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Calcium in PDB 3kmb: Complex of 3'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose- Binding Protein A

Protein crystallography data

The structure of Complex of 3'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose- Binding Protein A, PDB code: 3kmb 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 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 79.100, 84.900, 97.200, 90.00, 106.60, 90.00
R / Rfree (%) 20.4 / 25.4

Other elements in 3kmb:

The structure of Complex of 3'-Sulfo-Lewis-X with A Selectin-Like Mutant of Mannose- Binding Protein A also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 10 in 3kmb

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Calcium binding site 1 out of 10 in the Complex of 3'-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 3'-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:9.2
occ:1.00
 OD2 1:ASP161 2.3 10.6 1.0
O 1:HOH308 2.3 9.0 1.0
OD1 1:ASP194 2.4 11.0 1.0
O 1:GLU193 2.4 9.4 1.0
OD1 1:ASP161 2.6 7.2 1.0
OE2 1:GLU165 2.6 9.6 1.0
OE1 1:GLU165 2.6 9.3 1.0
OD1 1:ASP188 2.6 10.7 1.0
CG 1:ASP161 2.8 6.2 1.0
CD 1:GLU165 2.9 9.5 1.0
CG 1:ASP188 3.4 12.4 1.0
C 1:GLU193 3.4 8.8 1.0
CG 1:ASP194 3.5 9.2 1.0
CA 1:ASP194 3.8 7.9 1.0
CB 1:ASP188 3.9 10.2 1.0
CA 1:CA3 3.9 10.2 1.0
N 1:ASP194 4.0 8.2 1.0
O 1:HOH337 4.0 11.0 1.0
OD2 1:ASP188 4.2 11.4 1.0
CB 1:ASP194 4.2 8.7 1.0
CB 1:ASP161 4.3 8.5 1.0
N 1:GLU193 4.4 10.8 1.0
CG 1:GLU165 4.4 7.0 1.0
OD2 1:ASP194 4.5 9.9 1.0
CA 1:ASP188 4.5 11.1 1.0
O 1:HOH307 4.5 21.6 1.0
CA 1:GLU193 4.5 9.3 1.0
OD2 1:ASP206 4.6 7.1 1.0
CZ 1:PHE168 4.6 10.0 1.0
O 1:ASP161 4.7 10.1 1.0
O 1:HOH306 4.8 6.9 1.0
N 1:GLY166 4.8 11.9 1.0
C 1:ASP194 4.9 7.8 1.0

Calcium binding site 2 out of 10 in 3kmb

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Calcium binding site 2 out of 10 in the Complex of 3'-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 3'-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:13.3
occ:1.00
 OD1 1:ASP206 2.3 10.3 1.0
OD1 1:ASN187 2.3 16.7 1.0
OE1 1:GLU193 2.3 9.9 1.0
O2 1:FUC224 2.5 17.1 1.0
OE1 1:GLU185 2.5 13.2 1.0
OD1 1:ASN205 2.5 8.4 1.0
O 1:ASP206 2.6 10.8 1.0
O3 1:FUC224 2.7 15.6 1.0
CG 1:ASP206 3.3 8.6 1.0
C2 1:FUC224 3.3 17.7 1.0
CD 1:GLU193 3.3 6.8 1.0
CD 1:GLU185 3.4 14.7 1.0
CG 1:ASN187 3.4 12.8 1.0
C3 1:FUC224 3.4 19.9 1.0
CG 1:ASN205 3.6 10.5 1.0
C 1:ASP206 3.6 6.1 1.0
OE2 1:GLU193 3.7 8.0 1.0
OE2 1:GLU185 3.7 14.5 1.0
N 1:ASP206 3.8 8.5 1.0
ND2 1:ASN187 3.9 10.7 1.0
ND2 1:ASN205 4.0 11.2 1.0
OD2 1:ASP206 4.0 7.1 1.0
CA 1:ASP206 4.1 9.9 1.0
N 1:ASN187 4.2 12.8 1.0
CB 1:ASP206 4.3 8.4 1.0
CG 1:GLU185 4.6 12.9 1.0
CB 1:ASN187 4.6 10.6 1.0
CG 1:GLU193 4.6 8.4 1.0
C 1:ASN205 4.7 8.0 1.0
CB 1:HIS189 4.7 13.3 1.0
N 1:ILE207 4.7 7.2 1.0
N 1:ASP188 4.7 13.6 1.0
C1 1:FUC224 4.7 25.0 1.0
N 1:HIS189 4.8 11.7 1.0
CB 1:GLU193 4.8 5.9 1.0
CA 1:ASN187 4.8 13.1 1.0
C4 1:FUC224 4.8 26.4 1.0
CB 1:ASN205 4.9 6.1 1.0

Calcium binding site 3 out of 10 in 3kmb

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Calcium binding site 3 out of 10 in the Complex of 3'-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 3'-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:10.2
occ:1.00
 OE1 1:GLU165 2.3 9.3 1.0
O 1:HOH397 2.4 9.1 1.0
O 1:HOH337 2.4 11.0 1.0
O 1:HOH338 2.5 12.0 1.0
OD2 1:ASP194 2.5 9.9 1.0
OD1 1:ASP194 2.6 11.0 1.0
CG 1:ASP194 2.9 9.2 1.0
CD 1:GLU165 3.5 9.5 1.0
CA 1:CA1 3.9 9.2 1.0
CB 1:GLU165 4.1 9.7 1.0
O 1:HOH336 4.2 9.8 1.0
CG 1:GLU165 4.2 7.0 1.0
O 1:ASP161 4.3 10.1 1.0
OD1 1:ASP188 4.3 10.7 1.0
CB 1:ASP194 4.4 8.7 1.0
OE2 1:GLU165 4.4 9.6 1.0
CA 1:GLU165 4.5 8.5 1.0
O 1:HOH339 4.6 38.2 1.0
O 1:HOH340 4.8 19.8 1.0
OD2 1:ASP188 4.8 11.4 1.0
OD2 1:ASP161 4.9 10.6 1.0
OD1 1:ASP161 4.9 7.2 1.0
CG 1:ASP188 4.9 12.4 1.0
N 1:GLU165 5.0 7.6 1.0

Calcium binding site 4 out of 10 in 3kmb

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Calcium binding site 4 out of 10 in the Complex of 3'-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 3'-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:34.0
occ:1.00
 O 1:HOH282 2.4 15.9 1.0
O 2:HOH312 2.4 48.3 1.0
OE1 2:GLU93 2.4 21.5 1.0
O 2:HOH316 2.4 12.9 1.0
O 2:HOH311 2.5 20.3 1.0
O 2:HOH313 2.6 43.9 1.0
OE2 2:GLU93 2.9 21.6 1.0
CD 2:GLU93 3.0 24.1 1.0
O 2:HOH315 4.3 10.0 1.0
OD1 2:ASN96 4.4 17.3 1.0
NZ 1:LYS91 4.5 14.6 1.0
CD 1:LYS91 4.5 9.6 1.0
CG 2:GLU93 4.5 19.3 1.0
O 1:HOH284 4.6 40.5 1.0
O 2:HOH314 4.6 16.6 1.0
O 1:HOH283 4.7 23.0 1.0
CE 1:LYS91 4.9 12.1 1.0

