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Calcium in PDB 2jec: Crystal Structure of Recombinant Dioclea Grandiflora Lectin Mutant E123A-H131N-K132Q Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D- Mannose

Protein crystallography data

The structure of Crystal Structure of Recombinant Dioclea Grandiflora Lectin Mutant E123A-H131N-K132Q Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D- Mannose, PDB code: 2jec was solved by C.S.Nagano, L.Sanz, B.S.Cavada, J.J.Calvete, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 88.04 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.194, 84.552, 176.210, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 23

Other elements in 2jec:

The structure of Crystal Structure of Recombinant Dioclea Grandiflora Lectin Mutant E123A-H131N-K132Q Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D- Mannose also contains other interesting chemical elements:

Bromine (Br) 4 atoms
Manganese (Mn) 8 atoms
Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Recombinant Dioclea Grandiflora Lectin Mutant E123A-H131N-K132Q Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D- Mannose (pdb code 2jec). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Recombinant Dioclea Grandiflora Lectin Mutant E123A-H131N-K132Q Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D- Mannose, PDB code: 2jec:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2jec

Go back to Calcium Binding Sites List in 2jec
Calcium binding site 1 out of 4 in the Crystal Structure of Recombinant Dioclea Grandiflora Lectin Mutant E123A-H131N-K132Q Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D- Mannose


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 Recombinant Dioclea Grandiflora Lectin Mutant E123A-H131N-K132Q Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D- Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca240

b:8.8
occ:1.00
 O A:HOH2207 2.3 9.2 1.0
O A:HOH2189 2.3 5.2 1.0
O A:TYR14 2.3 10.1 1.0
OD2 A:ASP21 2.4 6.8 1.0
OD1 A:ASN16 2.4 10.6 1.0
OD2 A:ASP12 2.4 10.1 1.0
OD1 A:ASP12 2.5 9.6 1.0
CG A:ASP12 2.8 11.6 1.0
CG A:ASP21 3.5 11.3 1.0
C A:TYR14 3.5 9.6 1.0
CG A:ASN16 3.5 11.6 1.0
OD1 A:ASP21 3.9 11.3 1.0
N A:ASN16 3.9 11.8 1.0
CB A:ASN16 4.1 11.0 1.0
MN A:MN241 4.2 10.0 1.0
CB A:ASP12 4.3 9.5 1.0
CA A:TYR14 4.4 9.6 1.0
N A:PRO15 4.5 10.8 1.0
N A:TYR14 4.5 9.4 1.0
CB A:TYR14 4.5 9.7 1.0
CA A:PRO15 4.5 11.1 1.0
O A:ARG230 4.6 8.9 1.0
O A:HOH2217 4.6 7.2 1.0
C A:PRO15 4.6 12.5 1.0
CE1 A:HIS26 4.7 9.5 1.0
CA A:ASN16 4.7 12.3 1.0
ND2 A:ASN16 4.7 8.7 1.0
OD1 A:ASP210 4.7 7.8 1.0
O A:ASP210 4.7 6.4 1.0
CB A:ASP21 4.7 10.8 1.0
CB A:ARG230 4.7 8.9 1.0
CA A:ARG230 4.8 8.5 1.0
CD2 A:TYR14 4.9 8.6 1.0
NE2 A:HIS26 5.0 9.0 1.0

Calcium binding site 2 out of 4 in 2jec

Go back to Calcium Binding Sites List in 2jec
Calcium binding site 2 out of 4 in the Crystal Structure of Recombinant Dioclea Grandiflora Lectin Mutant E123A-H131N-K132Q Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D- Mannose


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 Recombinant Dioclea Grandiflora Lectin Mutant E123A-H131N-K132Q Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D- Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca240

b:17.1
occ:1.00
 O B:TYR14 2.4 15.4 1.0
O B:HOH2150 2.4 12.9 1.0
OD1 B:ASN16 2.4 15.7 1.0
OD2 B:ASP21 2.4 18.3 1.0
O B:HOH2162 2.4 11.4 1.0
OD1 B:ASP12 2.5 13.9 1.0
OD2 B:ASP12 2.5 16.5 1.0
CG B:ASP12 2.9 14.9 1.0
CG B:ASP21 3.5 19.0 1.0
CG B:ASN16 3.5 18.5 1.0
C B:TYR14 3.6 16.7 1.0
OD1 B:ASP21 3.9 19.0 1.0
N B:ASN16 3.9 20.2 1.0
CB B:ASN16 4.2 19.8 1.0
MN B:MN241 4.3 16.0 1.0
CA B:TYR14 4.4 16.4 1.0
CB B:ASP12 4.4 13.8 1.0
O B:HOH2171 4.4 12.6 1.0
N B:TYR14 4.5 15.0 1.0
O B:ARG230 4.5 16.3 1.0
N B:PRO15 4.5 18.2 1.0
CB B:ARG230 4.6 16.8 1.0
CA B:PRO15 4.6 18.8 1.0
ND2 B:ASN16 4.6 12.5 1.0
C B:PRO15 4.6 19.9 1.0
CB B:TYR14 4.6 16.7 1.0
CA B:ARG230 4.7 15.9 1.0
O B:ASP210 4.7 12.8 1.0
OD1 B:ASP210 4.7 13.8 1.0
CB B:ASP21 4.7 20.0 1.0
CA B:ASN16 4.7 20.4 1.0
CE1 B:HIS26 4.7 14.0 1.0
CD2 B:TYR14 4.9 15.9 1.0

Calcium binding site 3 out of 4 in 2jec

Go back to Calcium Binding Sites List in 2jec
Calcium binding site 3 out of 4 in the Crystal Structure of Recombinant Dioclea Grandiflora Lectin Mutant E123A-H131N-K132Q Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D- Mannose


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 Recombinant Dioclea Grandiflora Lectin Mutant E123A-H131N-K132Q Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D- Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca240

b:15.2
occ:1.00
 O C:HOH2134 2.3 10.4 1.0
O C:TYR14 2.3 18.2 1.0
O C:HOH2149 2.3 18.4 1.0
OD2 C:ASP12 2.4 14.6 1.0
OD2 C:ASP21 2.4 16.6 1.0
OD1 C:ASN16 2.5 17.6 1.0
OD1 C:ASP12 2.5 10.8 1.0
CG C:ASP12 2.8 13.6 1.0
C C:TYR14 3.5 17.2 1.0
CG C:ASP21 3.6 17.9 1.0
CG C:ASN16 3.6 20.9 1.0
N C:ASN16 3.9 19.8 1.0
OD1 C:ASP21 4.0 19.2 1.0
CB C:ASN16 4.1 20.2 1.0
MN C:MN241 4.2 14.1 1.0
CB C:ASP12 4.3 14.2 1.0
CA C:TYR14 4.4 17.3 1.0
N C:PRO15 4.4 17.8 1.0
C C:PRO15 4.5 19.4 1.0
O C:HOH2159 4.5 16.8 1.0
CA C:PRO15 4.5 18.0 1.0
N C:TYR14 4.5 15.9 1.0
CE1 C:HIS26 4.6 8.8 1.0
OD1 C:ASP210 4.6 15.3 1.0
O C:ASP210 4.6 17.1 1.0
CA C:ASN16 4.6 20.6 1.0
O C:ARG230 4.6 17.3 1.0
CB C:TYR14 4.6 18.1 1.0
ND2 C:ASN16 4.7 19.3 1.0
CB C:ASP21 4.8 17.7 1.0
CA C:ARG230 4.8 17.9 1.0
CB C:ARG230 4.8 17.7 1.0
NE2 C:HIS26 4.9 12.2 1.0
CD2 C:TYR14 4.9 20.2 1.0

Calcium binding site 4 out of 4 in 2jec

Go back to Calcium Binding Sites List in 2jec
Calcium binding site 4 out of 4 in the Crystal Structure of Recombinant Dioclea Grandiflora Lectin Mutant E123A-H131N-K132Q Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D- Mannose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Recombinant Dioclea Grandiflora Lectin Mutant E123A-H131N-K132Q Complexed with 5-Bromo-4-Chloro-3-Indolyl-A-D- Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca240

b:13.7
occ:1.00
 O D:HOH2009 2.2 11.4 1.0
OD2 D:ASP12 2.3 14.1 1.0
O D:TYR14 2.4 17.5 1.0
O D:HOH2164 2.4 11.0 1.0
OD2 D:ASP21 2.4 10.3 1.0
OD1 D:ASN16 2.5 19.4 1.0
OD1 D:ASP12 2.6 11.5 1.0
CG D:ASP12 2.8 14.5 1.0
CG D:ASP21 3.6 14.5 1.0
C D:TYR14 3.6 16.9 1.0
CG D:ASN16 3.6 18.4 1.0
N D:ASN16 4.0 17.1 1.0
OD1 D:ASP21 4.1 12.3 1.0
CB D:ASN16 4.1 17.4 1.0
MN D:MN241 4.2 13.0 1.0
CB D:ASP12 4.3 13.2 1.0
CA D:TYR14 4.4 16.8 1.0
N D:TYR14 4.5 15.6 1.0
O D:HOH2176 4.5 9.6 1.0
O D:ASP210 4.5 14.9 1.0
CB D:TYR14 4.6 17.3 1.0
N D:PRO15 4.6 17.5 1.0
CE1 D:HIS26 4.6 12.8 1.0
O D:ARG230 4.6 15.8 1.0
CA D:PRO15 4.6 17.4 1.0
C D:PRO15 4.7 18.4 1.0
OD1 D:ASP210 4.7 14.8 1.0
CA D:ASN16 4.7 17.3 1.0
ND2 D:ASN16 4.8 16.1 1.0
CB D:ARG230 4.8 15.8 1.0
CB D:ASP21 4.8 14.8 1.0
CA D:ARG230 4.8 16.0 1.0
NE2 D:HIS26 4.9 14.3 1.0
CD2 D:TYR14 5.0 19.1 1.0

Reference:

C.S.Nagano, J.J.Calvete, D.Barettino, A.Perez, B.S.Cavada, L.Sanz. Insights Into the Structural Basis of the pH- Dependent Dimer-Tetramer Equilibrium Through Crystallographic Analysis of Recombinant Diocleinae Lectins. Biochem.J. V. 409 417 2008.
ISSN: ISSN 0264-6021
PubMed: 17937659
DOI: 10.1042/BJ20070942
Page generated: Fri Jul 12 13:38:57 2024

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