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Calcium in PDB 8bpd: Structural and Functional Characterization of the Novel Endo-Alpha(1, 4)-Fucoidanase MEF1 From the Marine Bacterium Muricauda Eckloniae

Enzymatic activity of Structural and Functional Characterization of the Novel Endo-Alpha(1, 4)-Fucoidanase MEF1 From the Marine Bacterium Muricauda Eckloniae

All present enzymatic activity of Structural and Functional Characterization of the Novel Endo-Alpha(1, 4)-Fucoidanase MEF1 From the Marine Bacterium Muricauda Eckloniae:
3.2.1.212;

Protein crystallography data

The structure of Structural and Functional Characterization of the Novel Endo-Alpha(1, 4)-Fucoidanase MEF1 From the Marine Bacterium Muricauda Eckloniae, PDB code: 8bpd was solved by M.D.Mikkelsen, A.S.Meyer, J.P.Morth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.72 / 1.80
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 105.416, 105.416, 78.247, 90, 90, 120
R / Rfree (%) 16.5 / 20.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Structural and Functional Characterization of the Novel Endo-Alpha(1, 4)-Fucoidanase MEF1 From the Marine Bacterium Muricauda Eckloniae (pdb code 8bpd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structural and Functional Characterization of the Novel Endo-Alpha(1, 4)-Fucoidanase MEF1 From the Marine Bacterium Muricauda Eckloniae, PDB code: 8bpd:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 8bpd

Go back to Calcium Binding Sites List in 8bpd
Calcium binding site 1 out of 2 in the Structural and Functional Characterization of the Novel Endo-Alpha(1, 4)-Fucoidanase MEF1 From the Marine Bacterium Muricauda Eckloniae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural and Functional Characterization of the Novel Endo-Alpha(1, 4)-Fucoidanase MEF1 From the Marine Bacterium Muricauda Eckloniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:27.7
occ:1.00
 O A:ASP248 2.3 28.3 1.0
O A:HOH637 2.3 29.6 1.0
OD2 A:ASP242 2.3 27.9 1.0
OD1 A:ASP246 2.4 30.1 1.0
OD2 A:ASP246 2.4 31.6 1.0
O A:HOH528 2.4 29.8 1.0
O A:HOH534 2.4 31.4 1.0
CG A:ASP246 2.7 36.9 1.0
HB3 A:ASP248 3.2 39.1 1.0
C A:ASP248 3.5 33.5 1.0
CG A:ASP242 3.5 28.0 1.0
HB2 A:ASP242 3.6 32.5 1.0
HE1 A:TYR252 3.6 29.1 1.0
H A:ASP248 3.6 42.6 1.0
H A:ASP242 3.6 33.1 1.0
O A:ARG250 4.1 27.1 1.0
CB A:ASP248 4.1 32.6 1.0
CB A:ASP242 4.1 27.1 1.0
CA A:ASP248 4.2 35.0 1.0
HA2 A:GLY249 4.2 38.9 1.0
CB A:ASP246 4.2 41.4 1.0
N A:ASP242 4.3 27.6 1.0
N A:ASP248 4.3 35.5 1.0
HD3 A:PRO279 4.3 31.3 1.0
O A:GLY277 4.3 29.1 1.0
HA A:SER241 4.4 35.7 1.0
O A:HOH567 4.5 44.4 1.0
H A:ARG250 4.5 38.7 1.0
CE1 A:TYR252 4.5 24.2 1.0
HD2 A:PRO247 4.5 45.4 1.0
N A:GLY249 4.5 33.4 1.0
O A:HOH555 4.5 34.8 1.0
OD1 A:ASP242 4.6 27.0 1.0
HB3 A:ASP246 4.6 49.6 1.0
HB2 A:ASP246 4.6 49.6 1.0
HD1 A:TYR252 4.7 32.2 1.0
CA A:GLY249 4.7 32.4 1.0
N A:ARG250 4.7 32.2 1.0
HB2 A:ASP248 4.8 39.1 1.0
C A:GLY249 4.8 35.7 1.0
CG A:ASP248 4.8 33.2 1.0
CA A:ASP242 4.9 32.6 1.0
HB3 A:ASP242 4.9 32.5 1.0
HG3 A:PRO279 4.9 31.4 1.0
HA A:ASP246 4.9 50.5 1.0
O A:ASP240 4.9 29.0 1.0
HH A:TYR252 5.0 28.8 1.0

