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Calcium in PDB 6k54: Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide

Enzymatic activity of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide

All present enzymatic activity of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide:
3.2.1.91;

Protein crystallography data

The structure of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide, PDB code: 6k54 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) 35.94 / 1.91
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 170.582, 138.699, 110.636, 90.00, 101.99, 90.00
R / Rfree (%) 17.6 / 20.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide (pdb code 6k54). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide, PDB code: 6k54:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 6k54

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Calcium binding site 1 out of 7 in the Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:18.2
occ:1.00
 O A:HOH842 2.3 19.3 1.0
O A:HOH749 2.3 17.0 1.0
OD2 A:ASP260 2.4 19.4 1.0
O A:HOH853 2.4 19.7 1.0
OD2 A:ASP263 2.4 23.4 1.0
O A:HOH800 2.5 23.8 1.0
OD1 A:ASP263 2.6 18.9 1.0
CG A:ASP263 2.8 23.2 1.0
CG A:ASP260 3.2 19.8 1.0
OD1 A:ASP260 3.3 17.8 1.0
O A:HOH668 4.2 19.8 1.0
CB A:ASP263 4.2 18.4 1.0
O A:HOH944 4.5 22.5 1.0
O C:HOH1049 4.5 26.6 1.0
O A:PRO236 4.6 17.9 1.0
O A:HOH892 4.6 38.3 1.0
CB A:ASP260 4.6 15.4 1.0
CG A:GLU231 4.6 30.7 1.0
CA A:PRO236 4.6 17.1 1.0
N A:GLU232 4.7 16.8 1.0
O A:GLU232 4.7 15.9 1.0
O A:LEU235 4.8 18.5 1.0
N A:ASP263 5.0 13.0 1.0
C2 A:PGE513 5.0 30.4 1.0

Calcium binding site 2 out of 7 in 6k54

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Calcium binding site 2 out of 7 in the Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:22.5
occ:1.00
 O A:ASP2 2.3 26.4 1.0
O A:THR280 2.3 19.6 1.0
O A:HOH639 2.5 20.9 1.0
O A:HOH680 2.5 21.2 1.0
OD1 A:ASP2 2.5 26.6 1.0
O A:HOH912 2.5 26.0 1.0
O A:HOH676 2.5 35.0 1.0
O A:HOH748 3.0 40.5 1.0
C A:ASP2 3.3 24.5 1.0
C A:THR280 3.5 24.0 1.0
CG A:ASP2 3.7 41.4 1.0
CA A:ASP2 3.8 26.9 1.0
CB A:THR280 4.1 31.4 1.0
CA A:THR280 4.2 24.3 1.0
CB A:ASP2 4.3 30.3 1.0
OD2 A:ASP350 4.5 22.2 1.0
N A:ILE281 4.5 20.6 1.0
N A:ASN3 4.5 23.0 1.0
O A:ASP218 4.5 18.8 1.0
N A:GLY282 4.5 17.4 1.0
O A:HOH693 4.6 27.8 1.0
C A:ILE281 4.6 19.8 1.0
CA A:ILE281 4.6 22.5 1.0
O A:HOH1005 4.6 25.4 1.0
OD2 A:ASP2 4.6 41.1 1.0
O A:HOH753 4.6 25.6 1.0
O A:HOH958 4.6 36.4 1.0
OD1 A:ASP350 4.7 20.8 1.0
O A:LEU1 4.8 21.9 1.0
CA A:ASN3 4.9 20.2 1.0
OG1 A:THR280 5.0 24.0 1.0

Calcium binding site 3 out of 7 in 6k54

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Calcium binding site 3 out of 7 in the Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:21.2
occ:1.00
 OD2 B:ASP263 2.3 24.7 1.0
OD2 B:ASP260 2.4 21.4 1.0
O B:HOH771 2.4 21.3 1.0
O B:HOH785 2.4 20.9 1.0
O B:HOH847 2.4 28.6 1.0
O B:HOH685 2.4 20.0 1.0
OD1 B:ASP263 2.6 22.6 1.0
CG B:ASP263 2.8 22.6 1.0
CG B:ASP260 3.2 21.6 1.0
OD1 B:ASP260 3.4 22.6 1.0
CB B:ASP263 4.2 20.2 1.0
O B:HOH711 4.3 20.0 1.0
O B:PRO236 4.6 26.0 1.0
N B:GLU232 4.6 19.1 1.0
CA B:PRO236 4.6 20.6 1.0
CB B:ASP260 4.6 18.8 1.0
O B:HOH757 4.7 38.7 1.0
O B:GLU232 4.8 19.6 1.0
O B:LEU235 4.8 21.5 1.0
C4 B:PGE509 4.8 32.7 1.0
CG B:GLU231 4.8 31.3 1.0
O4 B:PGE509 4.9 51.2 1.0
N B:ASP263 5.0 17.1 1.0

Calcium binding site 4 out of 7 in 6k54

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Calcium binding site 4 out of 7 in the Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:24.6
occ:1.00
 O B:THR280 2.3 19.6 1.0
O B:ASP2 2.3 23.6 1.0
O B:HOH691 2.4 24.5 1.0
O B:HOH837 2.4 26.9 1.0
O B:HOH615 2.5 20.9 1.0
OD1 B:ASP2 2.6 32.9 1.0
O B:HOH733 2.9 35.6 1.0
C B:ASP2 3.4 25.4 1.0
C B:THR280 3.4 23.4 1.0
CG B:ASP2 3.6 44.8 1.0
CA B:ASP2 3.9 27.9 1.0
CB B:THR280 4.1 29.2 1.0
CA B:THR280 4.2 24.7 1.0
CB B:ASP2 4.4 29.7 1.0
OD2 B:ASP350 4.4 21.0 1.0
N B:ILE281 4.5 20.1 1.0
OD2 B:ASP2 4.5 53.0 1.0
O B:ASP218 4.5 23.4 1.0
N B:GLY282 4.5 19.8 1.0
N B:ASN3 4.5 20.7 1.0
CA B:ILE281 4.6 24.5 1.0
C B:ILE281 4.6 23.0 1.0
O B:HOH760 4.6 29.6 1.0
O B:HOH710 4.6 31.3 1.0
O B:HOH898 4.6 42.2 1.0
OD1 B:ASP350 4.7 22.2 1.0
O B:HOH936 4.7 27.9 1.0
O B:LEU1 4.9 27.2 1.0
CA B:ASN3 5.0 26.4 1.0
OG1 B:THR280 5.0 28.8 1.0
CG B:ASP350 5.0 22.7 1.0

Calcium binding site 5 out of 7 in 6k54

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Calcium binding site 5 out of 7 in the Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:27.5
occ:1.00
 O B:HOH943 2.3 33.3 1.0
O B:ALA113 2.4 19.0 1.0
O B:HOH750 2.5 25.1 1.0
O B:HOH972 2.6 26.4 1.0
O B:HOH1019 3.2 39.3 1.0
C B:ALA113 3.5 20.8 1.0
CA B:ALA113 4.2 21.4 1.0
CB B:ALA113 4.4 21.6 1.0
N B:GLU114 4.5 18.4 1.0
CB B:ASP117 4.5 17.1 1.0
CD B:PRO118 4.5 14.6 1.0
CA B:GLU114 4.6 18.5 1.0
OD2 B:ASP117 4.8 22.3 1.0
O B:HOH1021 4.9 42.1 1.0
O B:HOH1020 5.0 29.9 1.0

Calcium binding site 6 out of 7 in 6k54

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Calcium binding site 6 out of 7 in the Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:19.8
occ:1.00
 OD2 C:ASP263 2.3 21.6 1.0
OD2 C:ASP260 2.3 21.0 1.0
O C:HOH843 2.4 19.2 1.0
O C:HOH725 2.5 17.1 1.0
O C:HOH744 2.5 18.4 1.0
O C:HOH923 2.5 26.7 1.0
OD1 C:ASP263 2.6 21.7 1.0
CG C:ASP263 2.8 23.0 1.0
CG C:ASP260 3.2 19.0 1.0
OD1 C:ASP260 3.3 18.9 1.0
O C:HOH727 4.2 19.8 1.0
CB C:ASP263 4.2 17.4 1.0
O A:HOH1006 4.4 24.3 1.0
O C:HOH718 4.4 23.8 1.0
O C:PRO236 4.5 22.8 1.0
O C:HOH646 4.5 34.5 1.0
CA C:PRO236 4.6 18.6 1.0
CB C:ASP260 4.6 14.7 1.0
N C:GLU232 4.7 15.3 1.0
O C:GLU232 4.8 18.2 1.0
CG C:GLU231 4.8 25.9 1.0
O C:LEU235 4.8 18.2 1.0
C4 C:PEG508 5.0 30.0 1.0
C C:PRO236 5.0 19.4 1.0
N C:ASP263 5.0 17.1 1.0

Calcium binding site 7 out of 7 in 6k54

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Calcium binding site 7 out of 7 in the Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Hyperthermophilic GH6 Cellobiohydrolase II (HMCEL6A) in Complex with Trisaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:25.9
occ:1.00
 O C:ASP2 2.2 28.7 1.0
O C:THR280 2.3 21.1 1.0
O C:HOH716 2.4 24.2 1.0
O C:HOH623 2.5 22.6 1.0
O C:HOH903 2.5 30.1 1.0
O C:HOH611 2.5 38.6 1.0
OD1 C:ASP2 2.6 36.1 1.0
O C:HOH689 3.0 36.1 1.0
C C:ASP2 3.3 25.1 1.0
C C:THR280 3.5 25.1 1.0
CG C:ASP2 3.6 45.8 1.0
CA C:ASP2 3.8 29.8 1.0
CB C:THR280 4.2 31.3 1.0
CA C:THR280 4.2 28.2 1.0
CB C:ASP2 4.3 30.6 1.0
N C:ASN3 4.5 22.2 1.0
OD2 C:ASP350 4.5 20.8 1.0
N C:ILE281 4.5 22.8 1.0
O C:ASP218 4.5 23.6 1.0
N C:GLY282 4.5 20.0 1.0
OD2 C:ASP2 4.6 53.4 1.0
C C:ILE281 4.6 19.8 1.0
O C:HOH701 4.6 33.9 1.0
CA C:ILE281 4.6 20.7 1.0
O C:HOH922 4.6 30.3 1.0
O C:HOH924 4.7 39.3 1.0
OD1 C:ASP350 4.7 21.3 1.0
O C:HOH854 4.8 27.8 1.0
O C:LEU1 4.9 26.9 1.0
CA C:ASN3 4.9 20.6 1.0
OG1 C:THR280 5.0 27.2 1.0

Reference:

M.Takeda, S.Baba, J.Okuma, Y.Hirose, A.Nishimura, M.Takata, K.Oda, D.Shibata, Y.Kondo, T.Kumasaka. Novel Hyperthermophilic Cellobiohydrolase II Isolated From Hot Spring Microbial Community To Be Published.
Page generated: Tue Jul 16 10:14:24 2024

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