Atomistry » Calcium » PDB 3wt3-3zq4 » 3x17
Atomistry »
  Calcium »
    PDB 3wt3-3zq4 »
      3x17 »

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: Tue Jul 8 18:06:43 2025

Last articles

Mg in 5IQC
Mg in 5IQD
Mg in 5IQB
Mg in 5IQA
Mg in 5IPL
Mg in 5IPN
Mg in 5IPM
Mg in 5IN8
Mg in 5IOO
Mg in 5IP9
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy