Nickel in PDB 6fop: Glycoside Hydrolase Family 81 From Clostridium Thermocellum (CTLAM81A), Mutant E515A

The structure of Glycoside Hydrolase Family 81 From Clostridium Thermocellum (CTLAM81A), Mutant E515A, PDB code: 6fop was solved by M.A.S.C.Correia, A.L.Carvalho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.15 / 1.40
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.917, 139.033, 197.909, 90.00, 90.00, 90.00
R / Rfree (%)	10.8 / 13.3

The structure of Glycoside Hydrolase Family 81 From Clostridium Thermocellum (CTLAM81A), Mutant E515A also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Calcium	(Ca)	3 atoms
Chlorine	(Cl)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Nickel atom in the Glycoside Hydrolase Family 81 From Clostridium Thermocellum (CTLAM81A), Mutant E515A (pdb code 6fop). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Glycoside Hydrolase Family 81 From Clostridium Thermocellum (CTLAM81A), Mutant E515A, PDB code: 6fop:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Glycoside Hydrolase Family 81 From Clostridium Thermocellum (CTLAM81A), Mutant E515A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Glycoside Hydrolase Family 81 From Clostridium Thermocellum (CTLAM81A), Mutant E515A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni828 b:14.8 occ:1.00 OE1 A:GLU628 2.0 17.3 1.0 OE2 A:GLU624 2.0 15.3 1.0 NE2 A:HIS597 2.1 14.2 1.0 NE2 A:HIS585 2.1 15.8 1.0 CD A:GLU628 2.7 17.9 1.0 OE2 A:GLU628 2.8 20.0 1.0 CD A:GLU624 2.9 17.1 1.0 CE1 A:HIS585 3.0 17.5 1.0 CE1 A:HIS597 3.0 14.1 1.0 CD2 A:HIS597 3.1 14.4 1.0 CD2 A:HIS585 3.1 14.8 1.0 CG A:GLU624 3.2 18.1 1.0 ND1 A:HIS572 4.0 18.6 1.0 OE1 A:GLU624 4.1 18.7 1.0 ND1 A:HIS585 4.1 15.8 1.0 ND1 A:HIS597 4.1 14.0 1.0 CG A:GLU628 4.2 17.9 1.0 CG A:HIS597 4.2 13.3 1.0 CG A:HIS585 4.2 15.7 1.0 CD2 A:TYR574 4.3 14.4 1.0 CB A:GLU624 4.4 16.9 1.0 N A:MET625 4.6 14.8 1.0 C A:GLU624 4.7 15.2 1.0 CA A:MET625 4.7 14.5 1.0 CB A:HIS572 4.7 17.0 1.0 CG A:HIS572 4.7 18.1 1.0 O A:GLU624 4.8 16.6 1.0 CB A:GLU628 4.8 17.6 1.0 CB A:TYR574 4.8 14.4 1.0 CE1 A:HIS572 4.9 20.6 1.0 ND2 A:ASN593 5.0 16.1 1.0

Nickel binding site 2 out of 2 in the Glycoside Hydrolase Family 81 From Clostridium Thermocellum (CTLAM81A), Mutant E515A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Glycoside Hydrolase Family 81 From Clostridium Thermocellum (CTLAM81A), Mutant E515A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni829 b:21.1 occ:0.37 O A:HOH1546 3.2 18.5 1.0 N A:GLU659 3.3 16.7 1.0 CB A:ASN658 3.7 15.2 1.0 CA A:ASN658 3.7 13.9 1.0 CG A:GLU659 3.9 22.2 1.0 C A:ASN658 4.0 15.7 1.0 CB A:GLU659 4.1 21.2 1.0 CA A:GLU659 4.3 18.7 1.0 CZ3 A:TRP657 4.6 16.3 1.0 OE2 A:GLU659 4.6 18.1 1.0 CD A:GLU659 4.7 18.6 1.0 O A:HOH1263 4.8 21.0 1.0 O A:TRP657 4.9 15.4 1.0 CE3 A:TRP657 4.9 16.0 1.0

K.Kumar, M.A.S.Correia, V.M.R.Pires, A.Dhillon, K.Sharma, V.Rajulapati, C.M.G.A.Fontes, A.L.Carvalho, A.Goyal. Novel Insights Into the Degradation of Beta-1,3-Glucans By the Cellulosome of Clostridium Thermocellum Revealed By Structure and Function Studies of A Family 81 Glycoside Hydrolase. Int.J.Biol.Macromol. V. 117 890 2018.
ISSN: ISSN 0141-8130
PubMed: 29870811
DOI: 10.1016/J.IJBIOMAC.2018.06.003