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Calcium in PDB 4u6b: ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans

Protein crystallography data

The structure of ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans, PDB code: 4u6b was solved by E.Ficko-Blean, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.30
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 187.790, 223.520, 225.220, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.5

Other elements in 4u6b:

The structure of ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans (pdb code 4u6b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans, PDB code: 4u6b:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4u6b

Go back to Calcium Binding Sites List in 4u6b
Calcium binding site 1 out of 8 in the ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:49.8
occ:1.00
 O A:SER399 2.2 32.7 1.0
O A:VAL402 2.3 40.9 1.0
O A:HOH737 2.4 47.3 1.0
OE1 A:GLU78 2.4 83.9 1.0
OD1 A:ASP397 2.5 52.5 1.0
O A:HOH729 2.6 44.6 1.0
OD2 A:ASP397 2.7 53.1 1.0
CG A:ASP397 2.9 48.7 1.0
O A:HOH699 3.3 52.2 1.0
C A:SER399 3.4 38.1 1.0
C A:VAL402 3.4 44.1 1.0
CD A:GLU78 3.5 78.1 1.0
CA A:ASP403 3.9 61.6 1.0
N A:SER399 4.0 33.1 1.0
NZ A:LYS408 4.0 50.1 1.0
CG A:GLU78 4.1 77.1 1.0
N A:ASP403 4.1 49.0 1.0
CA A:SER399 4.1 37.0 1.0
OD1 A:ASP403 4.4 70.5 1.0
CB A:ASP403 4.4 64.8 1.0
CB A:ASP397 4.4 43.8 1.0
N A:LEU400 4.5 39.8 1.0
CB A:SER399 4.5 35.5 1.0
OE2 A:GLU78 4.5 79.3 1.0
N A:VAL402 4.5 43.7 1.0
O A:ASP397 4.5 39.5 1.0
CA A:VAL402 4.6 40.6 1.0
C A:ASP397 4.7 41.4 1.0
CA A:LEU400 4.7 48.2 1.0
CG A:ASP403 4.9 72.8 1.0
O A:GLU78 4.9 55.0 1.0
CB A:VAL402 4.9 47.4 1.0
C A:LEU400 5.0 56.4 1.0
C A:LEU398 5.0 33.6 1.0

Calcium binding site 2 out of 8 in 4u6b

Go back to Calcium Binding Sites List in 4u6b
Calcium binding site 2 out of 8 in the ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:28.0
occ:1.00
 O A:HOH635 2.2 29.9 1.0
O A:HOH637 2.3 25.2 1.0
O A:HOH636 2.3 32.0 1.0
O A:HOH634 2.4 19.3 1.0
O A:HOH633 2.5 17.6 1.0
O A:HOH638 2.5 23.7 1.0
O A:HOH671 2.6 36.2 1.0
O A:PRO105 4.0 21.5 1.0
OD2 A:ASP186 4.2 26.9 1.0
O A:HOH632 4.2 29.2 1.0
O1 A:EDO505 4.2 54.2 1.0
O A:ALA352 4.4 23.4 1.0
O A:PRO185 4.7 24.4 1.0
O A:ASP104 4.7 19.9 1.0
OD1 A:ASP104 4.8 24.5 1.0
NE2 A:GLN251 4.8 35.2 1.0
O A:ALA353 4.8 27.4 1.0
CA A:ASP104 4.8 18.5 1.0
C A:ASP104 4.8 20.0 1.0
CB A:ALA352 4.9 22.9 1.0
C A:ALA352 4.9 27.4 1.0
CB A:ASP104 4.9 19.2 1.0
CA A:ALA352 4.9 24.9 1.0

Calcium binding site 3 out of 8 in 4u6b

Go back to Calcium Binding Sites List in 4u6b
Calcium binding site 3 out of 8 in the ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:40.9
occ:1.00
 O B:VAL402 2.1 35.9 1.0
OE1 B:GLU78 2.2 53.8 1.0
O B:SER399 2.3 33.6 1.0
O B:HOH675 2.4 39.3 1.0
O B:HOH671 2.5 45.7 1.0
OD1 B:ASP397 2.6 37.2 1.0
OD2 B:ASP397 2.8 40.8 1.0
CG B:ASP397 3.0 42.9 1.0
C B:VAL402 3.3 36.8 1.0
CD B:GLU78 3.4 58.0 1.0
C B:SER399 3.5 39.5 1.0
N B:SER399 3.9 29.7 1.0
CA B:ASP403 4.0 52.2 1.0
NZ B:LYS408 4.0 44.8 1.0
N B:ASP403 4.1 41.8 1.0
OE2 B:GLU78 4.2 58.3 1.0
CA B:SER399 4.3 33.2 1.0
CG B:GLU78 4.3 56.1 1.0
O B:ASP397 4.4 33.3 1.0
CA B:VAL402 4.5 34.4 1.0
N B:VAL402 4.5 37.1 1.0
CB B:ASP397 4.5 35.1 1.0
N B:LEU400 4.6 37.1 1.0
C B:ASP397 4.6 34.0 1.0
OD1 B:ASP403 4.6 59.8 1.0
CB B:ASP403 4.6 54.1 1.0
CB B:SER399 4.7 30.4 1.0
CA B:LEU400 4.8 45.1 1.0
O B:GLU78 4.8 38.6 1.0
CB B:VAL402 4.9 40.8 1.0
C B:LEU398 5.0 31.8 1.0
CG B:ASP403 5.0 62.8 1.0

