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Calcium in PDB 1kmb: Selectin-Like Mutant of Mannose-Binding Protein A

Protein crystallography data

The structure of Selectin-Like Mutant of Mannose-Binding Protein A, PDB code: 1kmb 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 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 79.700, 84.900, 98.700, 90.00, 105.30, 90.00
R / Rfree (%) 20.2 / 26.5

Other elements in 1kmb:

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

Calcium binding site 1 out of 9 in 1kmb

Go back to Calcium Binding Sites List in 1kmb
Calcium binding site 1 out of 9 in the 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 Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca1

b:13.4
occ:1.00
O 1:HOH365 2.3 14.2 1.0
OD1 1:ASP194 2.3 16.7 1.0
OD2 1:ASP161 2.4 14.1 1.0
OD1 1:ASP188 2.4 18.4 1.0
O 1:GLU193 2.4 13.2 1.0
OE2 1:GLU165 2.5 15.3 1.0
OD1 1:ASP161 2.6 9.7 1.0
OE1 1:GLU165 2.6 19.2 1.0
CG 1:ASP161 2.8 9.2 1.0
CD 1:GLU165 2.9 16.8 1.0
CG 1:ASP188 3.3 16.5 1.0
C 1:GLU193 3.4 11.5 1.0
CG 1:ASP194 3.5 12.7 1.0
CB 1:ASP188 3.8 14.7 1.0
CA 1:ASP194 3.8 13.4 1.0
N 1:ASP194 4.0 10.5 1.0
O 1:HOH366 4.0 13.4 1.0
CA 1:CA3 4.1 13.2 1.0
CB 1:ASP194 4.2 12.4 1.0
OD2 1:ASP188 4.3 14.3 1.0
CB 1:ASP161 4.3 9.7 1.0
N 1:GLU193 4.3 16.0 1.0
CA 1:ASP188 4.4 14.5 1.0
CG 1:GLU165 4.4 18.7 1.0
OD2 1:ASP194 4.4 11.8 1.0
CA 1:GLU193 4.5 15.5 1.0
OD2 1:ASP206 4.6 13.7 1.0
CZ 1:PHE168 4.6 12.8 1.0
O 1:ASP161 4.7 12.9 1.0
O 1:HOH362 4.7 18.4 1.0
O 1:HOH363 4.8 16.3 1.0
N 1:GLY166 4.8 12.6 1.0
O 1:HOH373 4.9 7.3 1.0
C 1:ASP194 4.9 12.5 1.0

Calcium binding site 2 out of 9 in 1kmb

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Calcium binding site 2 out of 9 in the 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 Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca2

b:20.7
occ:1.00
OE1 1:GLU185 2.2 28.2 1.0
OD1 1:ASP206 2.2 17.6 1.0
OD1 1:ASN187 2.4 23.3 1.0
OE1 1:GLU193 2.6 13.6 1.0
OD1 1:ASN205 2.6 10.3 0.5
O 1:ASP206 2.6 20.1 1.0
O 1:HOH356 2.9 33.2 1.0
CD 1:GLU185 3.3 24.7 1.0
CG 1:ASP206 3.3 15.1 1.0
CG 1:ASN187 3.4 20.2 1.0
O 1:HOH355 3.5 45.6 1.0
CD 1:GLU193 3.5 12.9 1.0
C 1:ASP206 3.7 16.2 1.0
OE2 1:GLU185 3.7 26.6 1.0
CG 1:ASN205 3.7 9.9 0.5
N 1:ASP206 3.8 12.8 1.0
OE2 1:GLU193 3.9 12.2 1.0
ND2 1:ASN187 3.9 20.6 1.0
OD2 1:ASP206 4.0 13.7 1.0
CA 1:ASP206 4.1 13.0 1.0
N 1:ASN187 4.2 18.5 1.0
ND2 1:ASN205 4.3 13.6 0.5
CB 1:ASP206 4.3 11.9 1.0
CG 1:GLU185 4.5 22.1 1.0
C 1:ASN205 4.6 12.1 1.0
CB 1:HIS189 4.6 20.0 1.0
CB 1:ASN187 4.7 18.9 1.0
CG 1:GLU193 4.7 12.8 1.0
N 1:ASP188 4.8 18.0 1.0
N 1:HIS189 4.8 16.6 1.0
CB 1:GLU193 4.8 14.9 1.0
N 1:ILE207 4.8 15.7 1.0
CA 1:ASN187 4.9 20.0 1.0
CB 1:GLU185 4.9 20.2 1.0
CB 1:ASN205 4.9 16.8 1.0
CA 1:ASN205 5.0 15.4 1.0

Calcium binding site 3 out of 9 in 1kmb

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Calcium binding site 3 out of 9 in the 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 Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca3

b:13.2
occ:1.00
O 1:HOH372 2.2 20.0 1.0
O 1:HOH373 2.3 7.3 1.0
OE1 1:GLU165 2.4 19.2 1.0
OD2 1:ASP194 2.4 11.8 1.0
O 1:HOH366 2.4 13.4 1.0
OD1 1:ASP194 2.7 16.7 1.0
CG 1:ASP194 2.9 12.7 1.0
CD 1:GLU165 3.6 16.8 1.0
CA 1:CA1 4.1 13.4 1.0
OD1 1:ASP188 4.1 18.4 1.0
CB 1:GLU165 4.2 15.8 1.0
CG 1:GLU165 4.3 18.7 1.0
O 1:HOH367 4.3 9.8 1.0
O 1:ASP161 4.4 12.9 1.0
CB 1:ASP194 4.4 12.4 1.0
O 1:HOH371 4.5 20.0 1.0
OE2 1:GLU165 4.5 15.3 1.0
CA 1:GLU165 4.7 16.4 1.0
OD2 1:ASP188 4.9 14.3 1.0
CG 1:ASP188 4.9 16.5 1.0
O 1:HOH369 5.0 26.8 1.0
OD2 1:ASP161 5.0 14.1 1.0
OD1 1:ASP161 5.0 9.7 1.0

Calcium binding site 4 out of 9 in 1kmb

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Calcium binding site 4 out of 9 in the 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 Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca1

b:34.8
occ:1.00
OD2 2:ASP161 2.3 32.3 1.0
OD1 2:ASP188 2.5 35.6 1.0
O 2:HOH258 2.5 26.0 1.0
OD1 2:ASP161 2.6 27.9 1.0
OE1 2:GLU165 2.7 39.9 1.0
O 2:GLU193 2.7 28.6 1.0
OD1 2:ASP194 2.7 34.5 1.0
CG 2:ASP161 2.8 34.0 1.0
OE2 2:GLU165 2.9 45.2 1.0
CD 2:GLU165 3.1 43.8 1.0
CG 2:ASP188 3.4 36.1 1.0
C 2:GLU193 3.5 29.9 1.0
CA 2:CA3 3.8 48.1 1.0
CA 2:ASP194 3.9 27.5 1.0
CG 2:ASP194 3.9 34.7 1.0
CB 2:ASP188 3.9 36.0 1.0
N 2:ASP194 4.0 28.3 1.0
O 2:HOH259 4.1 43.1 1.0
O 2:HOH255 4.2 20.3 1.0
OD2 2:ASP188 4.3 37.2 1.0
CZ 2:PHE168 4.3 30.1 1.0
CB 2:ASP161 4.3 33.4 1.0
N 2:GLU193 4.4 35.7 1.0
CB 2:ASP194 4.4 29.1 1.0
OD2 2:ASP206 4.5 18.9 1.0
CA 2:GLU193 4.6 31.4 1.0
CA 2:ASP188 4.6 37.1 1.0
CG 2:GLU165 4.6 45.1 1.0
O 2:ASP161 4.8 38.9 1.0
OD2 2:ASP194 4.9 37.7 1.0
N 2:GLY166 4.9 42.4 1.0
CE2 2:PHE168 4.9 30.0 1.0
CE1 2:PHE168 4.9 31.4 1.0
C 2:ASP194 5.0 26.0 1.0
CA 2:GLU165 5.0 46.0 1.0

Calcium binding site 5 out of 9 in 1kmb

Go back to Calcium Binding Sites List in 1kmb
Calcium binding site 5 out of 9 in the 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 Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca2

b:40.1
occ:1.00
OE1 2:GLU193 2.2 32.0 1.0
OD1 2:ASN187 2.4 35.9 1.0
OD1 2:ASP206 2.5 26.1 1.0
OE1 2:GLU185 2.6 35.5 1.0
O 2:ASP206 2.7 26.2 1.0
OD1 2:ASN205 2.9 40.7 1.0
O 2:HOH265 3.0 31.4 1.0
CD 2:GLU193 3.2 31.1 1.0
CG 2:ASN187 3.3 35.0 1.0
CG 2:ASP206 3.5 29.1 1.0
CD 2:GLU185 3.5 33.9 1.0
OE2 2:GLU193 3.6 32.4 1.0
C 2:ASP206 3.7 28.6 1.0
ND2 2:ASN187 3.8 37.2 1.0
OE2 2:GLU185 3.8 36.9 1.0
CG 2:ASN205 3.8 34.7 1.0
N 2:ASP206 3.9 30.5 1.0
OD2 2:ASP206 4.1 18.9 1.0
ND2 2:ASN205 4.2 38.3 1.0
CA 2:ASP206 4.2 28.4 1.0
N 2:ASN187 4.3 30.7 1.0
CB 2:ASP206 4.5 28.6 1.0
CG 2:GLU193 4.5 30.1 1.0
CB 2:ASN187 4.5 32.3 1.0
CB 2:HIS189 4.5 45.5 1.0
N 2:ASP188 4.6 36.4 1.0
N 2:HIS189 4.6 39.5 1.0
CB 2:GLU193 4.7 28.4 1.0
C 2:ASN205 4.7 31.7 1.0
CA 2:ASN187 4.8 33.4 1.0
N 2:ILE207 4.9 29.2 1.0
CG 2:GLU185 4.9 30.9 1.0
C 2:ASN187 5.0 35.1 1.0

Calcium binding site 6 out of 9 in 1kmb

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Calcium binding site 6 out of 9 in the 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 Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca3

b:48.1
occ:1.00
OE1 2:GLU165 2.4 39.9 1.0
OD1 2:ASP194 2.5 34.5 1.0
O 2:HOH259 2.9 43.1 1.0
CG 2:ASP194 3.3 34.7 1.0
OD2 2:ASP194 3.3 37.7 1.0
CD 2:GLU165 3.6 43.8 1.0
CA 2:CA1 3.8 34.8 1.0
O 2:ASP161 3.8 38.9 1.0
CB 2:GLU165 4.0 45.9 1.0
OD2 2:ASP161 4.2 32.3 1.0
CA 2:GLU165 4.2 46.0 1.0
CG 2:GLU165 4.3 45.1 1.0
OD1 2:ASP188 4.3 35.6 1.0
OD1 2:ASP161 4.4 27.9 1.0
CG 2:ASP161 4.5 34.0 1.0
OE2 2:GLU165 4.5 45.2 1.0
C 2:ASP161 4.7 39.6 1.0
N 2:GLU165 4.7 47.9 1.0
CB 2:ASP194 4.7 29.1 1.0
CA 2:GLU162 4.8 50.4 1.0
O 2:GLU162 4.8 56.8 1.0
O 2:HOH261 4.9 42.8 1.0
OD2 2:ASP188 4.9 37.2 1.0
CG 2:ASP188 5.0 36.1 1.0

Calcium binding site 7 out of 9 in 1kmb

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Calcium binding site 7 out of 9 in the 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 Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca1

b:18.5
occ:1.00
O 3:GLU193 2.4 12.9 1.0
OD1 3:ASP188 2.4 11.9 1.0
OD1 3:ASP194 2.5 15.1 1.0
O 3:HOH294 2.5 21.5 1.0
OD2 3:ASP161 2.6 20.8 1.0
OE1 3:GLU165 2.6 16.9 1.0
OE2 3:GLU165 2.7 13.6 1.0
OD1 3:ASP161 2.7 21.0 1.0
CD 3:GLU165 3.0 12.3 1.0
CG 3:ASP161 3.0 17.0 1.0
CG 3:ASP188 3.3 13.5 1.0
C 3:GLU193 3.3 11.5 1.0
CG 3:ASP194 3.6 11.6 1.0
CB 3:ASP188 3.7 13.0 1.0
CA 3:ASP194 3.8 13.6 1.0
N 3:ASP194 3.9 12.2 1.0
CA 3:CA3 4.0 17.6 1.0
OD2 3:ASP188 4.3 13.6 1.0
CB 3:ASP194 4.3 10.9 1.0
CA 3:ASP188 4.3 14.7 1.0
N 3:GLU193 4.3 14.9 1.0
CA 3:GLU193 4.4 13.8 1.0
OD2 3:ASP206 4.4 17.3 1.0
CZ 3:PHE168 4.5 10.1 1.0
CB 3:ASP161 4.5 18.8 1.0
OD2 3:ASP194 4.5 12.8 1.0
CG 3:GLU165 4.5 10.5 1.0
O 3:HOH293 4.6 21.7 1.0
N 3:GLY166 4.8 22.5 1.0
O 3:HOH292 4.8 22.0 1.0
O 3:ASP161 4.8 18.4 1.0
N 3:ASP188 4.9 12.3 1.0
C 3:ASP194 5.0 13.7 1.0

