Magnesium in PDB 6k55: Inactivated Mutant (D140A) of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Hexasaccharide

The structure of Inactivated Mutant (D140A) of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Hexasaccharide, PDB code: 6k55 was solved by S.Baba, M.Takeda, J.Okuma, Y.Hirose, A.Nishimura, M.Takata, K.Oda, D.Shibata, Y.Kondo, T.Kumasaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.35 / 2.88
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	173.949, 140.010, 110.578, 90.00, 101.06, 90.00
R / Rfree (%)	17.9 / 21.8

The binding sites of Magnesium atom in the Inactivated Mutant (D140A) of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Hexasaccharide (pdb code 6k55). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Inactivated Mutant (D140A) of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Hexasaccharide, PDB code: 6k55:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Inactivated Mutant (D140A) of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Hexasaccharide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Inactivated Mutant (D140A) of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Hexasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:44.7 occ:1.00 OD2 A:ASP263 2.2 62.1 1.0 OD2 A:ASP260 2.6 58.4 1.0 CG A:ASP263 3.2 64.8 1.0 O A:HOH647 3.3 54.2 1.0 OD1 A:ASP263 3.4 59.6 1.0 CG A:ASP260 3.6 55.1 1.0 O A:PRO236 3.7 65.3 1.0 OD1 A:ASP260 3.8 58.0 1.0 CA A:PRO236 4.0 47.1 1.0 O A:LEU235 4.2 56.4 1.0 O A:GLU232 4.2 51.3 1.0 C A:PRO236 4.3 54.2 1.0 CB A:ASP263 4.5 52.8 1.0 N A:GLU232 4.7 54.7 1.0 CG A:GLU231 4.7 65.0 1.0 CB A:PRO236 4.9 45.9 1.0 C A:LEU235 4.9 54.5 1.0 CB A:ASP260 4.9 41.6 1.0 C A:GLU232 5.0 52.8 1.0 N A:PRO236 5.0 48.0 1.0

Magnesium binding site 2 out of 6 in the Inactivated Mutant (D140A) of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Hexasaccharide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Inactivated Mutant (D140A) of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Hexasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:50.7 occ:1.00 O A:ASP2 2.2 59.0 1.0 O A:THR280 2.2 59.5 1.0 OD1 A:ASP2 2.3 63.9 1.0 CG A:ASP2 3.3 69.2 1.0 C A:ASP2 3.3 61.2 1.0 C A:THR280 3.4 60.9 1.0 OD2 A:ASP350 3.6 59.5 1.0 OD1 A:ASP350 3.8 54.2 1.0 CA A:ASP2 3.8 61.0 1.0 O A:ASP218 3.9 67.0 1.0 N A:GLY282 4.0 58.5 1.0 C A:ILE281 4.0 61.4 1.0 OD2 A:ASP2 4.0 73.2 1.0 CG A:ASP350 4.1 57.7 1.0 CB A:ASP2 4.1 52.8 1.0 CA A:ILE281 4.1 57.6 1.0 N A:ILE281 4.2 51.8 1.0 CA A:THR280 4.4 61.4 1.0 N A:ASN3 4.4 54.9 1.0 O A:ILE281 4.5 60.7 1.0 CB A:THR280 4.6 60.9 1.0 CA A:GLY282 4.6 54.3 1.0 CA A:ASN3 4.8 51.2 1.0 C A:ASP218 5.0 58.8 1.0

Magnesium binding site 3 out of 6 in the Inactivated Mutant (D140A) of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Hexasaccharide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Inactivated Mutant (D140A) of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Hexasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:47.4 occ:1.00 OD2 B:ASP263 2.4 44.2 1.0 OD2 B:ASP260 2.5 59.0 1.0 CG B:ASP263 3.2 58.9 1.0 OD1 B:ASP263 3.3 58.8 1.0 CG B:ASP260 3.5 57.6 1.0 OD1 B:ASP260 3.8 56.5 1.0 O B:GLU232 4.0 58.7 1.0 CA B:PRO236 4.0 59.4 1.0 O B:PRO236 4.1 53.6 1.0 O B:LEU235 4.2 58.0 1.0 CG B:GLU231 4.2 79.0 1.0 N B:GLU232 4.5 63.4 1.0 C B:PRO236 4.5 49.7 1.0 CB B:ASP263 4.6 55.2 1.0 C B:GLU232 4.8 54.5 1.0 CB B:ASP260 4.8 51.6 1.0 CB B:PRO236 4.8 51.9 1.0 N B:PRO236 4.9 53.1 1.0 C B:LEU235 4.9 54.5 1.0 OE2 B:GLU231 5.0 97.1 1.0

