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Calcium in PDB 6dlh: Endo-Fucoidan Hydrolase MFFCNA4 From Glycoside Hydrolase Family 107

Protein crystallography data

The structure of Endo-Fucoidan Hydrolase MFFCNA4 From Glycoside Hydrolase Family 107, PDB code: 6dlh was solved by C.Vickers, K.Abe, O.Salama-Alber, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.23 / 2.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 156.600, 156.600, 84.571, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 25.3

Other elements in 6dlh:

The structure of Endo-Fucoidan Hydrolase MFFCNA4 From Glycoside Hydrolase Family 107 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Endo-Fucoidan Hydrolase MFFCNA4 From Glycoside Hydrolase Family 107 (pdb code 6dlh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Endo-Fucoidan Hydrolase MFFCNA4 From Glycoside Hydrolase Family 107, PDB code: 6dlh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6dlh

Go back to Calcium Binding Sites List in 6dlh
Calcium binding site 1 out of 5 in the Endo-Fucoidan Hydrolase MFFCNA4 From Glycoside Hydrolase Family 107


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Endo-Fucoidan Hydrolase MFFCNA4 From Glycoside Hydrolase Family 107 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca804

b:39.8
occ:1.00
 OD1 A:ASP336 2.2 39.9 1.0
O A:ARG332 2.3 52.2 1.0
OD1 A:ASN335 2.3 34.2 1.0
OD1 A:ASP330 2.4 37.9 1.0
O A:PHE327 2.4 37.9 1.0
O A:HOH1143 2.4 43.5 1.0
CG A:ASN335 3.4 35.9 1.0
CG A:ASP336 3.5 42.7 1.0
C A:ARG332 3.5 47.7 1.0
CG A:ASP330 3.5 38.3 1.0
C A:PHE327 3.6 36.4 1.0
ND2 A:ASN335 4.0 35.8 1.0
OD2 A:ASP330 4.0 36.2 1.0
O A:HOH933 4.1 49.6 1.0
OD2 A:ASP336 4.2 44.3 1.0
CA A:ARG328 4.2 39.8 1.0
N A:ARG332 4.3 49.0 1.0
CA A:ARG332 4.3 47.1 1.0
N A:ARG328 4.4 36.9 1.0
N A:ASP336 4.4 39.5 1.0
C A:ASN335 4.4 41.0 1.0
N A:ASP330 4.4 41.1 1.0
CA A:ASP336 4.4 38.4 1.0
N A:THR333 4.4 50.0 1.0
CB A:PHE327 4.4 31.6 1.0
O A:ASP330 4.4 41.4 1.0
CA A:THR333 4.5 49.3 1.0
CB A:ASP336 4.5 40.4 1.0
C A:ASP330 4.6 42.9 1.0
CA A:PHE327 4.6 34.9 1.0
N A:ASP329 4.6 43.4 1.0
O A:ASN335 4.6 42.7 1.0
CB A:ARG332 4.7 44.2 1.0
C A:ARG328 4.7 40.5 1.0
CB A:ASN335 4.7 37.4 1.0
N A:ASN335 4.7 42.3 1.0
CB A:ASP330 4.7 39.8 1.0
C A:THR333 4.7 47.1 1.0
CA A:ASP330 4.8 40.4 1.0
CA A:ASN335 4.8 41.0 1.0
O A:THR333 4.9 50.5 1.0

Calcium binding site 2 out of 5 in 6dlh

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Calcium binding site 2 out of 5 in the Endo-Fucoidan Hydrolase MFFCNA4 From Glycoside Hydrolase Family 107


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Endo-Fucoidan Hydrolase MFFCNA4 From Glycoside Hydrolase Family 107 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca805

b:60.1
occ:1.00
 OD2 A:ASP670 2.2 52.0 1.0
OD2 A:ASP715 2.3 71.1 1.0
O A:GLY634 2.4 49.6 1.0
OD1 A:ASP666 2.5 56.1 1.0
OE1 A:GLU668 2.7 46.6 1.0
CG A:ASP666 3.3 58.8 1.0
OD2 A:ASP666 3.4 58.9 1.0
CG A:ASP670 3.4 59.0 1.0
CG A:ASP715 3.5 76.9 1.0
C A:GLY634 3.5 53.6 1.0
CD A:GLU668 3.8 45.9 1.0
CB A:ASP670 4.1 60.4 1.0
CA A:GLY634 4.1 57.8 1.0
O A:HOH1012 4.2 53.1 1.0
CB A:ASP715 4.2 78.6 1.0
CB A:GLU668 4.2 51.7 1.0
CG A:GLU668 4.4 46.5 1.0
OD1 A:ASP715 4.4 76.8 1.0
OD1 A:ASP670 4.4 59.3 1.0
CD A:PRO636 4.6 66.8 1.0
N A:ALA635 4.6 52.0 1.0
OE2 A:GLU668 4.7 49.2 1.0
CB A:ASP666 4.7 55.9 1.0
N A:GLU668 4.9 53.0 1.0
CG A:PRO636 5.0 65.6 1.0
C A:ALA635 5.0 58.9 1.0
CA A:ALA635 5.0 56.0 1.0

Calcium binding site 3 out of 5 in 6dlh

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Calcium binding site 3 out of 5 in the Endo-Fucoidan Hydrolase MFFCNA4 From Glycoside Hydrolase Family 107


