Atomistry » Calcium » PDB 8bad-8brt » 8bpd
Atomistry »
  Calcium »
    PDB 8bad-8brt »
      8bpd »

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: Fri Jul 19 07:24:51 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy