Calcium in PDB 4kmb: Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A

Protein crystallography data

The structure of Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A, PDB code: 4kmb was solved by K.K.-S.Ng, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 79.100, 85.000, 97.500, 90.00, 106.30, 90.00
R / Rfree (%) 20.8 / 27.2

Other elements in 4kmb:

The structure of Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Zinc (Zn) 1 atom

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Calcium atom in the Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A (pdb code 4kmb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A, PDB code: 4kmb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in 4kmb

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Calcium binding site 1 out of 11 in the Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca1

b:11.5
occ:1.00
 OD2 1:ASP161 2.3 11.8 1.0
OD1 1:ASP194 2.3 9.1 1.0
O 1:HOH271 2.4 12.2 1.0
O 1:GLU193 2.5 10.4 1.0
OE2 1:GLU165 2.5 7.4 1.0
OD1 1:ASP188 2.5 11.5 1.0
OD1 1:ASP161 2.6 11.6 1.0
OE1 1:GLU165 2.6 10.3 1.0
CG 1:ASP161 2.8 9.6 1.0
CD 1:GLU165 2.9 11.0 1.0
CG 1:ASP188 3.3 13.7 1.0
C 1:GLU193 3.5 9.6 1.0
CG 1:ASP194 3.5 7.6 1.0
CA 1:ASP194 3.8 9.8 1.0
CB 1:ASP188 3.9 8.4 1.0
CA 1:CA3 3.9 10.9 1.0
O 1:HOH272 4.0 10.3 1.0
N 1:ASP194 4.0 12.1 1.0
OD2 1:ASP188 4.2 9.6 1.0
CB 1:ASP194 4.2 6.2 1.0
CB 1:ASP161 4.3 7.1 1.0
N 1:GLU193 4.4 9.4 1.0
CG 1:GLU165 4.4 8.3 1.0
OD2 1:ASP194 4.5 8.9 1.0
CA 1:ASP188 4.5 10.9 1.0
CA 1:GLU193 4.5 10.7 1.0
O 1:HOH269 4.6 15.4 1.0
CZ 1:PHE168 4.6 9.8 1.0
OD2 1:ASP206 4.7 10.5 1.0
N 1:GLY166 4.7 14.3 1.0
O 1:HOH270 4.7 9.2 1.0
O 1:ASP161 4.7 10.7 1.0
O 1:HOH277 4.9 9.0 1.0
CA 1:GLU165 5.0 9.8 1.0
C 1:ASP194 5.0 7.8 1.0

Calcium binding site 2 out of 11 in 4kmb

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Calcium binding site 2 out of 11 in the Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca2

b:15.8
occ:1.00
 OD1 1:ASP206 2.3 8.9 1.0
OD1 1:ASN187 2.4 19.7 1.0
OD1 1:ASN205 2.5 7.8 1.0
OE1 1:GLU185 2.5 15.3 1.0
OE1 1:GLU193 2.6 11.8 1.0
O 1:ASP206 2.6 12.9 1.0
O2 1:FUC224 2.6 22.5 1.0
O3 1:FUC224 2.8 17.6 1.0
CG 1:ASP206 3.3 9.7 1.0
CD 1:GLU185 3.3 14.7 1.0
C2 1:FUC224 3.4 25.5 1.0
CG 1:ASN187 3.4 17.5 1.0
CD 1:GLU193 3.5 8.0 1.0
CG 1:ASN205 3.5 10.9 1.0
C3 1:FUC224 3.6 23.3 1.0
C 1:ASP206 3.6 9.6 1.0
OE2 1:GLU185 3.6 15.4 1.0
N 1:ASP206 3.7 10.8 1.0
OE2 1:GLU193 3.9 10.2 1.0
ND2 1:ASN187 4.0 17.3 1.0
ND2 1:ASN205 4.0 13.9 1.0
OD2 1:ASP206 4.0 10.5 1.0
CA 1:ASP206 4.0 9.0 1.0
N 1:ASN187 4.2 14.3 1.0
CB 1:ASP206 4.3 8.3 1.0
CG 1:GLU185 4.5 13.1 1.0
C 1:ASN205 4.6 11.5 1.0
CB 1:ASN187 4.6 15.1 1.0
CB 1:HIS189 4.7 14.4 1.0
N 1:ILE207 4.7 8.5 1.0
CG 1:GLU193 4.8 8.8 1.0
CB 1:ASN205 4.8 10.4 1.0
C1 1:FUC224 4.8 31.2 1.0
N 1:ASP188 4.8 14.7 1.0
CA 1:ASN187 4.8 16.0 1.0
CB 1:GLU193 4.8 8.5 1.0
N 1:HIS189 4.8 11.8 1.0
CA 1:ASN205 4.9 11.9 1.0
C4 1:FUC224 4.9 28.1 1.0
CB 1:GLU185 5.0 13.4 1.0

Calcium binding site 3 out of 11 in 4kmb

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Calcium binding site 3 out of 11 in the Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca3

b:10.9
occ:1.00
 OE1 1:GLU165 2.2 10.3 1.0
O 1:HOH277 2.3 9.0 1.0
O 1:HOH272 2.4 10.3 1.0
OD2 1:ASP194 2.5 8.9 1.0
O 1:HOH276 2.5 13.4 1.0
OD1 1:ASP194 2.6 9.1 1.0
CG 1:ASP194 2.9 7.6 1.0
CD 1:GLU165 3.4 11.0 1.0
CA 1:CA1 3.9 11.5 1.0
CB 1:GLU165 4.0 9.7 1.0
CG 1:GLU165 4.1 8.3 1.0
OD1 1:ASP188 4.2 11.5 1.0
O 1:HOH273 4.2 7.9 1.0
O 1:ASP161 4.3 10.7 1.0
OE2 1:GLU165 4.4 7.4 1.0
CB 1:ASP194 4.4 6.2 1.0
CA 1:GLU165 4.5 9.8 1.0
OD2 1:ASP161 4.8 11.8 1.0
OD2 1:ASP188 4.8 9.6 1.0
O 1:HOH274 4.9 36.1 1.0
CG 1:ASP188 4.9 13.7 1.0
OD1 1:ASP161 5.0 11.6 1.0

Calcium binding site 4 out of 11 in 4kmb

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Calcium binding site 4 out of 11 in the Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca4

b:44.4
occ:1.00
 O 1:HOH305 2.7 23.4 1.0
O 1:HOH304 2.7 23.1 1.0
O 1:HOH306 4.2 35.8 1.0
O 1:ASN187 4.5 16.9 1.0
ND1 1:HIS189 4.7 16.8 1.0

Calcium binding site 5 out of 11 in 4kmb

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Calcium binding site 5 out of 11 in the Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca5

b:48.8
occ:1.00
 O3 3:G4S223 2.3 25.8 1.0
O 3:HOH272 2.4 17.6 1.0
O 3:SER191 2.6 18.8 1.0
O 3:HOH271 2.6 16.1 1.0
O 3:HOH269 2.6 26.0 1.0
C3 3:G4S223 3.4 29.4 1.0
O2 3:G4S223 3.7 29.4 1.0
C 3:SER191 3.7 16.2 1.0
O 3:HOH270 3.9 29.2 1.0
C2 3:G4S223 4.1 30.2 1.0
CA 3:GLY192 4.3 11.4 1.0
O 3:HOH273 4.4 14.6 1.0
N 3:GLY192 4.5 13.5 1.0
C4 3:G4S223 4.5 30.3 1.0
CA 3:SER191 4.8 19.6 1.0
CB 3:SER191 4.8 23.1 1.0
O8 3:G4S223 5.0 36.1 1.0

Calcium binding site 6 out of 11 in 4kmb

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Calcium binding site 6 out of 11 in the Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca1

b:19.8
occ:1.00
 O 2:HOH340 2.3 15.9 1.0
O 2:GLU193 2.4 22.9 1.0
OD2 2:ASP161 2.4 13.9 1.0
OE1 2:GLU165 2.4 27.1 1.0
OD1 2:ASP188 2.5 31.3 1.0
OD1 2:ASP194 2.6 30.3 1.0
OE2 2:GLU165 2.6 31.7 1.0
OD1 2:ASP161 2.7 18.0 1.0
CD 2:GLU165 2.9 26.9 1.0
CG 2:ASP161 2.9 17.2 1.0
C 2:GLU193 3.3 24.1 1.0
CG 2:ASP188 3.4 29.5 1.0
CG 2:ASP194 3.7 26.1 1.0
CA 2:ASP194 3.8 20.6 1.0
CA 2:CA3 3.8 42.1 1.0
CB 2:ASP188 3.9 28.1 1.0
N 2:ASP194 3.9 22.5 1.0
O 2:HOH341 4.0 20.9 1.0
O 2:HOH223 4.1 25.2 1.0
N 2:GLU193 4.3 29.3 1.0
CB 2:ASP194 4.3 22.3 1.0
OD2 2:ASP188 4.3 29.6 1.0
CG 2:GLU165 4.4 29.0 1.0
CB 2:ASP161 4.4 16.6 1.0
CA 2:GLU193 4.4 25.3 1.0
OD2 2:ASP206 4.4 12.9 1.0
CA 2:ASP188 4.5 28.7 1.0
CZ 2:PHE168 4.5 12.0 1.0
O 2:HOH225 4.7 29.9 1.0
OD2 2:ASP194 4.7 26.0 1.0
O 2:ASP161 4.7 22.4 1.0
N 2:GLY166 4.8 24.1 1.0
C 2:ASP194 4.9 20.0 1.0
CA 2:GLU165 4.9 27.4 1.0

Calcium binding site 7 out of 11 in 4kmb

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Calcium binding site 7 out of 11 in the Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca2

b:30.6
occ:1.00
 OE1 2:GLU193 2.2 25.2 1.0
OD1 2:ASN187 2.5 30.3 1.0
OD1 2:ASP206 2.6 17.5 1.0
OD1 2:ASN205 2.6 29.9 1.0
OE1 2:GLU185 2.6 31.4 1.0
O 2:ASP206 2.7 22.3 1.0
O2 2:FUC222 2.8 42.0 1.0
O3 2:FUC222 2.8 40.5 1.0
CD 2:GLU193 3.3 27.6 1.0
C3 2:FUC222 3.3 45.0 1.0
CG 2:ASN187 3.4 31.4 1.0
CG 2:ASP206 3.5 16.9 1.0
CD 2:GLU185 3.6 30.9 1.0
C2 2:FUC222 3.6 43.4 1.0
CG 2:ASN205 3.7 28.1 1.0
C 2:ASP206 3.7 21.8 1.0
OE2 2:GLU193 3.8 27.4 1.0
ND2 2:ASN187 3.9 31.0 1.0
N 2:ASP206 3.9 20.0 1.0
OE2 2:GLU185 4.0 33.7 1.0
OD2 2:ASP206 4.1 12.9 1.0
ND2 2:ASN205 4.2 29.2 1.0
CA 2:ASP206 4.2 20.1 1.0
N 2:ASN187 4.2 23.7 1.0
CB 2:ASP206 4.4 19.4 1.0
CB 2:HIS189 4.5 39.1 1.0
CG 2:GLU193 4.5 24.4 1.0
CB 2:ASN187 4.6 29.8 1.0
N 2:HIS189 4.7 34.1 1.0
N 2:ASP188 4.7 27.7 1.0
C 2:ASN205 4.7 23.4 1.0
CB 2:GLU193 4.7 21.3 1.0
C4 2:FUC222 4.8 47.6 1.0
CA 2:ASN187 4.8 26.3 1.0
CG 2:GLU185 4.8 27.9 1.0
C1 2:FUC222 4.8 42.2 1.0
N 2:ILE207 4.8 22.8 1.0
CB 2:ASN205 4.9 26.7 1.0

Calcium binding site 8 out of 11 in 4kmb

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Calcium binding site 8 out of 11 in the Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca3

b:42.1
occ:1.00
 O 2:HOH225 2.0 29.9 1.0
OE1 2:GLU165 2.4 27.1 1.0
OD1 2:ASP194 2.4 30.3 1.0
O 2:HOH223 2.4 25.2 1.0
OD2 2:ASP194 2.7 26.0 1.0
CG 2:ASP194 2.9 26.1 1.0
O 2:HOH224 2.9 35.1 1.0
CD 2:GLU165 3.6 26.9 1.0
CA 2:CA1 3.8 19.8 1.0
CB 2:GLU165 4.0 29.7 1.0
OD1 2:ASP188 4.1 31.3 1.0
O 2:ASP161 4.1 22.4 1.0
CG 2:GLU165 4.2 29.0 1.0
O 2:HOH226 4.2 41.7 1.0
CB 2:ASP194 4.4 22.3 1.0
CA 2:GLU165 4.4 27.4 1.0
OE2 2:GLU165 4.5 31.7 1.0
OD1 2:ASP161 4.8 18.0 1.0
OD2 2:ASP161 4.8 13.9 1.0
N 2:GLU165 4.8 28.9 1.0
CG 2:ASP188 4.8 29.5 1.0
OD2 2:ASP188 4.9 29.6 1.0
O 2:GLU162 4.9 36.7 1.0
CG 2:ASP161 4.9 17.2 1.0

Calcium binding site 9 out of 11 in 4kmb

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Calcium binding site 9 out of 11 in the Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca1

b:13.0
occ:1.00
 OD1 3:ASP194 2.3 11.8 1.0
O 3:HOH338 2.4 15.0 1.0
O 3:GLU193 2.4 12.7 1.0
OD1 3:ASP188 2.4 15.4 1.0
OD2 3:ASP161 2.4 16.8 1.0
OE2 3:GLU165 2.5 15.2 1.0
OE1 3:GLU165 2.6 15.6 1.0
OD1 3:ASP161 2.7 16.0 1.0
CD 3:GLU165 2.9 17.1 1.0
CG 3:ASP161 2.9 13.5 1.0
CG 3:ASP188 3.3 12.9 1.0
C 3:GLU193 3.4 11.7 1.0
CG 3:ASP194 3.5 12.5 1.0
CA 3:ASP194 3.7 10.8 1.0
CB 3:ASP188 3.8 13.9 1.0
N 3:ASP194 3.9 11.3 1.0
CA 3:CA3 4.0 13.2 1.0
CB 3:ASP194 4.2 11.7 1.0
OD2 3:ASP188 4.3 9.2 1.0
N 3:GLU193 4.4 11.7 1.0
CA 3:ASP188 4.4 13.1 1.0
CG 3:GLU165 4.4 13.7 1.0
CB 3:ASP161 4.4 13.0 1.0
OD2 3:ASP194 4.5 15.7 1.0
CZ 3:PHE168 4.5 10.9 1.0
OD2 3:ASP206 4.5 20.1 1.0
CA 3:GLU193 4.5 10.1 1.0
O 3:HOH339 4.7 19.4 1.0
N 3:GLY166 4.7 18.4 1.0
O 3:ASP161 4.8 16.9 1.0
O 3:HOH340 4.8 13.6 1.0
C 3:ASP194 4.9 10.6 1.0
CE1 3:PHE168 4.9 10.0 1.0
CA 3:GLU165 4.9 16.7 1.0
N 3:ASP188 5.0 14.0 1.0

Calcium binding site 10 out of 11 in 4kmb

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Calcium binding site 10 out of 11 in the Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Complex of 4'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca2

b:20.0
occ:1.00
 OD1 3:ASP206 2.3 18.2 1.0
OE1 3:GLU193 2.4 12.6 1.0
O3 3:FUC222 2.5 20.3 1.0
OD1 3:ASN187 2.5 15.0 1.0
OE1 3:GLU185 2.5 25.7 1.0
OD1 3:ASN205 2.5 14.5 1.0
O2 3:FUC222 2.6 29.2 1.0
O 3:ASP206 2.6 14.3 1.0
C3 3:FUC222 3.3 28.9 1.0
CG 3:ASP206 3.3 17.0 1.0
C2 3:FUC222 3.4 28.7 1.0
CD 3:GLU185 3.4 25.5 1.0
CD 3:GLU193 3.4 15.2 1.0
CG 3:ASN187 3.5 15.2 1.0
CG 3:ASN205 3.6 18.0 1.0
C 3:ASP206 3.6 14.0 1.0
OE2 3:GLU185 3.6 24.1 1.0
N 3:ASP206 3.8 18.8 1.0
OE2 3:GLU193 3.9 13.9 1.0
ND2 3:ASN205 4.0 17.4 1.0
OD2 3:ASP206 4.0 20.1 1.0
ND2 3:ASN187 4.0 16.7 1.0
CA 3:ASP206 4.1 15.4 1.0
N 3:ASN187 4.2 18.3 1.0
CB 3:ASP206 4.3 14.8 1.0
CB 3:HIS189 4.5 15.8 1.0
C 3:ASN205 4.6 18.2 1.0
CG 3:GLU193 4.7 14.0 1.0
C4 3:FUC222 4.7 29.8 1.0
CB 3:ASN187 4.7 20.7 1.0
CG 3:GLU185 4.7 20.1 1.0
C1 3:FUC222 4.8 33.1 1.0
CB 3:GLU193 4.8 10.0 1.0
N 3:HIS189 4.8 15.4 1.0
N 3:ASP188 4.8 14.0 1.0
N 3:ILE207 4.8 14.0 1.0
CB 3:ASN205 4.8 17.6 1.0
CA 3:ASN187 4.8 18.7 1.0
CA 3:ASN205 4.9 19.2 1.0

Reference:

K.K.Ng, W.I.Weis. Structure of A Selectin-Like Mutant of Mannose-Binding Protein Complexed with Sialylated and Sulfated Lewis(X) Oligosaccharides. Biochemistry V. 36 979 1997.
ISSN: ISSN 0006-2960
PubMed: 9033386
DOI: 10.1021/BI962564E
Page generated: Sat Dec 12 04:55:19 2020

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