Calcium binding site 4 out of 8 in 4u6b

Go back to Calcium Binding Sites List in 4u6b
Calcium binding site 4 out of 8 in the ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:27.6
occ:1.00
 O B:HOH636 2.3 14.9 1.0
O B:HOH640 2.4 30.5 1.0
O B:HOH638 2.4 30.6 1.0
O B:HOH641 2.5 23.8 1.0
O B:HOH634 2.5 22.0 1.0
O B:HOH635 2.5 17.0 1.0
O B:HOH639 2.6 31.1 1.0
O B:PRO105 3.9 19.6 1.0
O2 B:EDO504 4.1 52.1 1.0
OD2 B:ASP186 4.2 23.7 1.0
O B:HOH637 4.3 25.0 1.0
O B:ALA352 4.6 18.7 1.0
O B:PRO185 4.7 26.0 1.0
O B:ASP104 4.7 19.7 1.0
C B:ASP104 4.8 20.0 1.0
O B:HOH672 4.8 39.6 1.0
O B:ALA353 4.8 23.1 1.0
CA B:ASP104 4.8 20.0 1.0
NE2 B:GLN251 4.8 36.0 1.0
CB B:ALA352 4.8 20.1 1.0
OD1 B:ASP104 4.9 25.0 1.0
C B:ALA352 4.9 20.6 1.0
CB B:ASP104 4.9 18.8 1.0
CA B:ALA352 4.9 19.9 1.0
C B:PRO105 4.9 20.3 1.0

Calcium binding site 5 out of 8 in 4u6b

Go back to Calcium Binding Sites List in 4u6b
Calcium binding site 5 out of 8 in the ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:45.4
occ:1.00
 O C:VAL402 2.1 36.4 1.0
O C:SER399 2.2 41.3 1.0
OE1 C:GLU78 2.3 73.5 1.0
OD1 C:ASP397 2.5 47.6 1.0
O C:HOH683 2.5 36.9 1.0
O C:HOH762 2.6 51.4 1.0
OD2 C:ASP397 2.7 50.7 1.0
O C:HOH761 2.8 42.9 1.0
CG C:ASP397 3.0 46.5 1.0
CD C:GLU78 3.2 66.4 1.0
C C:VAL402 3.3 43.0 1.0
C C:SER399 3.4 40.2 1.0
OE2 C:GLU78 3.6 62.3 1.0
NZ C:LYS408 3.9 45.9 1.0
N C:SER399 4.0 30.8 1.0
CA C:ASP403 4.0 60.9 1.0
N C:ASP403 4.1 46.3 1.0
CA C:SER399 4.1 38.0 1.0
CG C:GLU78 4.3 71.3 1.0
N C:LEU400 4.4 42.6 1.0
CB C:ASP397 4.5 43.0 1.0
N C:VAL402 4.5 46.1 1.0
CA C:VAL402 4.5 41.1 1.0
CB C:SER399 4.5 37.4 1.0
CB C:ASP403 4.6 63.5 1.0
O C:ASP397 4.6 40.1 1.0
CA C:LEU400 4.7 47.5 1.0
OD1 C:ASP403 4.7 63.5 1.0
C C:ASP397 4.8 39.0 1.0
O C:GLU78 4.9 43.1 1.0
CB C:VAL402 4.9 46.1 1.0
C C:LEU400 5.0 46.8 1.0

Calcium binding site 6 out of 8 in 4u6b

Go back to Calcium Binding Sites List in 4u6b
Calcium binding site 6 out of 8 in the ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:25.4
occ:1.00
 O C:HOH632 2.3 18.3 1.0
O C:HOH631 2.3 29.2 1.0
O C:HOH636 2.3 5.9 0.5
O C:HOH633 2.4 23.3 1.0
O C:HOH630 2.5 13.8 1.0
O C:HOH637 2.5 27.0 1.0
O C:HOH635 2.5 34.0 1.0
O C:HOH636 3.2 32.6 0.5
O C:PRO105 3.9 20.6 1.0
OD2 C:ASP186 4.3 24.8 1.0
O C:HOH634 4.3 29.5 1.0
O1 C:EDO505 4.4 46.3 1.0
O C:ALA352 4.4 21.4 1.0
CB C:ALA352 4.7 21.8 1.0
C C:ASP104 4.7 19.8 1.0
O C:ASP104 4.7 20.2 1.0
C C:ALA352 4.7 23.1 1.0
CA C:ASP104 4.7 18.6 1.0
O C:ALA353 4.8 20.6 1.0
OD1 C:ASP104 4.8 25.2 1.0
CA C:ALA352 4.8 22.1 1.0
O C:PRO185 4.8 20.8 1.0
CB C:ASP104 4.8 19.1 1.0
NE2 C:GLN251 4.9 30.0 1.0
C C:PRO105 4.9 21.2 1.0

Calcium binding site 7 out of 8 in 4u6b

Go back to Calcium Binding Sites List in 4u6b
Calcium binding site 7 out of 8 in the ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:47.0
occ:1.00
 O D:HOH741 2.2 38.1 1.0
O D:VAL402 2.3 38.5 1.0
O D:SER399 2.4 44.3 1.0
OE1 D:GLU78 2.4 63.8 1.0
O D:HOH752 2.6 47.6 1.0
OD1 D:ASP397 2.6 48.0 1.0
OD2 D:ASP397 2.7 53.1 1.0
O D:HOH753 2.7 50.5 1.0
CG D:ASP397 3.0 50.6 1.0
CD D:GLU78 3.5 59.0 1.0
C D:VAL402 3.5 44.4 1.0
C D:SER399 3.6 42.6 1.0
CA D:ASP403 4.0 61.8 1.0
N D:SER399 4.0 35.1 1.0
N D:ASP403 4.2 52.2 1.0
OE2 D:GLU78 4.2 57.9 1.0
CA D:SER399 4.3 38.5 1.0
CG D:GLU78 4.4 59.8 1.0
NZ D:LYS408 4.4 47.1 1.0
CB D:ASP397 4.4 45.7 1.0
O D:ASP397 4.5 41.6 1.0
N D:VAL402 4.5 43.8 1.0
N D:LEU400 4.6 47.2 1.0
CA D:VAL402 4.6 43.6 1.0
C D:ASP397 4.6 44.1 1.0
OD1 D:ASP403 4.6 63.2 1.0
CB D:SER399 4.7 37.0 1.0
CB D:ASP403 4.7 62.3 1.0
CA D:LEU400 4.8 49.4 1.0
O D:GLU78 4.8 43.9 1.0
C D:LEU400 5.0 49.2 1.0
CE D:LYS408 5.0 53.0 1.0

Calcium binding site 8 out of 8 in 4u6b

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Calcium binding site 8 out of 8 in the ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:29.0
occ:1.00
 O D:HOH633 2.2 28.5 1.0
O D:HOH632 2.4 31.3 1.0
O D:HOH634 2.4 21.7 1.0
O D:HOH631 2.5 20.2 1.0
O D:HOH628 2.5 32.9 1.0
O D:HOH635 2.5 35.6 1.0
O D:HOH630 2.6 21.8 1.0
O D:PRO105 3.9 22.2 1.0
OD2 D:ASP186 4.2 24.9 1.0
O D:HOH629 4.4 20.8 1.0
O D:ALA352 4.5 25.2 1.0
NE2 D:GLN251 4.6 31.8 1.0
O D:ASP104 4.7 26.6 1.0
O D:PRO185 4.7 26.4 1.0
O D:ALA353 4.7 25.9 1.0
O D:HOH636 4.7 36.2 1.0
C D:ASP104 4.8 23.5 1.0
C D:ALA352 4.8 24.4 1.0
OD1 D:ASP104 4.8 28.5 1.0
CA D:ALA352 4.9 22.9 1.0
CA D:ASP104 4.9 23.8 1.0
CB D:ALA352 4.9 21.3 1.0
CB D:ASP104 5.0 21.9 1.0
C D:PRO105 5.0 24.4 1.0

Reference:

E.Ficko-Blean, D.Duffieux, E.Rebuffet, R.Larocque, A.Groisillier, G.Michel, M.Czjzek. Biochemical and Structural Investigation of Two Paralogous Glycoside Hydrolases From Zobellia Galactanivorans: Novel Insights Into the Evolution, Dimerization Plasticity and Catalytic Mechanism of the GH117 Family Acta Crystallogr.,Sect.D 2015.
ISSN: ESSN 1399-0047
DOI: 10.1107/S1399004714025024
Page generated: Wed Jul 9 02:13:37 2025

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