Calcium in PDB 6m8m: PA14 Sugar-Binding Domain From Rtx Adhesin

Protein crystallography data

The structure of PA14 Sugar-Binding Domain From Rtx Adhesin, PDB code: 6m8m was solved by T.D.R.Vance, B.Conroy, P.L.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.55 / 1.20
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 32.575, 61.309, 79.519, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 15.9

Other elements in 6m8m:

The structure of PA14 Sugar-Binding Domain From Rtx Adhesin also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the PA14 Sugar-Binding Domain From Rtx Adhesin (pdb code 6m8m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the PA14 Sugar-Binding Domain From Rtx Adhesin, PDB code: 6m8m:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6m8m

Go back to Calcium Binding Sites List in 6m8m
Calcium binding site 1 out of 3 in the PA14 Sugar-Binding Domain From Rtx Adhesin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of PA14 Sugar-Binding Domain From Rtx Adhesin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:6.1
occ:1.00
O A:PRO108 2.4 6.7 1.0
OD1 A:ASN110 2.4 6.6 1.0
OD1 A:ASP107 2.4 7.1 1.0
O A:HOH554 2.4 8.6 1.0
O A:HOH483 2.4 7.0 1.0
O A:HOH501 2.4 7.1 1.0
O A:HOH454 2.5 7.6 1.0
CG A:ASP107 3.4 8.0 1.0
CG A:ASN110 3.5 7.0 1.0
C A:PRO108 3.6 6.2 1.0
OD2 A:ASP107 3.7 9.1 1.0
H A:GLY91 3.7 7.8 1.0
HA A:ASN90 3.9 8.8 1.0
HD2 A:PRO108 3.9 8.8 1.0
HE22 A:GLN94 3.9 8.8 1.0
HG2 A:PRO108 4.0 8.5 1.0
HA A:ASN110 4.0 7.9 1.0
N A:ASN110 4.0 6.4 1.0
C A:GLU109 4.0 6.3 1.0
HD21 A:ASN110 4.0 9.5 1.0
H A:ASN110 4.2 7.7 1.0
HA A:GLU109 4.2 8.4 1.0
ND2 A:ASN110 4.2 7.9 1.0
N A:PRO108 4.3 6.3 1.0
O A:HOH428 4.3 5.8 1.0
O A:GLU109 4.3 7.0 1.0
C A:ASP107 4.4 7.1 1.0
CA A:ASN110 4.4 6.6 1.0
CD A:PRO108 4.4 7.3 1.0
O A:HOH447 4.4 14.2 1.0
CA A:GLU109 4.5 7.0 1.0
N A:GLU109 4.5 7.2 1.0
CA A:PRO108 4.5 7.5 1.0
N A:GLY91 4.5 6.5 1.0
HG12 A:VAL93 4.5 9.2 1.0
CB A:ASN110 4.5 7.1 1.0
OD1 A:ASN90 4.5 8.4 1.0
CG A:PRO108 4.6 7.1 1.0
CB A:ASP107 4.6 7.6 1.0
O A:HOH513 4.6 16.1 1.0
O A:ASP107 4.7 7.8 1.0
O A:GLY89 4.7 6.4 1.0
NE2 A:GLN94 4.8 7.4 1.0
OE1 A:GLN94 4.8 6.7 1.0
CA A:ASN90 4.8 7.3 1.0
HA A:ASP107 4.8 7.7 1.0
CA A:ASP107 4.9 6.4 1.0
HB3 A:ASP107 5.0 9.1 1.0

Calcium binding site 2 out of 3 in 6m8m

Go back to Calcium Binding Sites List in 6m8m
Calcium binding site 2 out of 3 in the PA14 Sugar-Binding Domain From Rtx Adhesin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of PA14 Sugar-Binding Domain From Rtx Adhesin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:4.6
occ:1.00
OE1 A:GLN47 2.3 5.8 1.0
OD1 A:ASN53 2.3 4.7 1.0
O A:GLN182 2.3 5.3 1.0
OD1 A:ASP113 2.4 5.6 1.0
O A:HOH435 2.5 5.6 1.0
OD2 A:ASP113 2.5 5.1 1.0
CG A:ASP113 2.8 5.0 1.0
CG A:ASN53 3.4 4.8 1.0
C A:GLN182 3.4 4.3 1.0
HA A:ASN53 3.5 6.1 1.0
HB2 A:GLN182 3.5 5.6 1.0
CD A:GLN47 3.5 5.3 1.0
HB2 A:GLN47 3.6 7.4 1.0
HA A:GLN182 3.6 5.8 1.0
H A:LEU54 3.9 6.1 1.0
CA A:GLN182 4.0 4.8 1.0
HG A:SER112 4.1 6.6 1.0
HB2 A:SER112 4.1 6.3 1.0
HE22 A:GLN47 4.2 7.7 1.0
CB A:ASN53 4.2 5.6 1.0
CB A:GLN182 4.2 4.6 1.0
OE1 A:GLN182 4.2 5.0 1.0
CA A:ASN53 4.2 5.1 1.0
HB2 A:ASN53 4.3 6.7 1.0
HD21 A:ASN53 4.3 6.7 1.0
ND2 A:ASN53 4.3 5.6 1.0
CB A:ASP113 4.3 4.8 1.0
CB A:GLN47 4.3 6.2 1.0
NE2 A:GLN47 4.3 6.4 1.0
HB3 A:GLN47 4.4 7.4 1.0
HA3 A:GLY183 4.4 6.5 1.0
O A:HOH500 4.5 8.4 1.0
CG A:GLN47 4.5 6.5 1.0
N A:LEU54 4.6 5.0 1.0
N A:GLY183 4.6 5.0 1.0
OG A:SER112 4.6 5.5 1.0
HB3 A:ASP113 4.7 5.8 1.0
O A:SER112 4.7 5.8 1.0
HA A:ASP113 4.7 5.4 1.0
HB2 A:ASP113 4.8 5.8 1.0
CB A:SER112 4.9 5.3 1.0
HB3 A:GLN182 4.9 5.6 1.0
CD A:GLN182 4.9 4.4 1.0
HG3 A:GLN47 4.9 7.8 1.0
C A:SER112 4.9 4.9 1.0
CA A:ASP113 5.0 4.5 1.0
C A:ASN53 5.0 5.6 1.0
CA A:GLY183 5.0 5.4 1.0

Calcium binding site 3 out of 3 in 6m8m

Go back to Calcium Binding Sites List in 6m8m
Calcium binding site 3 out of 3 in the PA14 Sugar-Binding Domain From Rtx Adhesin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of PA14 Sugar-Binding Domain From Rtx Adhesin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:4.5
occ:1.00
HA A:BGC301 2.0 5.5 1.0
OD1 A:ASP181 2.3 4.9 1.0
O A:ALA185 2.3 5.0 1.0
OD1 A:ASP136 2.3 5.2 1.0
O A:GLY183 2.4 5.2 1.0
OD2 A:ASP137 2.4 4.3 1.0
O2 A:BGC301 2.5 5.8 1.0
O1 A:BGC301 2.5 4.6 1.0
HB A:BGC301 3.0 7.0 1.0
H A:GLY183 3.3 6.0 1.0
CG A:ASP136 3.3 4.8 1.0
C1 A:BGC301 3.3 6.0 1.0
CG A:ASP137 3.4 4.0 1.0
C2 A:BGC301 3.4 5.7 1.0
H1 A:BGC301 3.4 7.2 1.0
HG3 A:GLN182 3.4 6.1 1.0
C A:GLY183 3.5 5.2 1.0
C A:ALA185 3.5 5.3 1.0
CG A:ASP181 3.5 4.6 1.0
OD2 A:ASP136 3.6 5.8 1.0
H2 A:BGC301 3.7 6.9 1.0
H A:ALA185 3.7 7.2 1.0
OD1 A:ASP137 3.7 4.2 1.0
H A:GLN182 3.8 4.7 1.0
HE21 A:GLN182 3.8 7.3 1.0
N A:ALA185 3.9 6.0 1.0
HA A:ASP181 3.9 4.4 1.0
N A:GLY183 3.9 5.0 1.0
HA A:ALA186 4.0 6.5 1.0
HA3 A:GLY184 4.1 7.7 1.0
N A:GLN182 4.3 3.9 1.0
C A:GLY184 4.3 6.2 1.0
OD2 A:ASP181 4.3 5.3 1.0
CA A:ALA185 4.3 5.8 1.0
N A:GLY184 4.3 6.0 1.0
CA A:GLY183 4.3 5.4 1.0
CG A:GLN182 4.3 5.1 1.0
C A:ASP136 4.4 4.0 1.0
CA A:GLY184 4.4 6.4 1.0
O A:ASP136 4.5 4.8 1.0
N A:ASP137 4.5 4.0 1.0
CB A:ASP181 4.5 4.5 1.0
HB2 A:ALA186 4.5 6.5 1.0
N A:ALA186 4.5 5.1 1.0
CA A:ASP181 4.5 3.7 1.0
NE2 A:GLN182 4.6 6.0 1.0
CB A:ASP137 4.6 4.1 1.0
CB A:ASP136 4.6 5.1 1.0
HB3 A:ALA185 4.6 8.2 1.0
HG2 A:GLN182 4.6 6.1 1.0
HB2 A:ASP181 4.6 5.4 1.0
H A:ASP137 4.6 4.8 1.0
O5 A:BGC301 4.6 6.6 1.0
CA A:ALA186 4.7 5.4 1.0
HB2 A:ASP137 4.7 4.9 1.0
C3 A:BGC301 4.7 8.0 1.0
C A:ASP181 4.8 4.4 1.0
HB3 A:ASP136 4.8 6.2 1.0
HA2 A:GLY183 4.8 6.5 1.0
HA A:ASP137 4.8 5.0 1.0
H3 A:BGC301 4.9 9.6 1.0
C A:GLN182 4.9 4.3 1.0
CA A:ASP137 4.9 4.1 1.0
O A:GLN155 5.0 5.8 1.0
CA A:ASP136 5.0 4.3 1.0

Reference:

T.D.R.Vance, S.Assaie-Ardakany, B.Conroy, P.L.Davies. Adhesin Sugar-Binding Domain Affinity Purification, Structure, and Ligand Analysis To Be Published.
Page generated: Sat Dec 12 06:48:16 2020

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