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Cadmium in PDB 4akd: High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb)

Protein crystallography data

The structure of High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb), PDB code: 4akd was solved by M.Gabrielsen, P.S.Abdul-Rahman, S.Othman, O.H.Hashim, R.J.Cogdell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.69 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.887, 86.222, 95.373, 90.00, 90.00, 90.00
R / Rfree (%) 19.34 / 23.57

Other elements in 4akd:

The structure of High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb) also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb) (pdb code 4akd). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb), PDB code: 4akd:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 4akd

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Cadmium binding site 1 out of 8 in the High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1151

b:0.3
occ:1.00
 OE2 A:GLU69 2.1 84.3 1.0
O A:HOH2043 2.6 41.5 1.0
CD A:GLU69 3.1 83.5 1.0
OE1 A:GLU69 3.4 75.2 1.0
O A:HOH2044 4.1 43.1 1.0
NH1 A:ARG28 4.2 31.3 1.0
CB A:ARG28 4.3 28.9 1.0
CG A:GLU69 4.5 54.9 1.0
O A:LEU70 4.6 32.4 1.0
CD A:ARG28 4.7 28.2 1.0
CG A:ARG28 4.7 26.8 1.0
O A:ARG28 4.7 30.7 1.0
C A:ARG28 5.0 29.5 1.0

Cadmium binding site 2 out of 8 in 4akd

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Cadmium binding site 2 out of 8 in the High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1151

b:63.5
occ:1.00
 OE2 B:GLU117 1.8 90.4 0.0
CD B:GLU117 2.3 94.1 0.0
OE1 B:GLU117 2.4 88.1 0.0
CL B:CL1155 2.8 61.2 1.0
CL B:CL1156 3.0 65.8 1.0
OD1 B:ASP115 3.2 74.6 1.0
OE2 B:GLU36 3.2 92.5 0.0
CL B:CL1154 3.5 95.9 1.0
CD B:CD1153 3.6 0.9 1.0
CG B:GLU117 3.7 71.3 0.0
CG B:ASP115 3.8 74.2 1.0
CD B:CD1152 3.8 69.0 1.0
OD2 B:ASP115 4.1 84.6 1.0
CD B:GLU36 4.3 98.1 0.0
NH2 B:ARG98 4.4 50.3 1.0
CG B:GLU36 4.6 75.4 0.0
CB B:GLU117 4.8 58.4 1.0
CB B:ASP115 4.9 58.5 1.0

Cadmium binding site 3 out of 8 in 4akd

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Cadmium binding site 3 out of 8 in the High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1152

b:69.0
occ:1.00
 CL B:CL1157 2.5 60.0 1.0
OD1 B:ASP115 2.6 74.6 1.0
CL B:CL1155 2.8 61.2 1.0
OE2 B:GLU117 3.2 90.4 0.0
CL B:CL1154 3.3 95.9 1.0
CG B:ASP115 3.4 74.2 1.0
OD2 B:ASP115 3.5 84.6 1.0
CD B:CD1151 3.8 63.5 1.0
CD B:GLU117 3.9 94.1 0.0
CG B:GLU117 4.0 71.3 0.0
CB B:ASP115 4.7 58.5 1.0
OE1 B:GLU117 4.9 88.1 0.0
N B:GLU116 4.9 55.0 1.0

Cadmium binding site 4 out of 8 in 4akd

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Cadmium binding site 4 out of 8 in the High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1153

b:0.9
occ:1.00
 CL B:CL1156 2.6 65.8 1.0
OE1 B:GLU117 2.9 88.1 0.0
CD B:CD1151 3.6 63.5 1.0
CD B:GLU117 3.7 94.1 0.0
OE2 B:GLU117 4.0 90.4 0.0
OG B:SER88 4.0 87.3 1.0
NH1 B:ARG98 4.5 49.5 1.0
NH2 B:ARG98 4.8 50.3 1.0
CG B:GLU117 4.9 71.3 0.0

Cadmium binding site 5 out of 8 in 4akd

Go back to Cadmium Binding Sites List in 4akd
Cadmium binding site 5 out of 8 in the High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1151

b:91.4
occ:1.00
 CL C:CL1155 1.6 34.4 1.0
OE1 C:GLU117 2.0 0.3 0.0
CL C:CL1154 2.8 74.5 1.0
CD C:GLU117 3.0 0.7 0.0
CD C:CD1152 3.1 94.4 1.0
CG C:GLU117 3.8 0.4 0.0
OE2 C:GLU117 3.9 0.5 0.0
OD2 C:ASP115 3.9 0.9 1.0
O C:HOH2040 4.1 62.0 1.0
CG C:ASP115 4.2 0.6 1.0
CB C:GLU117 4.6 1.0 0.0
CD C:CD2000 4.7 82.7 1.0
OD1 C:ASP115 4.7 0.4 1.0
CB C:ASP115 4.9 0.7 1.0

Cadmium binding site 6 out of 8 in 4akd

Go back to Cadmium Binding Sites List in 4akd
Cadmium binding site 6 out of 8 in the High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1152

b:94.4
occ:1.00
 OE2 C:GLU117 1.9 0.5 0.0
OE1 C:GLU117 2.3 0.3 0.0
CD C:GLU117 2.4 0.7 0.0
OD1 C:ASP115 2.7 0.4 1.0
CL C:CL1154 2.9 74.5 1.0
CL C:CL1153 2.9 0.2 1.0
CD C:CD1151 3.1 91.4 1.0
CG C:ASP115 3.2 0.6 1.0
OD2 C:ASP115 3.3 0.9 1.0
CG C:GLU117 3.8 0.4 0.0
CB C:ASP115 4.3 0.7 1.0
CL C:CL1155 4.6 34.4 1.0
O C:GLU116 4.8 1.0 1.0
CB C:GLU117 4.9 1.0 0.0
O C:HOH2040 4.9 62.0 1.0

Cadmium binding site 7 out of 8 in 4akd

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Cadmium binding site 7 out of 8 in the High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd2000

b:82.7
occ:1.00
 CL C:CL1155 3.2 34.4 1.0
CD C:CD1151 4.7 91.4 1.0
O C:HOH2036 4.8 43.4 1.0

Cadmium binding site 8 out of 8 in 4akd

Go back to Cadmium Binding Sites List in 4akd
Cadmium binding site 8 out of 8 in the High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of High Resolution Structure of Mannose Binding Lectin From Champedak (Cmb) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd1151

b:80.1
occ:1.00
 O D:HOH2047 2.6 36.1 1.0
OE2 D:GLU74 2.6 84.2 1.0
CD D:GLU74 2.6 81.8 1.0
O D:HOH2071 2.7 45.3 1.0
CG D:GLU74 2.9 46.1 1.0
O D:HOH2072 2.9 40.4 1.0
OE1 D:GLU74 3.3 90.3 1.0
O D:HOH2045 3.7 49.5 1.0
CB D:GLU74 4.4 33.8 1.0

Reference:

M.Gabrielsen, P.S.Abdul-Rahman, S.Othman, O.H.Hashim, R.J.Cogdell. Structures and Binding Specificity of Galactose- and Mannose-Binding Lectins From Champedak: Differences From Jackfruit Lectins Acta Crystallogr.,Sect.F V. 70 709 2014.
ISSN: ISSN 1744-3091
PubMed: 24915077
DOI: 10.1107/S2053230X14008966
Page generated: Sat Dec 12 08:23:55 2020

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