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Calcium in PDB 2jdu: Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside

Protein crystallography data

The structure of Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside, PDB code: 2jdu was solved by J.Adam, M.Pokorna, C.Sabin, E.P.Mitchell, A.Imberty, M.Wimmerova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.56 / 1.5
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.627, 74.886, 53.466, 90.00, 114.71, 90.00
R / Rfree (%) 14.9 / 19.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside (pdb code 2jdu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside, PDB code: 2jdu:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2jdu

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Calcium binding site 1 out of 4 in the Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1115

b:9.6
occ:0.70
 OD1 C:ASP101 2.3 16.9 1.0
O2 C:MFU1117 2.4 13.4 1.0
OD1 C:ASP99 2.4 17.9 1.0
O3 C:MFU1117 2.5 14.8 1.0
OE2 C:GLU95 2.5 12.6 1.0
OD2 C:ASP104 2.6 11.4 1.0
OE1 C:GLU95 2.6 12.2 1.0
OD1 C:ASP104 2.6 10.8 1.0
CD C:GLU95 2.9 11.9 1.0
CG C:ASP104 2.9 11.1 1.0
C2 C:MFU1117 3.2 14.1 1.0
C3 C:MFU1117 3.3 16.0 1.0
CG C:ASP101 3.4 16.8 1.0
CG C:ASP99 3.4 19.7 1.0
CA C:CA1116 3.7 8.2 0.7
OD2 C:ASP99 3.8 20.1 1.0
OD2 C:ASP101 3.9 17.1 1.0
N C:ASP101 4.1 15.5 1.0
OD1 C:ASP96 4.2 14.5 1.0
O C:HOH2120 4.3 21.2 1.0
CG C:GLU95 4.4 9.5 1.0
CB C:ASP104 4.4 5.8 1.0
N C:ASN100 4.5 19.9 1.0
OD1 C:ASN103 4.5 13.4 1.0
C1 C:MFU1117 4.6 14.1 1.0
N C:TYR102 4.6 11.5 1.0
CB C:ASP101 4.6 15.3 1.0
C4 C:MFU1117 4.7 17.6 1.0
N C:ASP96 4.7 10.1 1.0
N C:ASP99 4.7 20.4 1.0
CA C:ASP101 4.8 14.6 1.0
N C:GLY97 4.8 13.5 1.0
CB C:ASP99 4.8 19.7 1.0
CA C:GLU95 4.8 9.0 1.0
O4 C:MFU1117 4.9 13.4 1.0
CA C:GLY97 5.0 16.2 1.0
C C:ASP99 5.0 20.3 1.0

Calcium binding site 2 out of 4 in 2jdu

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Calcium binding site 2 out of 4 in the Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1116

b:8.2
occ:0.70
 OD1 C:ASN103 2.3 13.4 1.0
O3 C:MFU1117 2.3 14.8 1.0
O C:ASN21 2.4 7.0 1.0
OD2 C:ASP101 2.5 17.1 1.0
O4 C:MFU1117 2.5 13.4 1.0
O D:GLY114 2.5 12.1 1.0
OD1 C:ASP104 2.6 10.8 1.0
OD1 C:ASP101 3.1 16.9 1.0
CG C:ASP101 3.1 16.8 1.0
C3 C:MFU1117 3.3 16.0 1.0
CG C:ASN103 3.4 9.5 1.0
C4 C:MFU1117 3.4 17.6 1.0
C D:GLY114 3.5 12.6 1.0
C C:ASN21 3.6 6.0 1.0
ND2 C:ASN103 3.7 11.2 1.0
CA C:CA1115 3.7 9.6 0.7
OXT D:GLY114 3.7 13.9 1.0
C2 C:MFU1117 3.7 14.1 1.0
CG C:ASP104 3.8 11.1 1.0
CB C:ASN21 4.2 4.7 1.0
CA C:ASP104 4.3 5.4 1.0
N C:ASP104 4.4 5.7 1.0
O C:HOH2125 4.4 20.5 1.0
O2 C:MFU1117 4.4 13.4 1.0
CA C:SER22 4.4 8.0 1.0
C C:ASN103 4.4 5.8 1.0
N C:SER22 4.5 6.4 1.0
OD2 C:ASP99 4.6 20.1 1.0
CB C:ASP101 4.6 15.3 1.0
CA C:ASN21 4.6 4.3 1.0
CB C:ASP104 4.6 5.8 1.0
OD2 C:ASP104 4.7 11.4 1.0
CB C:ASN103 4.7 7.5 1.0
O C:ASN103 4.7 6.7 1.0
C5 C:MFU1117 4.7 17.6 1.0
CB C:SER22 4.7 7.7 1.0
CA D:GLY114 4.8 11.2 1.0
O5 C:MFU1117 4.9 14.6 1.0
C1 C:MFU1117 4.9 14.1 1.0
CA C:ASN103 5.0 7.7 1.0
N C:ASN103 5.0 7.2 1.0
OD1 C:ASP99 5.0 17.9 1.0

Calcium binding site 3 out of 4 in 2jdu

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Calcium binding site 3 out of 4 in the Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1115

b:9.4
occ:0.80
 OD1 D:ASN103 2.3 9.7 1.0
O3 D:MFU1117 2.4 13.2 1.0
O D:ASN21 2.4 10.8 1.0
O C:GLY114 2.4 14.1 1.0
O4 D:MFU1117 2.5 14.3 1.0
OD2 D:ASP101 2.5 14.0 1.0
OD1 D:ASP104 2.5 11.5 1.0
OD1 D:ASP101 3.1 14.1 1.0
CG D:ASP101 3.1 15.2 1.0
C3 D:MFU1117 3.3 14.6 1.0
CG D:ASN103 3.4 8.2 1.0
C C:GLY114 3.4 14.2 1.0
C4 D:MFU1117 3.4 14.7 1.0
C D:ASN21 3.6 8.9 1.0
OXT C:GLY114 3.7 15.5 1.0
ND2 D:ASN103 3.7 9.0 1.0
CG D:ASP104 3.7 8.8 1.0
CA D:CA1116 3.7 8.5 0.7
C2 D:MFU1117 3.8 13.2 1.0
CB D:ASN21 4.1 6.7 1.0
CA D:ASP104 4.2 6.4 1.0
N D:ASP104 4.3 6.0 1.0
O2 D:MFU1117 4.4 12.7 1.0
CA D:SER22 4.5 10.4 1.0
C D:ASN103 4.5 5.9 1.0
OD2 D:ASP99 4.5 16.5 1.0
N D:SER22 4.5 9.9 1.0
OD2 D:ASP104 4.5 9.4 1.0
CB D:ASP104 4.5 6.8 1.0
O D:HOH2133 4.6 26.1 1.0
CA D:ASN21 4.6 7.9 1.0
CB D:ASP101 4.6 12.9 1.0
CB D:ASN103 4.7 6.9 1.0
O D:ASN103 4.8 6.5 1.0
CA C:GLY114 4.8 11.7 1.0
CB D:SER22 4.8 9.8 1.0
C5 D:MFU1117 4.8 14.3 1.0
N D:ASN103 4.9 6.5 1.0
CA D:ASN103 4.9 6.4 1.0
OD1 D:ASP99 5.0 15.7 1.0
O5 D:MFU1117 5.0 14.0 1.0

Calcium binding site 4 out of 4 in 2jdu

Go back to Calcium Binding Sites List in 2jdu
Calcium binding site 4 out of 4 in the Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mutant (G24N) of Pseudomonas Aeruginosa Lectin II (Pa-Iil) Complexed with Methyl-A-L-Fucopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1116

b:8.5
occ:0.70
 O2 D:MFU1117 2.4 12.7 1.0
OD1 D:ASP101 2.4 14.1 1.0
OD1 D:ASP99 2.4 15.7 1.0
OE2 D:GLU95 2.4 10.3 1.0
OD2 D:ASP104 2.5 9.4 1.0
O3 D:MFU1117 2.6 13.2 1.0
OE1 D:GLU95 2.6 11.1 1.0
OD1 D:ASP104 2.7 11.5 1.0
CD D:GLU95 2.8 9.2 1.0
CG D:ASP104 2.9 8.8 1.0
C2 D:MFU1117 3.2 13.2 1.0
C3 D:MFU1117 3.3 14.6 1.0
CG D:ASP99 3.4 17.4 1.0
CG D:ASP101 3.5 15.2 1.0
CA D:CA1115 3.7 9.4 0.8
OD2 D:ASP99 3.8 16.5 1.0
OD2 D:ASP101 4.0 14.0 1.0
O D:HOH2139 4.2 21.5 1.0
N D:ASP101 4.2 15.2 1.0
OD1 D:ASP96 4.2 10.8 1.0
CG D:GLU95 4.3 9.1 1.0
CB D:ASP104 4.4 6.8 1.0
N D:ASP96 4.5 8.5 1.0
N D:ASN100 4.5 18.9 1.0
N D:TYR102 4.6 9.8 1.0
OD1 D:ASN103 4.6 9.7 1.0
N D:GLY97 4.6 11.5 1.0
CB D:ASP101 4.6 12.9 1.0
C1 D:MFU1117 4.7 14.7 1.0
C4 D:MFU1117 4.7 14.7 1.0
N D:ASP99 4.7 19.9 1.0
CA D:GLU95 4.8 7.5 1.0
CB D:ASP99 4.8 18.5 1.0
CA D:ASP101 4.8 14.3 1.0
O4 D:MFU1117 4.8 14.3 1.0

Reference:

J.Adam, M.Pokorna, C.Sabin, E.P.Mitchell, A.Imberty, M.Wimmerova. Engineering of Pa-Iil Lectin From Pseudomonas Aeruginosa - Unravelling the Role of the Specificity Loop For Sugar Preference. Bmc Struct.Biol. V. 7 36 2007.
ISSN: ISSN 1472-6807
PubMed: 17540045
DOI: 10.1186/1472-6807-7-36
Page generated: Fri Jul 12 13:38:14 2024

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