Calcium binding site 8 out of 9 in 1kmb

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Calcium binding site 8 out of 9 in the 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 Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca2

b:24.1
occ:1.00
OD1 3:ASP206 2.3 15.3 1.0
OE1 3:GLU185 2.4 30.2 1.0
OE1 3:GLU193 2.4 18.4 1.0
OD1 3:ASN187 2.5 17.2 1.0
O 3:ASP206 2.6 15.5 1.0
OD1 3:ASN205 2.7 36.2 1.0
O 3:HOH287 2.9 27.1 1.0
O 3:HOH286 3.0 23.1 1.0
CG 3:ASP206 3.4 14.2 1.0
CG 3:ASN187 3.4 14.4 1.0
CD 3:GLU193 3.4 11.1 1.0
CD 3:GLU185 3.5 33.1 1.0
C 3:ASP206 3.7 16.3 1.0
CG 3:ASN205 3.7 35.1 1.0
ND2 3:ASN187 3.8 16.4 1.0
OE2 3:GLU193 3.8 17.5 1.0
N 3:ASP206 3.8 19.8 1.0
OE2 3:GLU185 3.9 35.1 1.0
OD2 3:ASP206 4.1 17.3 1.0
CA 3:ASP206 4.2 16.4 1.0
ND2 3:ASN205 4.2 36.8 1.0
N 3:ASN187 4.2 14.8 1.0
CB 3:ASP206 4.4 15.9 1.0
CB 3:HIS189 4.5 11.7 1.0
C 3:ASN205 4.7 23.2 1.0
CG 3:GLU193 4.7 9.7 1.0
CG 3:GLU185 4.7 29.5 1.0
CB 3:ASN187 4.7 14.6 1.0
N 3:HIS189 4.7 15.3 1.0
N 3:ASP188 4.8 12.3 1.0
CB 3:GLU193 4.8 10.5 1.0
CA 3:ASN187 4.9 12.1 1.0
N 3:ILE207 4.9 16.3 1.0
CB 3:ASN205 5.0 31.1 1.0
CA 3:ASN205 5.0 28.0 1.0

Calcium binding site 9 out of 9 in 1kmb

Go back to Calcium Binding Sites List in 1kmb
Calcium binding site 9 out of 9 in the 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 Selectin-Like Mutant of Mannose-Binding Protein A within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca3

b:17.6
occ:1.00
OE1 3:GLU165 2.4 16.9 1.0
OD1 3:ASP194 2.6 15.1 1.0
OD2 3:ASP194 2.6 12.8 1.0
O 3:HOH350 2.7 37.5 1.0
CG 3:ASP194 3.0 11.6 1.0
CD 3:GLU165 3.6 12.3 1.0
CA 3:CA1 4.0 18.5 1.0
OD1 3:ASP188 4.1 11.9 1.0
CB 3:GLU165 4.2 16.8 1.0
O 3:ASP161 4.3 18.4 1.0
CG 3:GLU165 4.3 10.5 1.0
O 3:HOH349 4.3 21.9 1.0
O 3:HOH352 4.5 16.5 1.0
CB 3:ASP194 4.5 10.9 1.0
CA 3:GLU165 4.5 19.6 1.0
OE2 3:GLU165 4.5 13.6 1.0
CG 3:ASP188 4.9 13.5 1.0
OD1 3:ASP161 4.9 21.0 1.0
O 3:HOH353 4.9 20.0 1.0
OD2 3:ASP188 4.9 13.6 1.0
N 3:GLU165 5.0 19.3 1.0
OD2 3:ASP161 5.0 20.8 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 03:03:58 2020

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