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Calcium in PDB 2jdh: Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative

Protein crystallography data

The structure of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative, PDB code: 2jdh was solved by K.Marotte, C.Sabin, C.Preville, M.Pymbock, I.Deguise, M.Wimmerova, E.P.Mitchell, A.Imberty, R.Roy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.23 / 1.1
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.552, 72.829, 54.359, 90.00, 94.29, 90.00
R / Rfree (%) 10.7 / 13.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative (pdb code 2jdh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative, PDB code: 2jdh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2jdh

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Calcium binding site 1 out of 8 in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1116

b:4.4
occ:1.00
OD1 A:ASN103 2.3 4.5 1.0
O A:ASN21 2.3 4.4 1.0
OD1 A:ASP104 2.4 4.6 1.0
OD2 A:ASP101 2.4 5.2 1.0
O B:GLY114 2.4 5.1 1.0
O4 A:FUC1115 2.5 5.1 1.0
O3 A:FUC1115 2.5 5.1 1.0
CG A:ASP101 3.1 5.2 1.0
OD1 A:ASP101 3.1 5.9 1.0
CG A:ASN103 3.4 4.5 1.0
C B:GLY114 3.4 5.4 1.0
C3 A:FUC1115 3.4 5.3 1.0
C4 A:FUC1115 3.5 5.6 1.0
C A:ASN21 3.5 4.0 1.0
CG A:ASP104 3.6 4.2 1.0
OXT B:GLY114 3.7 7.1 1.0
ND2 A:ASN103 3.8 5.1 1.0
CA A:CA1117 3.8 5.0 1.0
C2 A:FUC1115 3.8 5.7 1.0
CB A:ASN21 4.1 4.2 1.0
CA A:ASP104 4.2 3.9 1.0
N A:ASP104 4.3 3.8 1.0
CA A:SER22 4.4 4.7 1.0
N A:SER22 4.4 4.1 1.0
OD2 A:ASP104 4.5 4.5 1.0
O A:HOH2184 4.5 15.4 1.0
O2 A:FUC1115 4.5 5.0 1.0
CB A:ASP104 4.5 4.6 1.0
C A:ASN103 4.5 3.8 1.0
CA A:ASN21 4.5 3.9 1.0
CB A:ASP101 4.5 6.2 1.0
OD2 A:ASP99 4.5 7.7 1.0
CB A:SER22 4.7 5.0 1.0
CB A:ASN103 4.7 4.5 1.0
CA B:GLY114 4.8 5.4 1.0
C5 A:FUC1115 4.8 5.6 1.0
O A:ASN103 4.8 4.3 1.0
N A:ASN103 4.8 4.1 1.0
CA A:ASN103 4.9 4.1 1.0

Calcium binding site 2 out of 8 in 2jdh

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Calcium binding site 2 out of 8 in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1117

b:5.0
occ:1.00
OD1 A:ASP99 2.4 7.3 1.0
OD1 A:ASP101 2.4 5.9 1.0
OE2 A:GLU95 2.4 6.2 1.0
OD2 A:ASP104 2.4 4.5 1.0
OE1 A:GLU95 2.5 5.3 1.0
O3 A:FUC1115 2.5 5.1 1.0
O2 A:FUC1115 2.6 5.0 1.0
OD1 A:ASP104 2.7 4.6 1.0
CD A:GLU95 2.8 5.1 1.0
CG A:ASP104 2.9 4.2 1.0
C2 A:FUC1115 3.3 5.7 1.0
CG A:ASP99 3.4 6.9 1.0
C3 A:FUC1115 3.4 5.3 1.0
CG A:ASP101 3.4 5.2 1.0
OD2 A:ASP99 3.7 7.7 1.0
CA A:CA1116 3.8 4.4 1.0
OD2 A:ASP101 4.0 5.2 1.0
N A:ASP101 4.1 6.8 1.0
O A:HOH2172 4.2 11.6 1.0
OD1 A:ASP96 4.2 5.6 1.0
CG A:GLU95 4.3 6.0 1.0
N A:TYR102 4.4 5.5 1.0
CB A:ASP104 4.4 4.6 1.0
N A:ASN100 4.4 7.7 1.0
N A:ASP96 4.5 4.8 1.0
CB A:ASP101 4.6 6.2 1.0
N A:GLY97 4.6 6.4 1.0
CA A:ASP101 4.7 6.0 1.0
CA A:GLU95 4.7 4.5 1.0
CB A:ASP99 4.7 9.2 1.0
C4 A:FUC1115 4.7 5.6 1.0
N A:ASP99 4.7 8.3 1.0
OD1 A:ASN103 4.8 4.5 1.0
C1 A:FUC1115 4.8 6.0 1.0
O4 A:FUC1115 4.8 5.1 1.0
CB A:GLU95 4.9 5.3 1.0
C A:ASP99 4.9 8.6 1.0
C A:ASP101 4.9 5.6 1.0
CG A:ASP96 5.0 4.8 1.0
CA A:ASP99 5.0 7.8 1.0
CA A:GLY97 5.0 7.2 1.0

Calcium binding site 3 out of 8 in 2jdh

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Calcium binding site 3 out of 8 in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1118

b:4.7
occ:1.00
OD1 B:ASP99 2.3 5.8 1.0
OD1 B:ASP101 2.4 4.9 1.0
OE2 B:GLU95 2.4 5.0 1.0
OD2 B:ASP104 2.4 5.0 1.0
OE1 B:GLU95 2.4 4.5 1.0
O3 B:FUC1115 2.5 4.8 1.0
O2 B:FUC1115 2.6 5.3 1.0
OD1 B:ASP104 2.7 4.9 1.0
CD B:GLU95 2.8 4.6 1.0
CG B:ASP104 2.9 4.3 1.0
C2 B:FUC1115 3.3 5.5 1.0
CG B:ASP99 3.4 5.9 1.0
CG B:ASP101 3.4 4.6 1.0
C3 B:FUC1115 3.4 6.0 1.0
OD2 B:ASP99 3.7 6.6 1.0
CA B:CA1119 3.7 4.7 1.0
OD2 B:ASP101 4.0 5.7 1.0
O B:HOH2169 4.1 8.1 1.0
N B:ASP101 4.1 5.2 1.0
OD1 B:ASP96 4.2 7.0 1.0
CG B:GLU95 4.3 4.5 1.0
N B:TYR102 4.4 4.4 1.0
CB B:ASP104 4.4 4.4 1.0
N B:ASN100 4.4 5.4 1.0
N B:ASP96 4.5 4.8 1.0
CB B:ASP101 4.5 5.7 1.0
N B:GLY97 4.7 5.7 1.0
CA B:GLU95 4.7 3.9 1.0
CA B:ASP101 4.7 5.2 1.0
CB B:ASP99 4.7 6.7 1.0
OD1 B:ASN103 4.7 4.4 1.0
C4 B:FUC1115 4.7 5.9 1.0
N B:ASP99 4.8 6.2 1.0
C1 B:FUC1115 4.8 6.7 1.0
O4 B:FUC1115 4.8 5.6 1.0
CB B:GLU95 4.9 4.2 1.0
C B:ASP101 4.9 4.8 1.0
C B:ASP99 5.0 6.1 1.0
CG B:ASP96 5.0 5.8 1.0
CA B:ASP99 5.0 6.5 1.0

Calcium binding site 4 out of 8 in 2jdh

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Calcium binding site 4 out of 8 in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1119

b:4.7
occ:1.00
OD1 B:ASN103 2.3 4.4 1.0
OD1 B:ASP104 2.4 4.9 1.0
O B:ASN21 2.4 4.7 1.0
OD2 B:ASP101 2.4 5.7 1.0
O A:GLY114 2.4 5.2 1.0
O4 B:FUC1115 2.5 5.6 1.0
O3 B:FUC1115 2.5 4.8 1.0
OD1 B:ASP101 3.0 4.9 1.0
CG B:ASP101 3.1 4.6 1.0
CG B:ASN103 3.4 4.7 1.0
C3 B:FUC1115 3.4 6.0 1.0
C A:GLY114 3.4 5.9 1.0
C4 B:FUC1115 3.4 5.9 1.0
C B:ASN21 3.6 5.0 1.0
CG B:ASP104 3.6 4.3 1.0
OXT A:GLY114 3.7 7.4 1.0
CA B:CA1118 3.7 4.7 1.0
ND2 B:ASN103 3.8 5.3 1.0
C2 B:FUC1115 3.8 5.5 1.0
CB B:ASN21 4.1 4.5 1.0
CA B:ASP104 4.2 4.1 1.0
N B:ASP104 4.2 3.6 1.0
CA B:SER22 4.4 5.7 1.0
N B:SER22 4.4 4.7 1.0
OD2 B:ASP104 4.4 5.0 1.0
C B:ASN103 4.4 3.7 1.0
CB B:ASP104 4.5 4.4 1.0
O B:HOH2177 4.5 14.2 1.0
O2 B:FUC1115 4.5 5.3 1.0
CB B:ASP101 4.5 5.7 1.0
CA B:ASN21 4.5 4.1 1.0
OD2 B:ASP99 4.6 6.6 1.0
CB B:SER22 4.6 5.5 1.0
CB B:ASN103 4.7 4.0 1.0
C5 B:FUC1115 4.8 6.9 1.0
CA A:GLY114 4.8 5.6 1.0
O B:ASN103 4.8 4.2 1.0
N B:ASN103 4.8 3.8 1.0
CA B:ASN103 4.9 3.6 1.0
O5 B:FUC1115 5.0 6.6 1.0

Calcium binding site 5 out of 8 in 2jdh

Go back to Calcium Binding Sites List in 2jdh
Calcium binding site 5 out of 8 in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1116

b:5.3
occ:1.00
OD1 C:ASN103 2.3 4.9 1.0
O C:ASN21 2.4 5.0 1.0
OD1 C:ASP104 2.4 5.1 1.0
O D:GLY114 2.4 6.0 1.0
OD2 C:ASP101 2.4 6.7 1.0
O4 C:FUC1118 2.5 6.4 1.0
O3 C:FUC1118 2.5 6.3 1.0
OD1 C:ASP101 3.0 6.3 1.0
CG C:ASP101 3.1 6.1 1.0
CG C:ASN103 3.4 5.2 1.0
C3 C:FUC1118 3.4 6.6 1.0
C D:GLY114 3.4 6.3 1.0
C4 C:FUC1118 3.4 6.7 1.0
C C:ASN21 3.6 4.5 1.0
CG C:ASP104 3.6 4.7 1.0
OXT D:GLY114 3.7 8.2 1.0
ND2 C:ASN103 3.7 5.4 1.0
CA C:CA1117 3.8 5.9 1.0
C2 C:FUC1118 3.8 7.1 1.0
CB C:ASN21 4.1 5.1 1.0
CA C:ASP104 4.2 4.1 1.0
N C:ASP104 4.3 4.5 1.0
CA C:SER22 4.4 5.2 1.0
N C:SER22 4.4 4.9 1.0
C C:ASN103 4.5 4.0 1.0
OD2 C:ASP104 4.5 5.5 1.0
O2 C:FUC1118 4.5 6.4 1.0
CB C:ASP104 4.5 4.8 1.0
CB C:ASP101 4.5 7.5 1.0
O C:HOH2165 4.5 15.8 1.0
CA C:ASN21 4.5 4.6 1.0
OD2 C:ASP99 4.6 8.6 1.0
CB C:SER22 4.6 6.2 1.0
CB C:ASN103 4.7 4.9 1.0
CA D:GLY114 4.8 6.8 1.0
C5 C:FUC1118 4.8 7.6 1.0
O C:ASN103 4.8 4.4 1.0
N C:ASN103 4.8 4.9 1.0
CA C:ASN103 4.9 4.8 1.0
O5 C:FUC1118 5.0 6.9 1.0

Calcium binding site 6 out of 8 in 2jdh

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Calcium binding site 6 out of 8 in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1117

b:5.9
occ:1.00
OD1 C:ASP99 2.3 8.5 1.0
OD1 C:ASP101 2.3 6.3 1.0
OE2 C:GLU95 2.4 6.5 1.0
OD2 C:ASP104 2.4 5.5 1.0
OE1 C:GLU95 2.4 6.0 1.0
O3 C:FUC1118 2.5 6.3 1.0
O2 C:FUC1118 2.6 6.4 1.0
OD1 C:ASP104 2.6 5.1 1.0
CD C:GLU95 2.8 6.3 1.0
CG C:ASP104 2.9 4.7 1.0
C2 C:FUC1118 3.3 7.1 1.0
CG C:ASP101 3.4 6.1 1.0
CG C:ASP99 3.4 8.3 1.0
C3 C:FUC1118 3.4 6.6 1.0
CA C:CA1116 3.8 5.3 1.0
OD2 C:ASP99 3.8 8.6 1.0
OD2 C:ASP101 4.0 6.7 1.0
N C:ASP101 4.1 8.0 1.0
O C:HOH2158 4.1 9.7 1.0
OD1 C:ASP96 4.2 7.3 1.0
CG C:GLU95 4.2 6.2 1.0
N C:TYR102 4.4 5.8 1.0
CB C:ASP104 4.4 4.8 1.0
N C:ASN100 4.5 9.4 1.0
N C:ASP96 4.5 5.3 1.0
CB C:ASP101 4.5 7.5 1.0
N C:GLY97 4.6 7.0 1.0
CA C:GLU95 4.7 5.1 1.0
CA C:ASP101 4.7 7.7 1.0
C4 C:FUC1118 4.7 6.7 1.0
OD1 C:ASN103 4.7 4.9 1.0
CB C:ASP99 4.7 9.3 1.0
N C:ASP99 4.8 9.0 1.0
C1 C:FUC1118 4.8 7.2 1.0
O4 C:FUC1118 4.8 6.4 1.0
CB C:GLU95 4.9 6.4 1.0
C C:ASP101 4.9 6.5 1.0
CG C:ASP96 5.0 6.5 1.0
C C:ASP99 5.0 8.6 1.0

Calcium binding site 7 out of 8 in 2jdh

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Calcium binding site 7 out of 8 in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1118

b:4.8
occ:1.00
OD1 D:ASN103 2.3 4.6 1.0
OD1 D:ASP104 2.4 5.1 1.0
O D:ASN21 2.4 5.3 1.0
O C:GLY114 2.4 5.2 1.0
OD2 D:ASP101 2.4 5.4 1.0
O4 D:FUC1115 2.5 5.8 1.0
O3 D:FUC1115 2.5 5.7 1.0
OD1 D:ASP101 3.1 5.5 1.0
CG D:ASP101 3.1 5.2 1.0
CG D:ASN103 3.4 4.2 1.0
C C:GLY114 3.4 5.9 1.0
C3 D:FUC1115 3.4 6.6 1.0
C4 D:FUC1115 3.4 6.1 1.0
C D:ASN21 3.5 4.8 1.0
CG D:ASP104 3.6 5.2 1.0
OXT C:GLY114 3.7 6.7 1.0
ND2 D:ASN103 3.7 5.3 1.0
CA D:CA1119 3.7 5.6 1.0
C2 D:FUC1115 3.8 6.4 1.0
CB D:ASN21 4.1 5.0 1.0
CA D:ASP104 4.2 4.8 1.0
N D:ASP104 4.3 4.6 1.0
CA D:SER22 4.4 6.0 1.0
OD2 D:ASP104 4.4 5.5 1.0
N D:SER22 4.4 5.5 1.0
O D:HOH2177 4.4 9.6 1.0
C D:ASN103 4.5 4.3 1.0
O2 D:FUC1115 4.5 6.8 1.0
CB D:ASP104 4.5 4.8 1.0
CA D:ASN21 4.5 5.0 1.0
CB D:ASP101 4.5 6.4 1.0
OD2 D:ASP99 4.6 7.3 1.0
CB D:SER22 4.7 5.8 1.0
CB D:ASN103 4.7 4.6 1.0
CA C:GLY114 4.8 6.1 1.0
C5 D:FUC1115 4.8 7.4 1.0
O D:ASN103 4.8 4.5 1.0
N D:ASN103 4.9 4.6 1.0
CA D:ASN103 4.9 3.9 1.0
O5 D:FUC1115 5.0 7.3 1.0

