3.9 34.9 1.0 CB A:ASP48 4.2 29.5 1.0 CD2 A:HIS0 4.3 47.3 1.0 NE2 A:HIS-2 4.3 58.3 1.0 NE2 A:HIS0 4.3 49.8 1.0 C A:HIS0 4.8 33.4 1.0 CE A:LYS74 4.9 47.3 1.0 CD2 A:HIS-2 5.0 66.9 1.0

Nickel binding site 4 out of 6 in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution


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 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni340 b:33.5 occ:1.00 ND1 B:HIS67 2.0 30.1 1.0 O B:HOH347 2.2 10.3 1.0 O B:HOH346 2.3 15.6 1.0 O B:HOH348 2.7 19.6 1.0 CE1 B:HIS67 2.9 26.6 1.0 CG B:HIS67 3.1 30.5 1.0 CB B:HIS67 3.5 27.9 1.0 CA B:HIS67 4.0 25.5 1.0 NE2 B:HIS67 4.0 29.8 1.0 CD2 B:HIS67 4.1 31.2 1.0 CD B:LYS70 4.5 32.0 1.0 O B:HOH501 4.8 33.9 1.0 CE1 B:PHE71 4.9 28.7 1.0 N B:HIS67 4.9 22.3 1.0

Nickel binding site 5 out of 6 in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni341 b:14.1 occ:0.33 NE2 B:HIS271 2.0 23.3 1.0 O B:HOH349 2.3 14.9 0.3 CE1 B:HIS271 3.0 24.6 1.0 CD2 B:HIS271 3.0 20.8 1.0 ND1 B:HIS271 4.1 25.3 1.0 CG B:HIS271 4.2 29.9 1.0 CG2 B:VAL249 4.2 31.6 1.0

Nickel binding site 6 out of 6 in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni342 b:50.3 occ:1.00 O B:HOH350 2.2 31.8 1.0 NE2 B:HIS263 2.2 28.1 1.0 O B:HOH351 2.8 29.6 1.0 CD2 B:HIS263 3.0 20.7 1.0 O B:HOH513 3.2 43.4 1.0 CE1 B:HIS263 3.3 27.4 1.0 CG B:HIS263 4.2 27.6 1.0 CB B:SER296 4.3 29.1 1.0 ND1 B:HIS263 4.3 28.5 1.0 O B:HOH505 4.3 39.1 1.0 O B:HOH493 4.6 48.6 1.0 OG B:SER296 4.6 22.2 1.0 CB B:GLN261 4.8 27.9 1.0

I.I.Mathews, D.Mcmullan, M.D.Miller, J.M.Canaves, M.A.Elsliger, R.Floyd, S.K.Grzechnik, L.Jaroszewski, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, T.M.Mcphillips, A.T.Morse, K.Quijano, C.L.Rife, R.Schwarzenbacher, G.Spraggon, R.C.Stevens, H.Van Den Bedem, D.Weekes, G.Wolf, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson. Crystal Structure of 2-Keto-3-Deoxygluconate Kinase (TM0067) From Thermotoga Maritima at 2.05 A Resolution. Proteins V. 70 603 2007.
ISSN: ISSN 0887-3585
PubMed: 18004772
DOI: 10.1002/PROT.21842