Calcium binding site 5 out of 10 in 3kmb

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Calcium binding site 5 out of 10 in the Complex of 3'-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 3'-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:20.3
occ:1.00
 OD2 2:ASP161 2.3 16.2 1.0
O 2:HOH374 2.3 20.9 1.0
OE1 2:GLU165 2.3 28.6 1.0
O 2:GLU193 2.4 19.0 1.0
OD1 2:ASP194 2.6 26.5 1.0
OE2 2:GLU165 2.6 33.3 1.0
OD1 2:ASP161 2.6 15.8 1.0
OD1 2:ASP188 2.7 25.0 1.0
CG 2:ASP161 2.8 16.2 1.0
CD 2:GLU165 2.8 28.9 1.0
C 2:GLU193 3.3 22.5 1.0
CG 2:ASP188 3.5 25.1 1.0
CG 2:ASP194 3.7 28.0 1.0
CA 2:ASP194 3.8 21.1 1.0
CA 2:CA3 3.8 41.1 1.0
N 2:ASP194 3.9 20.7 1.0
CB 2:ASP188 3.9 24.4 1.0
O 2:HOH364 4.2 33.1 1.0
O 2:HOH375 4.2 20.0 1.0
CB 2:ASP161 4.3 19.8 1.0
N 2:GLU193 4.3 29.0 1.0
CB 2:ASP194 4.3 22.4 1.0
CG 2:GLU165 4.3 30.7 1.0
CZ 2:PHE168 4.4 15.7 1.0
CA 2:GLU193 4.4 24.2 1.0
OD2 2:ASP188 4.4 22.3 1.0
CA 2:ASP188 4.5 26.6 1.0
OD2 2:ASP206 4.5 15.9 1.0
OD2 2:ASP194 4.7 28.8 1.0
N 2:GLY166 4.7 25.8 1.0
CA 2:GLU165 4.8 29.2 1.0
O 2:ASP161 4.9 23.2 1.0
C 2:ASP194 4.9 18.3 1.0
CB 2:GLU165 4.9 32.0 1.0
CE2 2:PHE168 4.9 18.9 1.0
O 2:HOH365 5.0 29.1 1.0

Calcium binding site 6 out of 10 in 3kmb

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Calcium binding site 6 out of 10 in the Complex of 3'-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 3'-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:24.1
occ:1.00
 OE1 2:GLU193 2.2 29.9 1.0
OD1 2:ASN187 2.5 20.8 1.0
OD1 2:ASN205 2.5 21.5 1.0
OD1 2:ASP206 2.5 16.1 1.0
O 2:ASP206 2.6 19.4 1.0
OE1 2:GLU185 2.6 18.9 1.0
O2 2:FUC222 2.9 82.3 1.0
O3 2:FUC222 2.9 80.5 1.0
CD 2:GLU193 3.3 26.8 1.0
CG 2:ASN187 3.4 25.5 1.0
C3 2:FUC222 3.4 84.0 1.0
CG 2:ASP206 3.4 16.2 1.0
CD 2:GLU185 3.5 21.1 1.0
CG 2:ASN205 3.6 22.2 1.0
C 2:ASP206 3.6 20.0 1.0
OE2 2:GLU193 3.7 23.3 1.0
C2 2:FUC222 3.7 83.8 1.0
N 2:ASP206 3.8 18.2 1.0
ND2 2:ASN187 3.8 19.9 1.0
OE2 2:GLU185 3.9 27.1 1.0
ND2 2:ASN205 4.1 22.8 1.0
OD2 2:ASP206 4.1 15.9 1.0
CA 2:ASP206 4.1 16.2 1.0
N 2:ASN187 4.2 20.8 1.0
CB 2:ASP206 4.4 17.3 1.0
CB 2:HIS189 4.5 40.0 1.0
CG 2:GLU193 4.5 23.2 1.0
CB 2:ASN187 4.6 25.3 1.0
N 2:HIS189 4.7 33.3 1.0
N 2:ASP188 4.7 25.5 1.0
C 2:ASN205 4.7 20.6 1.0
CB 2:GLU193 4.7 21.1 1.0
CG 2:GLU185 4.8 19.4 1.0
N 2:ILE207 4.8 19.0 1.0
CA 2:ASN187 4.8 23.9 1.0
C4 2:FUC222 4.9 86.1 1.0
CB 2:ASN205 4.9 21.4 1.0
C1 2:FUC222 4.9 83.6 1.0
CA 2:ASN205 5.0 20.3 1.0

Calcium binding site 7 out of 10 in 3kmb

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Calcium binding site 7 out of 10 in the Complex of 3'-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 3'-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:41.1
occ:1.00
 O 2:HOH365 2.3 29.1 1.0
OE1 2:GLU165 2.3 28.6 1.0
O 2:HOH364 2.3 33.1 1.0
OD1 2:ASP194 2.3 26.5 1.0
OD2 2:ASP194 2.6 28.8 1.0
CG 2:ASP194 2.8 28.0 1.0
CD 2:GLU165 3.5 28.9 1.0
CA 2:CA1 3.8 20.3 1.0
CB 2:GLU165 3.9 32.0 1.0
OD1 2:ASP188 4.0 25.0 1.0
CG 2:GLU165 4.1 30.7 1.0
O 2:ASP161 4.2 23.2 1.0
O 2:HOH366 4.3 25.8 1.0
CB 2:ASP194 4.3 22.4 1.0
CA 2:GLU165 4.4 29.2 1.0
OE2 2:GLU165 4.5 33.3 1.0
OD2 2:ASP161 4.7 16.2 1.0
OD1 2:ASP161 4.7 15.8 1.0
CG 2:ASP188 4.8 25.1 1.0
N 2:GLU165 4.8 30.1 1.0
OD2 2:ASP188 4.9 22.3 1.0
CG 2:ASP161 4.9 16.2 1.0
C 2:ASP161 5.0 22.4 1.0
O 2:GLU162 5.0 32.8 1.0

Calcium binding site 8 out of 10 in 3kmb

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Calcium binding site 8 out of 10 in the Complex of 3'-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 3'-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:15.2
occ:1.00
 OD1 3:ASP194 2.3 12.0 1.0
O 3:HOH278 2.4 12.1 1.0
O 3:GLU193 2.4 11.3 1.0
OD1 3:ASP188 2.5 13.8 1.0
OD2 3:ASP161 2.5 18.4 1.0
OE2 3:GLU165 2.5 11.4 1.0
OE1 3:GLU165 2.6 11.6 1.0
OD1 3:ASP161 2.7 12.6 1.0
CD 3:GLU165 2.9 13.0 1.0
CG 3:ASP161 3.0 12.5 1.0
CG 3:ASP188 3.4 12.5 1.0
C 3:GLU193 3.4 11.7 1.0
CG 3:ASP194 3.5 12.2 1.0
CA 3:ASP194 3.7 13.9 1.0
CB 3:ASP188 3.8 10.9 1.0
CA 3:CA3 3.9 14.7 1.0
N 3:ASP194 4.0 13.8 1.0
O 3:HOH331 4.0 13.3 1.0
CB 3:ASP194 4.2 15.1 1.0
OD2 3:ASP188 4.3 11.6 1.0
N 3:GLU193 4.3 11.6 1.0
CA 3:ASP188 4.4 12.2 1.0
CG 3:GLU165 4.4 14.6 1.0
OD2 3:ASP194 4.4 11.2 1.0
CB 3:ASP161 4.5 13.3 1.0
O 3:HOH277 4.5 19.1 1.0
CA 3:GLU193 4.5 11.2 1.0
OD2 3:ASP206 4.5 20.2 1.0
CZ 3:PHE168 4.5 15.6 1.0
N 3:GLY166 4.7 21.6 1.0
O 3:HOH279 4.7 16.4 1.0
O 3:ASP161 4.9 14.5 1.0
O 3:HOH330 4.9 14.8 1.0
CA 3:GLU165 4.9 20.9 1.0
C 3:ASP194 5.0 13.3 1.0
CE2 3:PHE168 5.0 13.5 1.0

Calcium binding site 9 out of 10 in 3kmb

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Calcium binding site 9 out of 10 in the Complex of 3'-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 3'-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 20.3 1.0
O3 3:FUC224 2.4 8.3 0.5
OD1 3:ASN187 2.5 17.6 1.0
OE1 3:GLU193 2.5 19.8 1.0
OD1 3:ASN205 2.6 27.3 1.0
O 3:ASP206 2.6 14.8 1.0
OE1 3:GLU185 2.6 25.8 1.0
O2 3:FUC224 2.7 16.8 0.5
CG 3:ASP206 3.3 19.9 1.0
C3 3:FUC224 3.4 17.5 0.5
C2 3:FUC224 3.4 20.0 0.5
CD 3:GLU185 3.4 27.6 1.0
CG 3:ASN187 3.5 15.2 1.0
OE2 3:GLU185 3.5 26.3 1.0
CD 3:GLU193 3.5 19.4 1.0
C 3:ASP206 3.7 14.4 1.0
CG 3:ASN205 3.7 27.4 1.0
N 3:ASP206 3.8 19.1 1.0
OE2 3:GLU193 3.9 18.9 1.0
OD2 3:ASP206 4.0 20.2 1.0
ND2 3:ASN187 4.1 14.4 1.0
CA 3:ASP206 4.2 15.6 1.0
N 3:ASN187 4.2 18.3 1.0
ND2 3:ASN205 4.2 27.4 1.0
CB 3:ASP206 4.4 14.2 1.0
CG 3:GLU185 4.7 21.4 1.0
CB 3:ASN187 4.7 17.2 1.0
CB 3:HIS189 4.7 16.0 1.0
C 3:ASN205 4.7 21.7 1.0
C4 3:FUC224 4.7 21.5 0.5
CG 3:GLU193 4.8 15.0 1.0
N 3:ASP188 4.8 14.4 1.0
O4 3:FUC224 4.8 27.0 0.5
N 3:HIS189 4.8 16.3 1.0
N 3:ILE207 4.8 15.0 1.0
CA 3:ASN187 4.8 16.2 1.0
C1 3:FUC224 4.8 25.8 0.5
CB 3:GLU193 4.9 11.4 1.0
CB 3:ASN205 4.9 23.4 1.0
CA 3:ASN205 5.0 24.7 1.0

Calcium binding site 10 out of 10 in 3kmb

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Calcium binding site 10 out of 10 in the Complex of 3'-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 3'-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:Ca3

b:14.7
occ:1.00
 OE1 3:GLU165 2.3 11.6 1.0
O 3:HOH330 2.3 14.8 1.0
O 3:HOH328 2.4 20.9 1.0
OD2 3:ASP194 2.4 11.2 1.0
O 3:HOH331 2.4 13.3 1.0
OD1 3:ASP194 2.6 12.0 1.0
CG 3:ASP194 2.9 12.2 1.0
CD 3:GLU165 3.5 13.0 1.0
CA 3:CA1 3.9 15.2 1.0
CB 3:GLU165 4.2 20.2 1.0
OD1 3:ASP188 4.2 13.8 1.0
CG 3:GLU165 4.2 14.6 1.0
O 3:HOH329 4.2 32.5 1.0
O 3:HOH332 4.3 19.8 1.0
CB 3:ASP194 4.4 15.1 1.0
O 3:ASP161 4.4 14.5 1.0
OE2 3:GLU165 4.4 11.4 1.0
CA 3:GLU165 4.5 20.9 1.0
O 3:HOH327 4.6 41.8 1.0
O 3:HOH334 4.8 31.6 1.0
OD1 3:ASP161 4.8 12.6 1.0
CG 3:ASP188 4.9 12.5 1.0
OD2 3:ASP188 4.9 11.6 1.0
OD2 3:ASP161 5.0 18.4 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 Jul 13 12:33:46 2024

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