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Calcium in PDB 2kmb: Complex of 3'-Neuac-Lewis-X with A Selectin-Like Mutant of Mannose- Binding Protein A

Protein crystallography data

The structure of Complex of 3'-Neuac-Lewis-X with A Selectin-Like Mutant of Mannose- Binding Protein A, PDB code: 2kmb 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, 98.800, 90.00, 107.10, 90.00
R / Rfree (%) 19 / 24.7

Other elements in 2kmb:

The structure of Complex of 3'-Neuac-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'-Neuac-Lewis-X with A Selectin-Like Mutant of Mannose- Binding Protein A (pdb code 2kmb). 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'-Neuac-Lewis-X with A Selectin-Like Mutant of Mannose- Binding Protein A, PDB code: 2kmb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 2kmb

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Calcium binding site 1 out of 10 in the Complex of 3'-Neuac-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'-Neuac-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:11.2
occ:1.00
 O 1:HOH298 2.3 10.6 1.0
OD2 1:ASP161 2.4 8.2 1.0
OD1 1:ASP194 2.4 12.5 1.0
OE2 1:GLU165 2.5 11.9 1.0
OD1 1:ASP188 2.5 12.9 1.0
O 1:GLU193 2.5 9.7 1.0
OD1 1:ASP161 2.6 5.5 1.0
OE1 1:GLU165 2.7 9.8 1.0
CG 1:ASP161 2.8 10.2 1.0
CD 1:GLU165 2.9 9.7 1.0
CG 1:ASP188 3.4 13.5 1.0
C 1:GLU193 3.5 8.5 1.0
CG 1:ASP194 3.6 11.8 1.0
CA 1:ASP194 3.8 8.1 1.0
CB 1:ASP188 3.9 10.3 1.0
N 1:ASP194 4.0 6.6 1.0
CA 1:CA3 4.0 10.1 1.0
O 1:HOH299 4.1 14.7 1.0
CB 1:ASP194 4.2 8.1 1.0
OD2 1:ASP188 4.3 9.3 1.0
CB 1:ASP161 4.3 5.7 1.0
N 1:GLU193 4.3 10.3 1.0
CG 1:GLU165 4.4 11.2 1.0
CA 1:ASP188 4.5 11.9 1.0
OD2 1:ASP194 4.5 9.0 1.0
CZ 1:PHE168 4.5 7.7 1.0
CA 1:GLU193 4.6 8.7 1.0
O 1:HOH296 4.6 17.0 1.0
O 1:HOH297 4.7 13.0 1.0
N 1:GLY166 4.7 10.1 1.0
OD2 1:ASP206 4.7 10.8 1.0
O 1:ASP161 4.7 6.8 1.0
C 1:ASP194 4.9 7.3 1.0
O 1:HOH318 4.9 6.7 1.0

Calcium binding site 2 out of 10 in 2kmb

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Calcium binding site 2 out of 10 in the Complex of 3'-Neuac-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'-Neuac-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:13.9
occ:1.00
 OD1 1:ASP206 2.2 12.3 1.0
OD1 1:ASN205 2.4 11.3 1.0
OE1 1:GLU193 2.5 11.0 1.0
OD1 1:ASN187 2.5 14.6 1.0
OE1 1:GLU185 2.5 17.2 1.0
O 1:ASP206 2.6 12.5 1.0
O2 1:FUC225 2.6 18.7 1.0
O3 1:FUC225 2.8 18.8 1.0
CG 1:ASP206 3.3 11.1 1.0
CD 1:GLU185 3.4 17.6 1.0
C2 1:FUC225 3.4 20.1 1.0
CD 1:GLU193 3.5 9.2 1.0
CG 1:ASN205 3.5 7.9 1.0
CG 1:ASN187 3.5 14.5 1.0
C3 1:FUC225 3.6 18.6 1.0
C 1:ASP206 3.6 13.7 1.0
OE2 1:GLU185 3.7 14.8 1.0
N 1:ASP206 3.7 13.1 1.0
OE2 1:GLU193 3.8 10.6 1.0
ND2 1:ASN205 3.9 6.6 1.0
OD2 1:ASP206 4.0 10.8 1.0
ND2 1:ASN187 4.0 11.6 1.0
CA 1:ASP206 4.1 11.7 1.0
N 1:ASN187 4.2 14.9 1.0
CB 1:ASP206 4.3 10.7 1.0
C 1:ASN205 4.6 10.6 1.0
CG 1:GLU185 4.6 12.7 1.0
CB 1:ASN187 4.6 9.4 1.0
CG 1:GLU193 4.7 10.6 1.0
CB 1:ASN205 4.7 6.3 1.0
N 1:ILE207 4.8 12.3 1.0
CA 1:ASN187 4.8 14.0 1.0
C1 1:FUC225 4.8 22.9 1.0
N 1:ASP188 4.8 16.4 1.0
CB 1:HIS189 4.9 10.6 1.0
CB 1:GLU193 4.9 8.4 1.0
CA 1:ASN205 4.9 10.9 1.0
N 1:HIS189 4.9 13.3 1.0
C4 1:FUC225 4.9 21.7 1.0

Calcium binding site 3 out of 10 in 2kmb

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Calcium binding site 3 out of 10 in the Complex of 3'-Neuac-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'-Neuac-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:10.1
occ:1.00
 OE1 1:GLU165 2.2 9.8 1.0
O 1:HOH318 2.3 6.7 1.0
O 1:HOH299 2.4 14.7 1.0
OD2 1:ASP194 2.4 9.0 1.0
OD1 1:ASP194 2.6 12.5 1.0
O 1:HOH319 2.6 13.0 1.0
CG 1:ASP194 2.9 11.8 1.0
CD 1:GLU165 3.4 9.7 1.0
CA 1:CA1 4.0 11.2 1.0
CB 1:GLU165 4.1 10.2 1.0
CG 1:GLU165 4.1 11.2 1.0
O 1:HOH300 4.2 8.4 1.0
OD1 1:ASP188 4.2 12.9 1.0
O 1:ASP161 4.3 6.8 1.0
OE2 1:GLU165 4.3 11.9 1.0
CB 1:ASP194 4.4 8.1 1.0
CA 1:GLU165 4.5 9.5 1.0
O 1:HOH320 4.6 23.4 1.0
O 1:HOH321 4.8 21.0 1.0
OD2 1:ASP188 4.9 9.3 1.0
OD1 1:ASP161 4.9 5.5 1.0
CG 1:ASP188 4.9 13.5 1.0
OD2 1:ASP161 5.0 8.2 1.0

Calcium binding site 4 out of 10 in 2kmb

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Calcium binding site 4 out of 10 in the Complex of 3'-Neuac-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'-Neuac-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:27.7
occ:1.00
 O 1:HOH312 2.4 18.2 1.0
O 1:HOH311 2.6 27.8 1.0
O 1:HOH313 2.9 40.4 1.0
O 1:HOH310 4.3 59.9 1.0
O 1:ASN187 4.5 18.7 1.0
ND1 1:HIS189 4.6 12.5 1.0
N 1:GLY190 4.8 11.3 1.0
CA 1:HIS189 4.9 11.5 1.0

Calcium binding site 5 out of 10 in 2kmb

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Calcium binding site 5 out of 10 in the Complex of 3'-Neuac-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'-Neuac-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:17.7
occ:1.00
 O 2:HOH261 2.2 12.2 1.0
OD1 2:ASP194 2.4 19.4 1.0
OD2 2:ASP161 2.4 17.7 1.0
O 2:GLU193 2.5 18.8 1.0
OD1 2:ASP188 2.5 29.7 1.0
OE2 2:GLU165 2.6 20.6 1.0
OE1 2:GLU165 2.6 18.8 1.0
OD1 2:ASP161 2.8 15.4 1.0
CD 2:GLU165 2.9 18.9 1.0
CG 2:ASP161 3.0 17.9 1.0
CG 2:ASP188 3.4 25.4 1.0
C 2:GLU193 3.5 18.4 1.0
CG 2:ASP194 3.6 21.3 1.0
CA 2:CA3 3.8 25.2 1.0
CA 2:ASP194 3.9 18.7 1.0
CB 2:ASP188 3.9 24.3 1.0
O 2:HOH262 4.0 17.1 1.0
N 2:ASP194 4.1 17.9 1.0
O 2:HOH233 4.1 24.3 1.0
CB 2:ASP194 4.3 19.1 1.0
OD2 2:ASP188 4.3 24.8 1.0
CG 2:GLU165 4.4 18.6 1.0
N 2:GLU193 4.4 22.0 1.0
CB 2:ASP161 4.5 18.4 1.0
OD2 2:ASP206 4.5 15.5 1.0
OD2 2:ASP194 4.5 23.2 1.0
CA 2:ASP188 4.5 25.5 1.0
CA 2:GLU193 4.6 20.0 1.0
CZ 2:PHE168 4.6 15.0 1.0
O 2:ASP161 4.8 23.9 1.0
N 2:GLY166 4.9 17.9 1.0
CA 2:GLU165 5.0 18.1 1.0

Calcium binding site 6 out of 10 in 2kmb

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Calcium binding site 6 out of 10 in the Complex of 3'-Neuac-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'-Neuac-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:23.2
occ:1.00
 OE1 2:GLU193 2.3 22.6 1.0
OD1 2:ASP206 2.5 17.6 1.0
OD1 2:ASN187 2.5 21.5 1.0
OE1 2:GLU185 2.5 19.7 1.0
O 2:ASP206 2.6 18.5 1.0
OD1 2:ASN205 2.6 20.4 1.0
O3 2:FUC225 2.6 9.4 0.5
O2 2:FUC225 2.7 18.3 0.5
CD 2:GLU193 3.4 21.6 1.0
C2 2:FUC225 3.4 19.0 0.5
CG 2:ASP206 3.4 17.5 1.0
CD 2:GLU185 3.4 20.8 1.0
C3 2:FUC225 3.5 17.0 0.5
CG 2:ASN187 3.5 21.6 1.0
CG 2:ASN205 3.6 19.5 1.0
C 2:ASP206 3.6 19.4 1.0
OE2 2:GLU185 3.7 19.5 1.0
OE2 2:GLU193 3.8 23.4 1.0
N 2:ASP206 3.9 18.4 1.0
ND2 2:ASN187 4.0 18.6 1.0
OD2 2:ASP206 4.0 15.5 1.0
ND2 2:ASN205 4.0 19.3 1.0
CA 2:ASP206 4.2 17.7 1.0
N 2:ASN187 4.3 21.6 1.0
CB 2:ASP206 4.4 18.7 1.0
CB 2:HIS189 4.7 33.5 1.0
CG 2:GLU193 4.7 19.0 1.0
CG 2:GLU185 4.7 20.0 1.0
C 2:ASN205 4.7 18.3 1.0
CB 2:ASN187 4.7 22.8 1.0
N 2:ASP188 4.7 24.4 1.0
N 2:ILE207 4.7 19.8 1.0
N 2:HIS189 4.8 29.7 1.0
CB 2:GLU193 4.8 15.9 1.0
C4 2:FUC225 4.8 18.8 0.5
C1 2:FUC225 4.9 21.4 0.5
CB 2:ASN205 4.9 18.0 1.0
CA 2:ASN187 4.9 23.1 1.0

Calcium binding site 7 out of 10 in 2kmb

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Calcium binding site 7 out of 10 in the Complex of 3'-Neuac-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'-Neuac-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:25.2
occ:1.00
 OE1 2:GLU165 2.2 18.8 1.0
O 2:HOH232 2.3 30.7 1.0
O 2:HOH230 2.4 17.8 1.0
O 2:HOH231 2.4 23.0 1.0
O 2:HOH233 2.4 24.3 1.0
OD1 2:ASP194 2.6 19.4 1.0
OD2 2:ASP194 2.7 23.2 1.0
CG 2:ASP194 3.0 21.3 1.0
CD 2:GLU165 3.4 18.9 1.0
CA 2:CA1 3.8 17.7 1.0
OD1 2:ASP188 4.0 29.7 1.0
CB 2:GLU165 4.1 20.2 1.0
O 2:ASP161 4.1 23.9 1.0
CG 2:GLU165 4.2 18.6 1.0
OE2 2:GLU165 4.4 20.6 1.0
O 2:HOH258 4.4 30.9 1.0
CB 2:ASP194 4.5 19.1 1.0
CA 2:GLU165 4.5 18.1 1.0
OD2 2:ASP161 4.5 17.7 1.0
O 2:HOH234 4.6 41.3 1.0
OD2 2:ASP188 4.7 24.8 1.0
CG 2:ASP188 4.7 25.4 1.0
OD1 2:ASP161 4.7 15.4 1.0
O 2:HOH229 4.8 24.1 1.0
CG 2:ASP161 4.8 17.9 1.0

Calcium binding site 8 out of 10 in 2kmb

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Calcium binding site 8 out of 10 in the Complex of 3'-Neuac-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'-Neuac-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:13.8
occ:1.00
 O 3:HOH302 2.3 9.5 1.0
OD1 3:ASP194 2.4 15.9 1.0
O 3:GLU193 2.4 8.5 1.0
OD1 3:ASP188 2.4 14.7 1.0
OD2 3:ASP161 2.5 14.8 1.0
OE2 3:GLU165 2.5 9.2 1.0
OE1 3:GLU165 2.6 12.8 1.0
OD1 3:ASP161 2.8 15.4 1.0
CD 3:GLU165 2.9 10.7 1.0
CG 3:ASP161 3.0 14.5 1.0
CG 3:ASP188 3.3 11.3 1.0
C 3:GLU193 3.4 11.3 1.0
CG 3:ASP194 3.6 12.5 1.0
CB 3:ASP188 3.7 12.1 1.0
CA 3:ASP194 3.8 13.1 1.0
N 3:ASP194 4.0 10.9 1.0
CA 3:CA3 4.0 14.3 1.0
OD2 3:ASP188 4.2 8.9 1.0
CB 3:ASP194 4.3 10.6 1.0
CA 3:ASP188 4.3 11.1 1.0
N 3:GLU193 4.4 13.7 1.0
CZ 3:PHE168 4.4 14.7 1.0
CG 3:GLU165 4.4 11.8 1.0
O 3:HOH301 4.5 18.3 1.0
CA 3:GLU193 4.5 11.2 1.0
OD2 3:ASP206 4.5 14.3 1.0
CB 3:ASP161 4.5 12.6 1.0
OD2 3:ASP194 4.5 12.1 1.0
O 3:HOH300 4.7 14.2 1.0
N 3:GLY166 4.8 12.7 1.0
O 3:ASP161 4.8 12.7 1.0
CE1 3:PHE168 4.8 13.7 1.0
C 3:ASP194 5.0 12.8 1.0
N 3:ASP188 5.0 11.6 1.0

Calcium binding site 9 out of 10 in 2kmb

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Calcium binding site 9 out of 10 in the Complex of 3'-Neuac-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'-Neuac-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:15.3
occ:1.00
 OE1 3:GLU193 2.3 15.6 1.0
OD1 3:ASP206 2.4 12.4 1.0
OD1 3:ASN187 2.5 9.0 1.0
O3 3:FUC225 2.5 7.0 0.5
OD1 3:ASN205 2.5 18.5 1.0
O 3:ASP206 2.6 18.4 1.0
OE1 3:GLU185 2.6 19.4 1.0
O2 3:FUC225 2.9 9.5 0.5
CD 3:GLU193 3.3 13.1 1.0
CG 3:ASP206 3.4 11.3 1.0
C3 3:FUC225 3.4 13.8 0.5
CG 3:ASN187 3.5 11.1 1.0
C2 3:FUC225 3.5 15.2 0.5
CG 3:ASN205 3.5 19.9 1.0
CD 3:GLU185 3.6 18.9 1.0
OE2 3:GLU193 3.6 13.4 1.0
C 3:ASP206 3.6 15.7 1.0
N 3:ASP206 3.8 14.9 1.0
OE2 3:GLU185 3.9 18.7 1.0
ND2 3:ASN187 4.0 12.5 1.0
ND2 3:ASN205 4.0 17.2 1.0
OD2 3:ASP206 4.1 14.3 1.0
CA 3:ASP206 4.2 14.6 1.0
N 3:ASN187 4.2 11.6 1.0
CB 3:ASP206 4.4 10.9 1.0
CG 3:GLU193 4.6 8.7 1.0
C 3:ASN205 4.6 17.6 1.0
CB 3:HIS189 4.7 12.6 1.0
CB 3:ASN187 4.7 12.9 1.0
CG 3:GLU185 4.8 17.2 1.0
CB 3:GLU193 4.8 12.1 1.0
N 3:ASP188 4.8 11.6 1.0
N 3:HIS189 4.8 12.5 1.0
C4 3:FUC225 4.8 18.6 0.5
N 3:ILE207 4.8 15.1 1.0
CB 3:ASN205 4.8 16.5 1.0
CA 3:ASN187 4.8 11.4 1.0
CA 3:ASN205 4.9 19.7 1.0
C1 3:FUC225 5.0 20.9 0.5
O4 3:FUC225 5.0 23.1 0.5

Calcium binding site 10 out of 10 in 2kmb

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Calcium binding site 10 out of 10 in the Complex of 3'-Neuac-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'-Neuac-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:14.3
occ:1.00
 OE1 3:GLU165 2.3 12.8 1.0
O 3:HOH315 2.4 17.8 1.0
OD2 3:ASP194 2.5 12.1 1.0
OD1 3:ASP194 2.6 15.9 1.0
CG 3:ASP194 2.9 12.5 1.0
CD 3:GLU165 3.5 10.7 1.0
CA 3:CA1 4.0 13.8 1.0
CB 3:GLU165 4.2 13.2 1.0
OD1 3:ASP188 4.2 14.7 1.0
CG 3:GLU165 4.3 11.8 1.0
O 3:HOH318 4.3 11.4 1.0
O 3:ASP161 4.3 12.7 1.0
O 3:HOH316 4.3 25.5 1.0
CB 3:ASP194 4.4 10.6 1.0
OE2 3:GLU165 4.5 9.2 1.0
CA 3:GLU165 4.6 12.9 1.0
OD1 3:ASP161 4.9 15.4 1.0
CG 3:ASP188 4.9 11.3 1.0
OD2 3:ASP188 4.9 8.9 1.0
O 3:HOH314 4.9 56.7 1.0
OD2 3:ASP161 4.9 14.8 1.0
O 3:HOH313 5.0 22.1 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: Fri Jul 12 13:59:04 2024

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