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Endo-Fucoidan Hydrolase MFFCNA4 From Glycoside Hydrolase Family 107 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca806

b:42.1
occ:1.00
 OD2 A:ASP609 2.3 31.4 1.0
OE1 A:GLU562 2.3 35.5 1.0
O A:GLY528 2.4 41.0 1.0
OD2 A:ASP564 2.5 47.6 1.0
OD2 A:ASP560 2.5 36.0 1.0
O A:HOH1192 2.6 23.4 1.0
OD1 A:ASP560 2.9 39.8 1.0
CG A:ASP560 3.1 37.5 1.0
C A:GLY528 3.4 41.3 1.0
O A:HOH935 3.4 23.9 1.0
CG A:ASP609 3.5 34.9 1.0
CD A:GLU562 3.5 41.0 1.0
CG A:ASP564 3.6 46.8 1.0
CA A:GLY528 3.8 43.8 1.0
CB A:ASP564 4.1 45.6 1.0
CB A:GLU562 4.1 41.5 1.0
CB A:ASP609 4.2 33.5 1.0
CG A:GLU562 4.2 41.5 1.0
OE2 A:GLU562 4.5 44.1 1.0
OD1 A:ASP609 4.5 32.5 1.0
CB A:ASP560 4.6 36.4 1.0
O A:HOH969 4.6 45.0 1.0
OD1 A:ASP564 4.6 49.8 1.0
N A:THR529 4.6 40.3 1.0
N A:GLU562 4.6 42.1 1.0
O A:HOH1321 4.7 43.5 1.0
CD A:PRO530 4.8 40.4 1.0
N A:PRO530 4.9 40.7 1.0
C A:THR529 4.9 41.3 1.0
CA A:GLU562 4.9 43.0 1.0

Calcium binding site 4 out of 5 in 6dlh

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Calcium binding site 4 out of 5 in the Endo-Fucoidan Hydrolase MFFCNA4 From Glycoside Hydrolase Family 107


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Endo-Fucoidan Hydrolase MFFCNA4 From Glycoside Hydrolase Family 107 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca807

b:28.9
occ:1.00
 O A:HOH1243 2.3 47.3 1.0
O A:HOH1097 2.4 25.9 1.0
OD1 A:ASP79 2.4 25.1 1.0
OD2 A:ASP79 2.4 25.9 1.0
O A:THR77 2.4 27.0 1.0
O A:HOH1004 2.4 23.9 1.0
O A:HOH1007 2.6 27.2 1.0
CG A:ASP79 2.7 25.2 1.0
C A:THR77 3.5 25.6 1.0
CA A:THR77 4.1 26.0 1.0
CB A:ASP79 4.2 24.0 1.0
O A:HOH1161 4.2 39.9 1.0
OE1 A:GLN416 4.2 28.4 1.0
CB A:THR77 4.3 26.4 1.0
O A:GLY44 4.3 30.5 1.0
O A:HOH1228 4.5 39.6 1.0
C A:VAL78 4.6 25.5 1.0
N A:VAL78 4.6 25.3 1.0
O A:ARG425 4.7 25.0 1.0
N A:ASP79 4.7 26.8 1.0
O A:VAL78 4.7 24.2 1.0
NE2 A:GLN426 4.8 27.9 1.0
CA A:ASP79 4.8 24.7 1.0
N A:LEU46 4.9 25.9 1.0
CA A:VAL78 4.9 24.9 1.0
O A:HOH1291 4.9 41.2 1.0

Calcium binding site 5 out of 5 in 6dlh

Go back to Calcium Binding Sites List in 6dlh
Calcium binding site 5 out of 5 in the Endo-Fucoidan Hydrolase MFFCNA4 From Glycoside Hydrolase Family 107


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Endo-Fucoidan Hydrolase MFFCNA4 From Glycoside Hydrolase Family 107 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca808

b:67.2
occ:1.00
 O A:GLY419 2.1 39.3 1.0
OE1 A:GLU453 2.4 36.5 1.0
O A:HOH1088 2.5 40.8 1.0
OD1 A:ASP451 2.7 38.8 1.0
OD2 A:ASP502 2.8 44.0 1.0
C A:GLY419 3.2 40.6 1.0
CG A:ASP451 3.5 37.6 1.0
CD A:GLU453 3.5 36.2 1.0
CG A:ASP502 3.6 41.6 1.0
CA A:GLY419 3.6 38.6 1.0
CB A:ASP504 4.0 54.7 1.0
OD1 A:ASP502 4.0 39.5 1.0
OD2 A:ASP451 4.0 40.2 1.0
CB A:GLU453 4.0 36.4 1.0
N A:GLY419 4.1 39.1 1.0
CG A:GLU453 4.2 35.9 1.0
N A:GLU453 4.2 36.3 1.0
CD A:PRO452 4.3 30.8 1.0
N A:LYS420 4.4 40.2 1.0
OE2 A:GLU453 4.4 41.3 1.0
CB A:ASP451 4.5 36.3 1.0
N A:PRO452 4.5 32.3 1.0
CB A:ASP502 4.6 38.6 1.0
CA A:GLU453 4.7 36.1 1.0
CG A:ASP504 4.8 60.5 1.0
CA A:ASP451 4.8 34.4 1.0
C A:ASP451 4.8 32.4 1.0
CA A:LYS420 4.9 40.5 1.0
OG A:SER503 4.9 38.0 1.0

Reference:

C.Vickers, F.Liu, K.Abe, O.Salama-Alber, M.Jenkins, C.M.K.Springate, J.E.Burke, S.G.Withers, A.B.Boraston. Endo-Fucoidan Hydrolases From Glycoside Hydrolase Family 107 (GH107) Display Structural and Mechanistic Similarities to Alpha-L-Fucosidases From GH29. J. Biol. Chem. V. 293 18296 2018.
ISSN: ESSN 1083-351X
PubMed: 30282808
DOI: 10.1074/JBC.RA118.005134
Page generated: Mon Jul 15 17:58:59 2024

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