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Calcium in PDB 6aq5: X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with Epilactose

Protein crystallography data

The structure of X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with Epilactose, PDB code: 6aq5 was solved by O.Gerlits, R.J.Woods, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.17 / 2.19
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 134.950, 134.950, 81.794, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 20.8

Other elements in 6aq5:

The structure of X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with Epilactose also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with Epilactose (pdb code 6aq5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with Epilactose, PDB code: 6aq5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6aq5

Go back to Calcium Binding Sites List in 6aq5
Calcium binding site 1 out of 2 in the X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with Epilactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with Epilactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca310

b:22.4
occ:1.00
OD2 A:ASP136 2.3 21.2 1.0
ND2 A:ASN133 2.3 21.7 1.0
O A:PHE131 2.3 19.3 1.0
O A:HOH427 2.4 20.8 1.0
OD2 A:ASP129 2.4 24.4 1.0
O A:HOH409 2.4 17.8 1.0
OD1 A:ASP129 2.5 20.9 1.0
CG A:ASP129 2.8 26.1 1.0
CG A:ASP136 3.4 21.2 1.0
CG A:ASN133 3.5 24.3 1.0
C A:PHE131 3.5 22.4 1.0
OD1 A:ASP136 3.8 26.0 1.0
N A:ASN133 3.9 23.9 1.0
CB A:ASN133 4.0 22.4 1.0
MN A:MN309 4.2 26.5 1.0
CB A:ASP129 4.3 22.6 1.0
N A:PHE131 4.4 20.1 1.0
CA A:PHE131 4.4 20.3 1.0
O A:HOH413 4.4 21.7 1.0
CA A:GLY107 4.5 20.5 1.0
O A:GLY107 4.5 22.4 1.0
N A:SER132 4.5 18.8 1.0
OD1 A:ASN133 4.6 24.9 1.0
NE1 A:TRP135 4.6 22.6 1.0
CB A:PHE131 4.6 20.4 1.0
CB A:ASP136 4.6 24.4 1.0
CA A:ASN133 4.6 24.9 1.0
CA A:SER132 4.6 20.8 1.0
O A:ASP89 4.6 22.3 1.0
OD2 A:ASP89 4.6 17.9 1.0
C A:SER132 4.7 26.4 1.0
CD2 A:PHE131 4.8 24.2 1.0

Calcium binding site 2 out of 2 in 6aq5

Go back to Calcium Binding Sites List in 6aq5
Calcium binding site 2 out of 2 in the X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with Epilactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with Epilactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:18.2
occ:1.00
O B:PHE131 2.2 18.1 1.0
OD2 B:ASP136 2.3 17.8 1.0
ND2 B:ASN133 2.4 16.3 1.0
O B:HOH431 2.4 17.1 1.0
OD2 B:ASP129 2.4 21.0 1.0
O B:HOH447 2.4 19.2 1.0
OD1 B:ASP129 2.5 19.6 1.0
CG B:ASP129 2.8 17.9 1.0
CG B:ASP136 3.4 19.8 1.0
C B:PHE131 3.5 17.6 1.0
CG B:ASN133 3.6 20.3 1.0
N B:ASN133 3.9 20.9 1.0
OD1 B:ASP136 3.9 20.4 1.0
CB B:ASN133 4.1 17.5 1.0
MN B:MN304 4.2 25.7 1.0
CA B:PHE131 4.3 20.1 1.0
N B:PHE131 4.3 18.3 1.0
CB B:ASP129 4.3 17.6 1.0
N B:SER132 4.4 17.6 1.0
NE1 B:TRP135 4.5 21.4 1.0
CB B:PHE131 4.5 19.4 1.0
O B:GLY107 4.5 22.2 1.0
CA B:GLY107 4.5 19.1 1.0
CA B:SER132 4.5 19.1 1.0
OD1 B:ASN133 4.6 23.3 1.0
O B:ASP89 4.6 21.3 1.0
CB B:ASP136 4.6 18.4 1.0
OD2 B:ASP89 4.6 21.5 1.0
C B:SER132 4.6 21.0 1.0
CA B:ASN133 4.7 21.5 1.0
O B:HOH406 4.7 18.2 1.0
CD2 B:PHE131 4.7 18.4 1.0
CZ2 B:TRP135 4.9 24.2 1.0
CE2 B:TRP135 5.0 22.4 1.0

Reference:

O.Gerlits, R.J.Woods, A.Sood. X-Ray Crystal Structure of Erythrina Crista-Galli Lectin in Complex with Epilactose To Be Published.
Page generated: Mon Jul 15 16:35:42 2024

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