Calcium binding site 2 out of 2 in 8bpd

Go back to Calcium Binding Sites List in 8bpd
Calcium binding site 2 out of 2 in the Structural and Functional Characterization of the Novel Endo-Alpha(1, 4)-Fucoidanase MEF1 From the Marine Bacterium Muricauda Eckloniae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural and Functional Characterization of the Novel Endo-Alpha(1, 4)-Fucoidanase MEF1 From the Marine Bacterium Muricauda Eckloniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:32.9
occ:1.00
 O A:ALA136 2.3 20.9 1.0
O A:THR140 2.4 19.6 1.0
OD1 A:ASN142 2.5 25.5 1.0
O A:SER138 2.5 19.6 1.0
HB1 A:ALA136 3.1 25.1 1.0
C A:ALA136 3.4 18.6 1.0
C A:THR140 3.6 20.9 1.0
CG A:ASN142 3.6 24.9 1.0
C A:SER138 3.6 20.9 1.0
CB A:ALA136 3.9 20.9 1.0
C A:ARG137 4.0 22.9 0.5
N A:THR140 4.1 18.2 1.0
HD21 A:ASN142 4.1 35.8 1.0
HA A:ARG137 4.1 24.5 0.5
N A:SER138 4.1 21.0 1.0
H A:SER138 4.1 25.2 0.5
H A:THR140 4.1 21.8 1.0
H A:ASN142 4.1 24.1 1.0
HB3 A:ALA136 4.1 25.1 1.0
CA A:ALA136 4.2 19.6 1.0
N A:ASN142 4.2 20.1 1.0
HA A:ARG137 4.2 24.6 0.5
H A:SER138 4.3 25.2 0.5
O A:ARG137 4.3 24.5 0.5
HA A:ARG141 4.3 23.2 1.0
C A:GLY139 4.3 18.4 1.0
C A:ARG137 4.3 22.8 0.5
ND2 A:ASN142 4.3 29.9 1.0
O A:HOH744 4.3 30.4 1.0
HB A:THR140 4.3 21.6 1.0
N A:ARG137 4.3 18.7 0.5
CA A:THR140 4.4 18.9 1.0
N A:ARG137 4.4 18.8 0.5
HA A:ASN142 4.4 23.8 1.0
O A:HOH742 4.4 19.1 1.0
HA A:ALA136 4.4 23.5 1.0
O A:HOH804 4.4 37.7 1.0
CA A:SER138 4.4 22.3 1.0
CA A:ARG137 4.5 20.4 0.5
CA A:ARG137 4.5 20.4 0.5
HA2 A:GLY139 4.5 24.6 1.0
C A:ARG141 4.5 20.8 1.0
O A:HOH532 4.5 27.5 1.0
N A:ARG141 4.5 19.8 1.0
N A:GLY139 4.5 20.5 1.0
CA A:ARG141 4.7 19.3 1.0
OD2 A:ASP132 4.7 20.9 1.0
CA A:ASN142 4.7 19.8 1.0
CA A:GLY139 4.7 20.5 1.0
HB2 A:ALA136 4.7 25.1 1.0
HA A:SER138 4.7 26.8 1.0
O A:GLY139 4.7 19.7 1.0
CB A:ASN142 4.7 21.1 1.0
O A:ARG137 4.9 22.7 0.5
CB A:THR140 4.9 18.0 1.0

Reference:

M.D.Mikkelsen, V.H.N.Tran, S.Meier, T.T.Nguyen, J.Holck, H.T.T.Cao, T.T.T.Van, P.D.Thinh, A.S.Meyer, J.P.Morth. Structural and Functional Characterization of the Novel Endo-Alpha (1,4)-Fucoidanase MEF1 From the Marine Bacterium Muricauda Eckloniae. Acta Crystallogr D Struct 2023BIOL.
ISSN: ISSN 2059-7983
PubMed: 37877949
DOI: 10.1107/S2059798323008732
Page generated: Thu Dec 28 01:35:48 2023

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