Calcium binding site 8 out of 8 in 2jdh

Go back to Calcium Binding Sites List in 2jdh
Calcium binding site 8 out of 8 in the Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Lectin Pa-Iil of P.Aeruginosa Complexed with Disaccharide Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1119

b:5.6
occ:1.00
OD1 D:ASP101 2.3 5.5 1.0
OD1 D:ASP99 2.3 7.0 1.0
OE2 D:GLU95 2.4 6.5 1.0
OE1 D:GLU95 2.5 6.4 1.0
OD2 D:ASP104 2.5 5.5 1.0
O3 D:FUC1115 2.5 5.7 1.0
O2 D:FUC1115 2.6 6.8 1.0
OD1 D:ASP104 2.7 5.1 1.0
CD D:GLU95 2.8 6.2 1.0
CG D:ASP104 3.0 5.2 1.0
C2 D:FUC1115 3.3 6.4 1.0
CG D:ASP99 3.4 6.7 1.0
CG D:ASP101 3.4 5.2 1.0
C3 D:FUC1115 3.4 6.6 1.0
OD2 D:ASP99 3.7 7.3 1.0
CA D:CA1118 3.7 4.8 1.0
OD2 D:ASP101 3.9 5.4 1.0
O D:HOH2170 4.0 9.5 1.0
N D:ASP101 4.1 7.5 1.0
OD1 D:ASP96 4.2 7.8 1.0
CG D:GLU95 4.3 6.5 1.0
N D:TYR102 4.4 5.8 1.0
N D:ASN100 4.4 8.5 1.0
CB D:ASP104 4.4 4.8 1.0
CB D:ASP101 4.5 6.4 1.0
N D:ASP96 4.5 5.8 1.0
N D:GLY97 4.6 7.9 1.0
CA D:ASP101 4.7 6.6 1.0
CB D:ASP99 4.7 7.5 1.0
CA D:GLU95 4.7 5.2 1.0
OD1 D:ASN103 4.7 4.6 1.0
C4 D:FUC1115 4.7 6.1 1.0
N D:ASP99 4.7 8.2 1.0
C1 D:FUC1115 4.8 7.0 1.0
O4 D:FUC1115 4.8 5.8 1.0
CB D:GLU95 4.9 6.0 1.0
C D:ASP101 5.0 6.7 1.0
C D:ASP99 5.0 8.0 1.0
CA D:ASP99 5.0 8.4 1.0
CG D:ASP96 5.0 6.4 1.0

Reference:

K.Marotte, C.Sabin, C.Preville, M.Pymbock, M.Wimmerova, E.P.Mitchell, A.Imberty, R.Roy. X-Ray Structures and Thermodynamics of the Interaction of Pa-Iil From Pseudomonas Aeruginosa with Disaccharide Derivatives. Chemmedchem V. 2 1328 2007.
ISSN: ISSN 1860-7179
PubMed: 17623286
DOI: 10.1002/CMDC.200700100
Page generated: Fri Jul 12 13:34:11 2024

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