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Calcium in PDB 3x17: Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase

Enzymatic activity of Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase

All present enzymatic activity of Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase:
3.2.1.4;

Protein crystallography data

The structure of Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase, PDB code: 3x17 was solved by H.Okano, C.Angkawidjaja, S.Kanaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.96 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.631, 89.913, 151.157, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 24.6

Other elements in 3x17:

The structure of Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase (pdb code 3x17). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase, PDB code: 3x17:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3x17

Go back to Calcium Binding Sites List in 3x17
Calcium binding site 1 out of 4 in the Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:56.8
occ:1.00
 O B:VAL237 2.3 32.5 1.0
OD2 B:ASP242 2.5 37.7 1.0
OD1 B:ASN235 2.5 37.0 1.0
OD1 B:ASP225 2.5 34.2 1.0
OD1 B:ASP239 2.6 28.7 1.0
O B:GLU232 2.7 37.6 1.0
CG B:ASN235 3.3 42.8 1.0
C B:VAL237 3.5 34.6 1.0
CG B:ASP225 3.5 38.1 1.0
C B:GLU232 3.6 36.8 1.0
CG B:ASP242 3.7 39.2 1.0
CG B:ASP239 3.8 33.1 1.0
N B:GLY234 3.8 42.4 1.0
ND2 B:ASN235 3.8 39.9 1.0
CA B:SER233 3.9 38.2 1.0
N B:VAL237 3.9 36.9 1.0
N B:ASN235 4.0 43.0 1.0
N B:ASP239 4.0 31.8 1.0
CA B:ASP239 4.1 31.4 1.0
N B:SER233 4.1 37.0 1.0
CA B:VAL237 4.1 36.0 1.0
CA B:ASP225 4.2 33.7 1.0
C B:PRO238 4.2 32.3 1.0
C B:SER233 4.2 41.2 1.0
N B:GLY226 4.3 33.0 1.0
CB B:ASP225 4.3 34.6 1.0
OD1 B:ASP242 4.3 31.5 1.0
OD2 B:ASP225 4.3 44.9 1.0
CB B:VAL237 4.4 36.3 1.0
CB B:ASN235 4.5 42.5 1.0
O B:PRO238 4.5 32.5 1.0
CB B:GLU232 4.5 38.7 1.0
CB B:ASP239 4.6 32.1 1.0
N B:PRO238 4.6 33.2 1.0
N B:GLY236 4.6 39.5 1.0
CA B:ASN235 4.7 40.9 1.0
OD2 B:ASP239 4.7 33.1 1.0
CA B:GLU232 4.7 38.2 1.0
CA B:PRO238 4.7 33.1 1.0
CB B:ASP242 4.7 31.5 1.0
C B:ASP225 4.8 32.9 1.0
C B:ASN235 4.8 41.1 1.0
CA B:GLY234 4.8 44.1 1.0
C B:GLY234 4.9 44.6 1.0

Calcium binding site 2 out of 4 in 3x17

Go back to Calcium Binding Sites List in 3x17
Calcium binding site 2 out of 4 in the Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:33.6
occ:1.00
 OD2 B:ASP357 2.2 32.2 1.0
O B:ASP353 2.3 39.1 1.0
O B:VAL395 2.4 29.6 1.0
OD1 B:ASP356 2.4 31.2 1.0
OD2 B:ASP351 2.5 38.9 1.0
O B:HOH785 2.5 30.4 1.0
OD1 B:ASP351 2.6 40.1 1.0
CG B:ASP351 2.9 35.6 1.0
CG B:ASP357 3.2 30.6 1.0
CG B:ASP356 3.3 36.4 1.0
OD2 B:ASP356 3.4 32.6 1.0
C B:ASP353 3.5 36.1 1.0
OD1 B:ASP357 3.5 32.3 1.0
C B:VAL395 3.6 32.1 1.0
NZ B:LYS295 4.2 31.9 1.0
CA B:ASP354 4.4 33.7 1.0
N B:ASP354 4.4 33.2 1.0
CB B:ASP351 4.4 34.0 1.0
CA B:ASP353 4.4 38.0 1.0
N B:ASP357 4.5 34.3 1.0
CA B:VAL395 4.5 32.0 1.0
N B:ASP353 4.5 36.8 1.0
CB B:ASP357 4.6 32.1 1.0
N B:ASN396 4.6 32.5 1.0
CB B:ASP353 4.7 39.2 1.0
CB B:ASP356 4.7 31.2 1.0
CG1 B:VAL395 4.7 35.4 1.0
CA B:ASN396 4.8 31.3 1.0
CB B:GLN291 4.8 32.3 1.0
CD B:PRO397 4.8 31.4 1.0
C B:ASP354 4.9 35.0 1.0
N B:ASP356 5.0 28.6 1.0
O B:TRP394 5.0 34.1 1.0

Calcium binding site 3 out of 4 in 3x17

Go back to Calcium Binding Sites List in 3x17
Calcium binding site 3 out of 4 in the Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:79.3
occ:1.00
 O A:VAL237 2.2 55.3 1.0
OD1 A:ASP225 2.3 61.2 1.0
OD2 A:ASP242 2.6 60.3 1.0
OD1 A:ASN235 2.6 64.6 1.0
O A:GLU232 2.7 59.8 1.0
OD1 A:ASP239 2.7 53.1 1.0
CG A:ASP225 3.2 61.9 1.0
C A:VAL237 3.3 54.6 1.0
CG A:ASN235 3.5 63.4 1.0
CG A:ASP242 3.7 53.1 1.0
N A:ASP239 3.7 48.3 1.0
C A:GLU232 3.7 58.8 1.0
CG A:ASP239 3.8 51.2 1.0
CA A:SER233 3.9 59.4 1.0
CA A:ASP239 3.9 48.7 1.0
OD2 A:ASP225 3.9 60.7 1.0
N A:GLY234 3.9 61.5 1.0
N A:VAL237 3.9 57.7 1.0
CA A:VAL237 3.9 55.6 1.0
N A:ASN235 4.0 63.1 1.0
ND2 A:ASN235 4.1 63.7 1.0
C A:PRO238 4.1 51.0 1.0
CA A:ASP225 4.1 58.4 1.0
CB A:ASP225 4.1 58.8 1.0
CB A:VAL237 4.1 54.5 1.0
N A:SER233 4.2 58.9 1.0
C A:SER233 4.3 60.9 1.0
OD1 A:ASP242 4.3 47.3 1.0
N A:GLY226 4.4 56.9 1.0
N A:PRO238 4.4 52.8 1.0
CB A:ASP239 4.4 46.7 1.0
CB A:ASN235 4.5 62.5 1.0
O A:PRO238 4.5 52.0 1.0
CA A:PRO238 4.6 52.3 1.0
OD2 A:ASP239 4.6 50.1 1.0
CA A:ASN235 4.7 61.7 1.0
CB A:ASP242 4.7 42.5 1.0
CB A:GLU232 4.7 58.2 1.0
N A:GLY236 4.7 60.5 1.0
C A:ASP225 4.8 56.6 1.0
C A:ASN235 4.8 61.1 1.0
CA A:GLU232 4.8 57.1 1.0
CA A:GLY234 4.9 62.7 1.0
C A:GLY234 4.9 62.4 1.0
CG1 A:VAL237 5.0 54.0 1.0

Calcium binding site 4 out of 4 in 3x17

Go back to Calcium Binding Sites List in 3x17
Calcium binding site 4 out of 4 in the Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:46.0
occ:1.00
 OD2 A:ASP357 2.2 39.5 1.0
O A:ASP353 2.3 51.2 1.0
OD2 A:ASP351 2.3 36.8 1.0
OD1 A:ASP351 2.4 42.4 1.0
O A:VAL395 2.5 45.7 1.0
O A:HOH846 2.5 45.8 1.0
OD1 A:ASP356 2.7 50.3 1.0
CG A:ASP351 2.7 40.2 1.0
CG A:ASP357 3.3 40.5 1.0
C A:ASP353 3.5 50.0 1.0
CG A:ASP356 3.5 47.0 1.0
C A:VAL395 3.6 43.7 1.0
OD2 A:ASP356 3.7 51.4 1.0
OD1 A:ASP357 3.7 42.0 1.0
NZ A:LYS295 4.1 33.2 1.0
CB A:ASP351 4.2 40.7 1.0
CA A:ASP354 4.3 47.2 1.0
CA A:VAL395 4.4 40.7 1.0
N A:ASP354 4.4 47.7 1.0
CA A:ASP353 4.5 51.7 1.0
N A:ASP353 4.5 51.0 1.0
CG1 A:VAL395 4.5 40.9 1.0
CB A:ASP357 4.5 42.1 1.0
N A:ASP357 4.6 43.6 1.0
N A:ASN396 4.6 44.3 1.0
CB A:ASP353 4.7 52.7 1.0
CB A:GLN291 4.8 39.9 1.0
CA A:ASN396 4.8 44.9 1.0
C A:ASP354 4.8 47.4 1.0
CD A:PRO397 4.9 42.2 1.0
CB A:ASP356 5.0 46.6 1.0

Reference:

H.Okano, E.Kanaya, M.Ozaki, C.Angkawidjaja, S.Kanaya. Structure, Activity and Stability of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase with An N-Terminal Ig-Like Domain Protein Sci. 2014.
ISSN: ESSN 1469-896X
PubMed: 25545469
DOI: 10.1002/PRO.2632
Page generated: Sat Dec 12 04:36:22 2020

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