Calcium in PDB 6bia: Crystal Structure of Ps I-Cgsb

Protein crystallography data

The structure of Crystal Structure of Ps I-Cgsb, PDB code: 6bia 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) 114.86 / 2.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 133.850, 133.850, 223.695, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 26.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Ps I-Cgsb (pdb code 6bia). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Ps I-Cgsb, PDB code: 6bia:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6bia

Go back to Calcium Binding Sites List in 6bia
Calcium binding site 1 out of 3 in the Crystal Structure of Ps I-Cgsb


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 Ps I-Cgsb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:43.2
occ:1.00
OD1 A:ASP39 2.2 41.1 1.0
OD1 A:ASP38 2.3 39.6 1.0
OD2 A:ASP291 2.4 43.9 1.0
OD1 A:ASN292 2.4 34.4 1.0
SG A:CYS78 2.6 48.5 1.0
OD1 A:ASP291 2.6 42.9 1.0
CG A:ASP291 2.9 42.0 1.0
CG A:ASN292 3.2 35.2 1.0
CG A:ASP39 3.3 41.1 1.0
ND2 A:ASN292 3.4 33.2 1.0
CG A:ASP38 3.5 39.7 1.0
N A:ASP39 3.6 40.5 1.0
CB A:CYS78 3.6 41.6 1.0
CA A:CYS78 3.8 39.6 1.0
OD2 A:ASP39 4.0 41.8 1.0
N A:CYS78 4.0 38.7 1.0
C A:ASP38 4.2 39.4 1.0
CE A:LYS309 4.2 41.7 1.0
CA A:ASP39 4.2 40.7 1.0
CA A:ASP38 4.3 39.1 1.0
NZ A:LYS309 4.3 41.5 1.0
OD2 A:ASP38 4.3 40.4 1.0
CB A:ASP39 4.3 41.1 1.0
CB A:ASP291 4.3 39.2 1.0
CB A:ASP38 4.5 40.3 1.0
CB A:ASN292 4.6 35.4 1.0
CD2 A:HIS233 4.6 43.2 1.0
NZ A:LYS132 4.7 43.3 1.0
N A:ASN292 4.7 36.1 1.0
C A:PHE77 4.8 36.8 1.0
NH2 A:ARG82 4.9 45.7 1.0
NE A:ARG82 5.0 43.4 1.0

Calcium binding site 2 out of 3 in 6bia

Go back to Calcium Binding Sites List in 6bia
Calcium binding site 2 out of 3 in the Crystal Structure of Ps I-Cgsb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Ps I-Cgsb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:45.4
occ:1.00
OD1 B:ASP39 2.2 39.2 1.0
OD1 B:ASP38 2.3 41.3 1.0
OD2 B:ASP291 2.4 35.3 1.0
OD1 B:ASN292 2.4 40.6 1.0
SG B:CYS78 2.5 43.6 1.0
OD1 B:ASP291 2.7 37.4 1.0
CG B:ASP291 2.9 36.5 1.0
CG B:ASN292 3.3 37.2 1.0
CG B:ASP39 3.3 38.0 1.0
ND2 B:ASN292 3.5 34.2 1.0
CG B:ASP38 3.5 41.9 1.0
CB B:CYS78 3.5 40.5 1.0
N B:ASP39 3.6 40.3 1.0
CA B:CYS78 3.8 40.4 1.0
N B:CYS78 3.9 39.4 1.0
OD2 B:ASP39 4.0 36.9 1.0
CE B:LYS309 4.1 38.1 1.0
NZ B:LYS309 4.2 37.3 1.0
C B:ASP38 4.3 40.9 1.0
OD2 B:ASP38 4.3 41.8 1.0
CA B:ASP39 4.3 39.6 1.0
CA B:ASP38 4.3 41.4 1.0
CB B:ASP291 4.4 36.1 1.0
CB B:ASP39 4.4 38.6 1.0
CB B:ASP38 4.5 42.7 1.0
CD2 B:HIS233 4.6 34.8 1.0
NZ B:LYS132 4.6 47.4 1.0
CB B:ASN292 4.6 37.2 1.0
N B:ASN292 4.8 36.2 1.0
C B:PHE77 4.8 37.7 1.0
NH2 B:ARG82 4.9 42.5 1.0
NE B:ARG82 4.9 38.4 1.0

Calcium binding site 3 out of 3 in 6bia

Go back to Calcium Binding Sites List in 6bia
Calcium binding site 3 out of 3 in the Crystal Structure of Ps I-Cgsb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Ps I-Cgsb within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:47.7
occ:1.00
OD1 C:ASP38 2.1 57.0 1.0
OD1 C:ASP39 2.2 49.7 1.0
OD2 C:ASP291 2.4 50.5 1.0
OD1 C:ASN292 2.5 51.4 1.0
SG C:CYS78 2.6 60.0 1.0
OD1 C:ASP291 2.7 53.4 1.0
CG C:ASP291 2.9 49.4 1.0
CG C:ASP39 3.3 50.7 1.0
CG C:ASP38 3.4 59.4 1.0
CG C:ASN292 3.4 50.7 1.0
CB C:CYS78 3.6 52.5 1.0
N C:ASP39 3.6 56.0 1.0
ND2 C:ASN292 3.6 49.9 1.0
CA C:CYS78 3.8 50.7 1.0
OD2 C:ASP39 3.9 47.8 1.0
N C:CYS78 4.0 50.0 1.0
C C:ASP38 4.1 58.2 1.0
OD2 C:ASP38 4.1 61.7 1.0
CA C:ASP38 4.2 58.3 1.0
CE C:LYS309 4.2 44.1 1.0
CA C:ASP39 4.2 54.3 1.0
NZ C:LYS309 4.3 44.4 1.0
CB C:ASP39 4.3 52.5 1.0
CB C:ASP38 4.4 59.0 1.0
CB C:ASP291 4.4 48.6 1.0
NZ C:LYS132 4.6 53.3 1.0
ND1 C:HIS233 4.8 67.0 1.0
NH2 C:ARG82 4.8 54.6 1.0
CB C:ASN292 4.8 48.9 1.0
N C:ASN292 4.9 48.9 1.0
NE C:ARG82 4.9 48.7 1.0
C C:PHE77 4.9 47.5 1.0

Reference:

A.G.Hettle, C.Vickers, C.S.Robb, F.Liu, S.G.Withers, J.H.Hehemann, A.B.Boraston. The Molecular Basis of Polysaccharide Sulfatase Activity and A Nomenclature For Catalytic Subsites in This Class of Enzyme. Structure V. 26 747 2018.
ISSN: ISSN 1878-4186
PubMed: 29681469
DOI: 10.1016/J.STR.2018.03.012
Page generated: Sat Dec 12 05:58:51 2020

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