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Manganese 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
Chlorine (Cl) 4 atoms
Calcium (Ca) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 8 binding sites of Manganese 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 Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 2jec

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Manganese binding site 1 out of 8 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 Manganese with other atoms in the Mn 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:Mn241

b:10.0
occ:1.00
 OD1 A:ASP12 2.1 9.6 1.0
OD1 A:ASP21 2.2 11.3 1.0
OE2 A:GLU10 2.2 8.0 1.0
O A:HOH2217 2.2 7.2 1.0
NE2 A:HIS26 2.2 9.0 1.0
O A:HOH2216 2.3 8.5 1.0
CG A:ASP12 3.1 11.6 1.0
CG A:ASP21 3.2 11.3 1.0
CE1 A:HIS26 3.2 9.5 1.0
CD A:GLU10 3.2 10.2 1.0
CD2 A:HIS26 3.2 6.4 1.0
CB A:ASP12 3.5 9.5 1.0
OE1 A:GLU10 3.5 11.3 1.0
OD2 A:ASP21 3.6 6.8 1.0
O A:HOH2207 3.9 9.2 1.0
O A:HOH2028 4.0 19.1 1.0
OG A:SER36 4.2 8.5 1.0
CA A:CA240 4.2 8.8 1.0
OD2 A:ASP12 4.2 10.1 1.0
O A:HOH2030 4.3 23.6 1.0
ND1 A:HIS26 4.3 8.2 1.0
CG A:HIS26 4.4 9.2 1.0
CB A:ASP21 4.4 10.8 1.0
CG A:GLU10 4.5 9.1 1.0
O A:ILE34 4.5 11.8 1.0
CA A:ASP21 4.7 12.2 1.0

Manganese binding site 2 out of 8 in 2jec

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Manganese binding site 2 out of 8 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 Manganese with other atoms in the Mn 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
A:Mn243

b:29.4
occ:0.50
 CE1 A:HIS53 1.8 10.8 0.5
O A:HOH2223 2.1 39.4 1.0
NE2 A:HIS53 2.4 10.1 0.5
O A:HOH2172 2.4 27.1 1.0
O A:HOH2221 2.4 25.7 1.0
O A:HOH2222 2.6 29.9 1.0
ND1 A:HIS53 2.9 12.3 0.5
CD2 A:HIS53 3.6 11.2 0.5
OD2 A:ASP194 3.6 15.9 0.5
CG A:HIS53 3.9 11.0 0.5
CG2 D:VAL190 4.0 15.7 1.0
OG D:SER192 4.0 17.5 1.0
CB D:SER192 4.1 14.6 1.0
CB A:SER55 4.2 11.2 1.0
OG A:SER55 4.4 16.6 1.0
CG A:ASP194 4.6 14.4 0.5
CB A:ASP194 4.7 11.9 0.5
CB D:ASN57 4.8 15.3 1.0
O A:HOH2077 4.9 26.0 1.0
CB A:ASP194 4.9 12.5 0.5
CG1 D:VAL190 5.0 16.6 1.0

Manganese binding site 3 out of 8 in 2jec

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Manganese binding site 3 out of 8 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 Manganese with other atoms in the Mn 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
B:Mn241

