Atomistry » Calcium » PDB 4k9m-4ko1 » 4kmb
Atomistry »
  Calcium »
    PDB 4k9m-4ko1 »
      4kmb »

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

Go back to Calcium Binding Sites List in 4kmb
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

Go back to Calcium Binding Sites List in 4kmb
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

Go back to Calcium Binding Sites List in 4kmb
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

Go back to Calcium Binding Sites List in 4kmb
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

Go back to Calcium Binding Sites List in 4kmb
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

Go back to Calcium Binding Sites List in 4kmb
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

Go back to Calcium Binding Sites List in 4kmb
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

Go back to Calcium Binding Sites List in 4kmb
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

Go back to Calcium Binding Sites List in 4kmb
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

Go back to Calcium Binding Sites List in 4kmb
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: Sun Jul 14 09:10:35 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy