Calcium in PDB 5a3l: Structure of CEA1A in Complex with N-Acetylglucosamine

Protein crystallography data

The structure of Structure of CEA1A in Complex with N-Acetylglucosamine, PDB code: 5a3l was solved by M.Kock, S.Brueckner, N.Wozniak, M.Veelders, J.Schlereth, H.-U.Moesch, L.-O.Essen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.84 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 102.340, 106.210, 107.600, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.2

Other elements in 5a3l:

The structure of Structure of CEA1A in Complex with N-Acetylglucosamine also contains other interesting chemical elements:

Sodium (Na) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of CEA1A in Complex with N-Acetylglucosamine (pdb code 5a3l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of CEA1A in Complex with N-Acetylglucosamine, PDB code: 5a3l:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5a3l

Go back to Calcium Binding Sites List in 5a3l
Calcium binding site 1 out of 4 in the Structure of CEA1A in Complex with N-Acetylglucosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of CEA1A in Complex with N-Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1242

b:8.3
occ:1.00
O A:LEU204 2.3 8.4 1.0
OD1 A:ASP136 2.3 7.0 1.0
OD1 A:ASN202 2.3 8.5 1.0
O4 A:NDG1244 2.3 9.2 0.5
O4 A:NAG1243 2.3 8.4 0.5
O3 A:NDG1244 2.4 9.3 0.5
O3 A:NAG1243 2.4 8.5 0.5
O A:ARG206 2.4 8.7 1.0
OD2 A:ASP137 2.5 7.6 1.0
CG A:ASP136 3.2 7.3 1.0
C3 A:NDG1244 3.3 10.0 0.5
C4 A:NDG1244 3.3 9.7 0.5
C3 A:NAG1243 3.3 8.7 0.5
C4 A:NAG1243 3.3 8.5 0.5
CG A:ASP137 3.3 7.2 1.0
CG A:ASN202 3.5 8.1 1.0
C A:ARG206 3.5 9.1 1.0
C A:LEU204 3.5 8.9 1.0
OD2 A:ASP136 3.6 7.9 1.0
OD1 A:ASP137 3.7 7.2 1.0
N A:ARG206 3.8 9.5 1.0
N A:LEU204 3.9 8.8 1.0
ND2 A:ASN202 4.1 8.3 1.0
C A:GLU205 4.1 10.1 1.0
CA A:ARG206 4.2 9.7 1.0
C A:ASP136 4.2 6.9 1.0
O A:ASP136 4.3 7.2 1.0
N A:ASP137 4.4 6.9 1.0
CA A:LEU204 4.4 9.0 1.0
N A:ALA203 4.4 8.7 1.0
CB A:ASP136 4.5 7.2 1.0
N A:GLU205 4.5 9.4 1.0
O A:GLU205 4.5 9.4 1.0
CB A:ASP137 4.5 7.2 1.0
N A:ALA207 4.6 8.6 1.0
CB A:ASN202 4.6 8.2 1.0
CA A:GLU205 4.7 10.5 1.0
C2 A:NDG1244 4.7 10.3 0.5
C5 A:NAG1243 4.7 8.8 0.5
C5 A:NDG1244 4.7 10.2 0.5
C2 A:NAG1243 4.7 8.9 0.5
CA A:ASN202 4.7 8.0 1.0
CB A:ARG206 4.8 10.2 1.0
CA A:ASP137 4.8 7.2 1.0
CA A:ASP136 4.8 7.0 1.0
CD2 A:LEU204 4.9 10.7 1.0
CB A:GLU205 4.9 11.8 1.0
CG A:LEU204 4.9 10.4 1.0
CA A:ALA207 4.9 8.2 1.0
C A:ASN202 5.0 8.4 1.0

Calcium binding site 2 out of 4 in 5a3l

Go back to Calcium Binding Sites List in 5a3l
Calcium binding site 2 out of 4 in the Structure of CEA1A in Complex with N-Acetylglucosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of CEA1A in Complex with N-Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1242

b:8.3
occ:1.00
OD1 B:ASP136 2.3 6.8 1.0
OD1 B:ASN202 2.3 8.7 1.0
O B:LEU204 2.3 8.7 1.0
O4 B:NDG1244 2.4 9.0 0.5
O4 B:NAG1243 2.4 8.4 0.5
O3 B:NDG1244 2.4 9.0 0.5
O3 B:NAG1243 2.4 8.4 0.5
O B:ARG206 2.4 9.2 1.0
OD2 B:ASP137 2.4 7.8 1.0
C3 B:NDG1244 3.2 9.6 0.5
CG B:ASP136 3.2 7.1 1.0
C4 B:NDG1244 3.2 9.4 0.5
C3 B:NAG1243 3.3 8.7 0.5
C4 B:NAG1243 3.3 8.6 0.5
CG B:ASP137 3.3 7.6 1.0
CG B:ASN202 3.4 8.4 1.0
C B:ARG206 3.5 8.5 1.0
C B:LEU204 3.5 9.7 1.0
OD2 B:ASP136 3.6 7.5 1.0
OD1 B:ASP137 3.7 7.9 1.0
N B:ARG206 3.8 9.4 1.0
N B:LEU204 3.9 9.8 1.0
ND2 B:ASN202 4.0 8.7 1.0
C B:GLU205 4.1 9.9 1.0
C B:ASP136 4.2 7.2 1.0
CA B:ARG206 4.2 9.5 1.0
O B:ASP136 4.3 7.3 1.0
N B:ASP137 4.3 7.4 1.0
CA B:LEU204 4.4 10.0 1.0
N B:ALA203 4.4 8.5 1.0
CB B:ASP136 4.5 7.3 1.0
CB B:ASP137 4.5 7.8 1.0
N B:GLU205 4.5 9.9 1.0
O B:GLU205 4.5 9.9 1.0
N B:ALA207 4.6 8.3 1.0
CB B:ASN202 4.6 8.1 1.0
C5 B:NDG1244 4.6 9.9 0.5
C2 B:NDG1244 4.7 9.8 0.5
C5 B:NAG1243 4.7 9.0 0.5
CA B:GLU205 4.7 10.5 1.0
C2 B:NAG1243 4.7 8.9 0.5
CA B:ASN202 4.7 8.2 1.0
CA B:ASP137 4.7 7.7 1.0
CB B:ARG206 4.8 10.0 1.0
CA B:ASP136 4.8 7.2 1.0
CD2 B:LEU204 4.9 11.8 1.0
CA B:ALA207 4.9 8.0 1.0
CB B:GLU205 4.9 11.6 1.0
CG B:LEU204 4.9 11.3 1.0
C B:ASN202 5.0 8.3 1.0

Calcium binding site 3 out of 4 in 5a3l

Go back to Calcium Binding Sites List in 5a3l
Calcium binding site 3 out of 4 in the Structure of CEA1A in Complex with N-Acetylglucosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of CEA1A in Complex with N-Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1235

b:9.2
occ:1.00
OD1 C:ASP136 2.3 8.6 1.0
O C:LEU204 2.3 10.5 1.0
OD1 C:ASN202 2.3 10.8 1.0
O4 C:NDG1237 2.4 9.9 0.5
O4 C:NAG1236 2.4 8.7 0.5
O3 C:NDG1237 2.4 10.5 0.5
O C:ARG206 2.4 8.8 1.0
O3 C:NAG1236 2.4 9.2 0.5
OD2 C:ASP137 2.5 9.0 1.0
CG C:ASP136 3.2 8.4 1.0
C3 C:NDG1237 3.2 10.8 0.5
C4 C:NDG1237 3.2 10.8 0.5
C3 C:NAG1236 3.3 8.9 0.5
C4 C:NAG1236 3.3 9.0 0.5
CG C:ASP137 3.3 8.7 1.0
CG C:ASN202 3.5 9.2 1.0
C C:ARG206 3.5 8.8 1.0
C C:LEU204 3.5 11.7 1.0
OD2 C:ASP136 3.6 8.7 1.0
OD1 C:ASP137 3.7 9.4 1.0
N C:ARG206 3.8 9.2 1.0
N C:LEU204 4.0 12.0 1.0
C C:GLU205 4.1 9.7 1.0
ND2 C:ASN202 4.1 10.2 1.0
CA C:ARG206 4.2 9.1 1.0
C C:ASP136 4.2 7.8 1.0
O C:ASP136 4.2 7.7 1.0
N C:ASP137 4.3 7.8 1.0
CA C:LEU204 4.4 12.2 1.0
N C:ALA203 4.5 10.6 1.0
CB C:ASP136 4.5 7.9 1.0
CB C:ASP137 4.5 8.5 1.0
N C:GLU205 4.5 11.1 1.0
O C:GLU205 4.5 9.4 1.0
N C:ALA207 4.6 8.2 1.0
CB C:ASN202 4.6 9.2 1.0
CA C:GLU205 4.6 10.8 1.0
C5 C:NDG1237 4.6 11.3 0.5
C2 C:NDG1237 4.7 11.3 0.5
C5 C:NAG1236 4.7 9.3 0.5
CA C:ASN202 4.7 8.9 1.0
C2 C:NAG1236 4.7 9.1 0.5
CA C:ASP137 4.8 8.0 1.0
CB C:ARG206 4.8 9.5 1.0
CA C:ASP136 4.8 8.0 1.0
CB C:GLU205 4.9 11.6 1.0
CD2 C:LEU204 4.9 14.6 1.0
CA C:ALA207 4.9 8.0 1.0
CG C:LEU204 5.0 14.0 1.0

Calcium binding site 4 out of 4 in 5a3l

Go back to Calcium Binding Sites List in 5a3l
Calcium binding site 4 out of 4 in the Structure of CEA1A in Complex with N-Acetylglucosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of CEA1A in Complex with N-Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1235

b:9.8
occ:1.00
OD1 D:ASP136 2.3 8.3 1.0
OD1 D:ASN202 2.3 8.5 1.0
O D:LEU204 2.3 10.3 1.0
O4 D:NDG1237 2.4 10.4 0.5
O3 D:NDG1237 2.4 10.8 0.5
O4 D:NAG1236 2.4 9.7 0.5
O3 D:NAG1236 2.4 10.1 0.5
O D:ARG206 2.4 9.1 1.0
OD2 D:ASP137 2.4 9.6 1.0
CG D:ASP136 3.2 8.1 1.0
C3 D:NDG1237 3.2 11.2 0.5
C4 D:NDG1237 3.2 11.1 0.5
C3 D:NAG1236 3.3 10.2 0.5
C4 D:NAG1236 3.3 10.1 0.5
CG D:ASP137 3.3 9.5 1.0
CG D:ASN202 3.5 8.3 1.0
C D:LEU204 3.5 10.4 1.0
C D:ARG206 3.5 9.4 1.0
OD2 D:ASP136 3.6 8.3 1.0
OD1 D:ASP137 3.7 9.3 1.0
N D:ARG206 3.9 9.6 1.0
N D:LEU204 4.0 10.4 1.0
ND2 D:ASN202 4.1 7.7 1.0
C D:GLU205 4.1 9.6 1.0
O D:ASP136 4.2 8.7 1.0
C D:ASP136 4.2 8.7 1.0
CA D:ARG206 4.2 9.8 1.0
N D:ASP137 4.3 8.7 1.0
CA D:LEU204 4.4 10.8 1.0
N D:ALA203 4.4 10.0 1.0
CB D:ASP136 4.5 8.4 1.0
CB D:ASP137 4.5 9.3 1.0
N D:GLU205 4.5 9.9 1.0
O D:GLU205 4.5 9.2 1.0
N D:ALA207 4.6 8.7 1.0
CB D:ASN202 4.6 8.6 1.0
C5 D:NDG1237 4.6 11.5 0.5
CA D:GLU205 4.7 10.3 1.0
C2 D:NDG1237 4.7 11.6 0.5
C5 D:NAG1236 4.7 10.4 0.5
CA D:ASN202 4.7 8.7 1.0
C2 D:NAG1236 4.7 10.4 0.5
CA D:ASP137 4.7 9.1 1.0
CA D:ASP136 4.8 8.5 1.0
CB D:ARG206 4.8 10.3 1.0
CD2 D:LEU204 4.9 12.7 1.0
CA D:ALA207 4.9 8.8 1.0
CG D:LEU204 4.9 12.2 1.0
CB D:GLU205 4.9 11.9 1.0
C D:ASN202 5.0 9.2 1.0

Reference:

M.Kock, S.Brueckner, N.Wozniak, M.Veelders, J.Schlereth, H.-U.Moesch, L.-O.Essen. High-Affinity Recognition of Non-Reducing Chitinous Ends By the Yeast Adhesin CEA1 To Be Published.
Page generated: Sat Dec 12 05:16:36 2020

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