b:16.0
occ:1.00
 O B:HOH2171 2.0 12.6 1.0
NE2 B:HIS26 2.1 13.3 1.0
OD1 B:ASP12 2.2 13.9 1.0
O B:HOH2172 2.2 14.4 1.0
OD1 B:ASP21 2.2 19.0 1.0
OE2 B:GLU10 2.2 13.9 1.0
CE1 B:HIS26 2.9 14.0 1.0
CG B:ASP12 3.1 14.9 1.0
CG B:ASP21 3.1 19.0 1.0
CD B:GLU10 3.2 14.0 1.0
CD2 B:HIS26 3.3 11.9 1.0
CB B:ASP12 3.5 13.8 1.0
OE1 B:GLU10 3.5 14.3 1.0
OD2 B:ASP21 3.7 18.3 1.0
O B:HOH2162 4.0 11.4 1.0
O B:HOH2014 4.1 25.6 1.0
ND1 B:HIS26 4.1 14.1 1.0
OG B:SER36 4.1 14.9 1.0
OD2 B:ASP12 4.2 16.5 1.0
CA B:CA240 4.3 17.1 1.0
CB B:ASP21 4.3 20.0 1.0
CG B:HIS26 4.3 12.7 1.0
O B:HOH2015 4.5 26.7 1.0
CG B:GLU10 4.6 13.8 1.0
CA B:ASP21 4.6 20.4 1.0
O B:ILE34 4.6 20.0 1.0
CA B:ASP12 5.0 14.0 1.0

Manganese binding site 4 out of 8 in 2jec

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Manganese binding site 4 out of 8 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 Manganese with other atoms in the Mn 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
B:Mn243

b:43.4
occ:0.50
 NE2 B:HIS53 2.0 15.9 0.5
CE1 B:HIS53 2.3 13.5 0.5
O B:HOH2176 2.7 30.0 1.0
CD2 B:HIS53 3.3 14.5 0.5
O B:HOH2045 3.5 49.5 1.0
ND1 B:HIS53 3.5 13.3 0.5
O B:HOH2044 4.0 37.6 1.0
CG B:HIS53 4.0 12.7 0.5
OG C:SER192 4.1 19.0 1.0
CB B:ASP194 4.1 16.9 1.0
CG B:ASP194 4.3 23.6 1.0
CB C:SER192 4.3 15.4 1.0
OD1 B:ASP194 4.4 30.5 1.0
CB B:SER55 4.5 13.2 1.0
CG2 C:VAL190 4.6 21.7 1.0
OD2 B:ASP194 4.9 29.2 1.0

Manganese binding site 5 out of 8 in 2jec

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Manganese binding site 5 out of 8 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 Manganese with other atoms in the Mn binding site number 5 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:Mn241

b:14.1
occ:1.00
 O C:HOH2158 2.0 12.0 1.0
O C:HOH2159 2.1 16.8 1.0
OD1 C:ASP12 2.2 10.8 1.0
OE2 C:GLU10 2.2 13.9 1.0
NE2 C:HIS26 2.2 12.2 1.0
OD1 C:ASP21 2.3 19.2 1.0
CG C:ASP12 3.1 13.6 1.0
CD C:GLU10 3.2 13.4 1.0
CG C:ASP21 3.2 17.9 1.0
CE1 C:HIS26 3.2 8.8 1.0
CD2 C:HIS26 3.2 10.4 1.0
OE1 C:GLU10 3.5 14.2 1.0
CB C:ASP12 3.5 14.2 1.0
OD2 C:ASP21 3.6 16.6 1.0
O C:HOH2149 3.9 18.4 1.0
OG C:SER36 4.2 16.2 1.0
CA C:CA240 4.2 15.2 1.0
OD2 C:ASP12 4.2 14.6 1.0
O C:HOH2015 4.3 21.1 1.0
ND1 C:HIS26 4.3 13.0 1.0
CG C:HIS26 4.3 13.9 1.0
O C:HOH2016 4.4 26.0 1.0
CB C:ASP21 4.4 17.7 1.0
CG C:GLU10 4.6 10.1 1.0
O C:ILE34 4.6 16.9 1.0
CA C:ASP21 4.7 18.1 1.0

Manganese binding site 6 out of 8 in 2jec

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Manganese binding site 6 out of 8 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 Manganese with other atoms in the Mn binding site number 6 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:Mn243

b:43.7
occ:0.50
 NE2 C:HIS53 2.2 14.6 0.5
O C:HOH2162 2.4 47.6 1.0
O C:HOH2125 3.0 19.1 1.0
OD2 C:ASP194 3.0 16.2 0.5
CE1 C:HIS53 3.1 12.5 0.5
CD2 C:HIS53 3.2 14.1 0.5
O B:HOH2087 3.3 43.7 1.0
NZ B:LYS118 3.4 35.6 1.0
OG B:SER192 3.7 17.1 1.0
CG C:ASP194 3.8 16.4 0.5
OD1 C:ASP194 3.9 22.5 0.5
CB C:ASP194 4.1 15.8 0.5
CG C:ASP194 4.1 18.3 0.5
CB C:ASP194 4.2 15.0 0.5
ND1 C:HIS53 4.2 12.9 0.5
CB B:SER192 4.3 13.6 1.0
CG C:HIS53 4.3 13.1 0.5
OD1 C:ASP194 4.7 17.6 0.5
CE B:LYS118 4.7 30.7 1.0
CD B:LYS116 4.8 26.8 1.0
OD2 C:ASP194 4.8 21.8 0.5

Manganese binding site 7 out of 8 in 2jec

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Manganese binding site 7 out of 8 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 Manganese with other atoms in the Mn binding site number 7 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:Mn241

b:13.0
occ:1.00
 O D:HOH2175 1.9 10.1 1.0
OD1 D:ASP12 1.9 11.5 1.0
O D:HOH2176 2.1 9.6 1.0
NE2 D:HIS26 2.2 14.3 1.0
OE2 D:GLU10 2.3 15.8 1.0
OD1 D:ASP21 2.3 12.3 1.0
CG D:ASP12 3.0 14.5 1.0
CE1 D:HIS26 3.2 12.8 1.0
CG D:ASP21 3.2 14.5 1.0
CD2 D:HIS26 3.2 14.2 1.0
CD D:GLU10 3.2 14.7 1.0
OE1 D:GLU10 3.5 12.4 1.0
OD2 D:ASP21 3.5 10.3 1.0
CB D:ASP12 3.5 13.2 1.0
O D:HOH2164 3.9 11.0 1.0
OD2 D:ASP12 4.1 14.1 1.0
O D:HOH2021 4.1 25.4 1.0
CA D:CA240 4.2 13.7 1.0
ND1 D:HIS26 4.3 13.3 1.0
OG D:SER36 4.3 13.1 1.0
CG D:HIS26 4.3 12.9 1.0
O D:HOH2020 4.4 33.4 1.0
CB D:ASP21 4.4 14.8 1.0
O D:ILE34 4.6 15.6 1.0
CG D:GLU10 4.6 11.7 1.0
CA D:ASP21 4.7 15.4 1.0

Manganese binding site 8 out of 8 in 2jec

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Manganese binding site 8 out of 8 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 Manganese with other atoms in the Mn binding site number 8 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:Mn243

b:44.5
occ:0.50
 NE2 D:HIS53 2.1 16.1 0.5
OD1 D:ASP194 2.1 21.9 0.5
O D:HOH2179 2.1 37.6 1.0
CD2 D:HIS53 2.8 16.9 0.5
O A:HOH2171 2.9 43.1 1.0
CG D:ASP194 3.2 18.1 0.5
CE1 D:HIS53 3.2 16.8 0.5
OD2 D:ASP194 3.6 20.1 0.5
OD2 D:ASP194 3.7 16.4 0.5
CG D:HIS53 4.0 15.3 0.5
ND1 D:HIS53 4.2 17.5 0.5
CB D:ASP194 4.2 16.1 0.5
CG D:ASP194 4.2 16.9 0.5
O D:HOH2142 4.3 18.4 1.0
OG A:SER192 4.3 14.1 1.0
O D:HOH2060 4.4 37.8 1.0
CB D:ASP194 4.5 17.2 0.5
CE A:LYS116 4.8 33.1 1.0
O D:HOH2141 4.9 36.4 1.0
CG2 D:THR196 5.0 16.2 0.5

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: Sat Oct 5 14:33:52 2024

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