Magnesium binding site 4 out of 6 in the Inactivated Mutant (D140A) of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Hexasaccharide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Inactivated Mutant (D140A) of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Hexasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:49.5 occ:1.00 O B:ASP2 2.0 62.6 1.0 O B:THR280 2.2 68.0 1.0 OD1 B:ASP2 2.7 62.7 1.0 OD2 B:ASP350 3.2 56.4 1.0 C B:ASP2 3.2 60.1 1.0 C B:THR280 3.4 64.8 1.0 OD1 B:ASP350 3.6 57.2 1.0 CG B:ASP2 3.6 65.1 1.0 CG B:ASP350 3.8 55.6 1.0 CA B:ASP2 3.9 54.7 1.0 N B:GLY282 3.9 45.3 1.0 C B:ILE281 4.0 56.4 1.0 O B:ASP218 4.0 55.1 1.0 CA B:ILE281 4.1 52.7 1.0 N B:ILE281 4.3 56.6 1.0 N B:ASN3 4.3 54.1 1.0 CB B:ASP2 4.3 50.2 1.0 CA B:THR280 4.5 56.7 1.0 OD2 B:ASP2 4.5 60.2 1.0 O B:ILE281 4.5 62.8 1.0 CA B:ASN3 4.6 50.6 1.0 CA B:GLY282 4.6 43.4 1.0 CB B:THR280 4.7 58.4 1.0 OG1 B:THR280 4.8 75.2 1.0 OH B:TYR181 4.9 56.0 1.0 CB B:ASN3 4.9 42.2 1.0

Magnesium binding site 5 out of 6 in the Inactivated Mutant (D140A) of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Hexasaccharide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Inactivated Mutant (D140A) of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Hexasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:44.6 occ:1.00 OD2 C:ASP263 2.4 43.3 1.0 OD2 C:ASP260 2.5 60.3 1.0 CG C:ASP263 3.3 54.4 1.0 OD1 C:ASP263 3.5 62.1 1.0 CG C:ASP260 3.6 54.6 1.0 O C:PRO236 3.8 61.0 1.0 O C:GLU232 3.9 54.0 1.0 CA C:PRO236 3.9 56.1 1.0 OD1 C:ASP260 4.0 47.8 1.0 O C:LEU235 4.1 64.9 1.0 C C:PRO236 4.3 54.3 1.0 N C:GLU232 4.3 56.6 1.0 C C:GLU232 4.6 53.7 1.0 CB C:ASP263 4.7 45.0 1.0 CB C:PRO236 4.8 46.9 1.0 C C:LEU235 4.8 58.4 1.0 N C:PRO236 4.8 60.2 1.0 CB C:ASP260 4.8 44.4 1.0 CA C:GLU232 4.9 48.5 1.0 CB C:GLU232 4.9 50.4 1.0 CG C:GLU231 5.0 81.5 1.0

Magnesium binding site 6 out of 6 in the Inactivated Mutant (D140A) of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Hexasaccharide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Inactivated Mutant (D140A) of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Hexasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:53.1 occ:1.00 O C:THR280 2.1 59.5 1.0 O C:ASP2 2.4 56.6 1.0 O C:HOH604 2.4 58.0 1.0 O C:HOH626 2.4 56.5 1.0 O C:HOH606 2.6 51.4 1.0 OD1 C:ASP2 2.6 53.0 1.0 C C:THR280 3.2 67.0 1.0 OD2 C:ASP350 3.3 53.9 1.0 OD1 C:ASP350 3.5 56.7 1.0 C C:ASP2 3.5 55.9 1.0 CG C:ASP2 3.5 55.0 1.0 N C:GLY282 3.7 56.6 1.0 C C:ILE281 3.7 57.2 1.0 CG C:ASP350 3.8 48.2 1.0 CA C:ILE281 4.0 53.6 1.0 N C:ILE281 4.1 56.8 1.0 O C:ILE281 4.1 64.6 1.0 CA C:ASP2 4.2 51.0 1.0 OD2 C:ASP2 4.2 57.9 1.0 CA C:THR280 4.2 63.0 1.0 CA C:GLY282 4.2 51.2 1.0 O C:ASP218 4.3 56.6 1.0 CB C:ASP2 4.4 49.0 1.0 N C:ASN3 4.6 51.9 1.0 CB C:THR280 4.7 54.6 1.0 CA C:ASN3 4.8 47.3 1.0

M.Takeda, S.Baba, J.Okuma, Y.Hirose, A.Nishimura, M.Takata, K.Oda, D.Shibata, Y.Kondo, T.Kumasaka. A Hyperthermophilic Cellobiohydrolase Mined From A Hot Spring Metagenomic Data To Be Published.