Calcium in PDB 7jwf: Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose

Protein crystallography data

The structure of Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose, PDB code: 7jwf was solved by A.G.Hettle, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.76 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.517, 124.763, 142.423, 90.00, 93.86, 90.00
R / Rfree (%) 20.5 / 23.7

Other elements in 7jwf:

The structure of Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose also contains other interesting chemical elements:

Iodine (I) 120 atoms
Chlorine (Cl) 10 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose (pdb code 7jwf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose, PDB code: 7jwf:

Calcium binding site 1 out of 1 in 7jwf

Go back to Calcium Binding Sites List in 7jwf
Calcium binding site 1 out of 1 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca746

b:54.8
occ:1.00
O A:ASP274 2.5 27.6 1.0
O A:HOH1055 2.5 32.0 1.0
O A:HOH1143 2.6 41.8 1.0
OE2 A:GLU125 2.7 41.1 1.0
C A:ASP274 3.5 30.2 1.0
CD A:GLU125 3.5 44.0 1.0
OE1 A:GLU125 4.0 47.0 1.0
CA A:GLU125 4.2 27.9 1.0
N A:SER275 4.3 27.8 1.0
O A:HOH1036 4.4 34.9 1.0
CA A:SER275 4.4 29.5 1.0
CA A:ASP274 4.4 29.9 1.0
CB A:ASP274 4.5 30.7 1.0
ND2 A:ASN276 4.5 30.4 1.0
CG A:GLU125 4.6 36.5 1.0
CB A:GLU125 4.7 30.3 1.0
C A:GLU125 4.8 27.8 1.0
O A:HOH818 4.8 33.4 1.0
C A:SER275 4.8 27.6 1.0

Reference:

B.E.Mcguire, A.Hettle, C.Vickers, D.T.King, D.J.Vocadlo, A.B.Boraston. The Structure of A Family 110 Glycoside Hydrolase Provides Insight Into the Hydrolysis of Alpha-(1,3)-Galactosidic Linkages in Lambda-Carrageenan and Blood Group Antigens. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 33127644
DOI: 10.1074/JBC.RA120.015776
Page generated: Sat Dec 12 08:07:16 2020

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