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Calcium in PDB 1kwy: Rat Mannose Protein A Complexed with Man-A13-Man.

Protein crystallography data

The structure of Rat Mannose Protein A Complexed with Man-A13-Man., PDB code: 1kwy was solved by K.K.Ng, A.R.Kolatkar, S.Park-Snyder, H.Feinberg, D.A.Clark, K.Drickamer, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.860, 85.250, 98.130, 90.00, 107.34, 90.00
R / Rfree (%) 19.8 / 23.1

Other elements in 1kwy:

The structure of Rat Mannose Protein A Complexed with Man-A13-Man. also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Rat Mannose Protein A Complexed with Man-A13-Man. (pdb code 1kwy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Rat Mannose Protein A Complexed with Man-A13-Man., PDB code: 1kwy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 1kwy

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Calcium binding site 1 out of 10 in the Rat Mannose Protein A Complexed with Man-A13-Man.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rat Mannose Protein A Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:17.1
occ:1.00
 OD2 A:ASP161 2.3 17.0 1.0
O A:HOH626 2.4 14.7 1.0
OD2 A:ASP194 2.4 15.0 1.0
O A:GLU193 2.4 18.3 1.0
OD2 A:ASP188 2.5 19.6 1.0
OE2 A:GLU165 2.5 16.6 1.0
OE1 A:GLU165 2.6 15.7 1.0
OD1 A:ASP161 2.6 13.4 1.0
CG A:ASP161 2.8 16.3 1.0
CD A:GLU165 2.9 16.9 1.0
CG A:ASP188 3.3 19.7 1.0
C A:GLU193 3.3 18.5 1.0
CG A:ASP194 3.5 16.3 1.0
CA A:ASP194 3.7 15.8 1.0
CB A:ASP188 3.8 20.2 1.0
N A:ASP194 3.9 16.6 1.0
CA A:CA505 3.9 17.6 1.0
O A:HOH686 4.0 21.2 1.0
OD1 A:ASP188 4.2 20.3 1.0
CB A:ASP194 4.2 17.2 1.0
N A:GLU193 4.3 18.0 1.0
CB A:ASP161 4.3 15.1 1.0
CA A:ASP188 4.4 20.2 1.0
CG A:GLU165 4.4 16.3 1.0
CA A:GLU193 4.4 17.4 1.0
OD1 A:ASP194 4.5 15.5 1.0
CZ A:PHE168 4.6 13.4 1.0
N A:GLY166 4.6 18.8 1.0
O A:HOH652 4.7 18.5 1.0
O A:ASP161 4.7 18.8 1.0
O A:HOH625 4.7 21.5 1.0
OD1 A:ASP206 4.7 16.5 1.0
CA A:GLU165 4.9 17.5 1.0
C A:ASP194 5.0 16.7 1.0

Calcium binding site 2 out of 10 in 1kwy

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Calcium binding site 2 out of 10 in the Rat Mannose Protein A Complexed with Man-A13-Man.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rat Mannose Protein A Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:20.3
occ:1.00
 OD2 A:ASP206 2.3 16.2 1.0
OD1 A:ASN205 2.4 17.2 1.0
OE2 A:GLU193 2.5 22.2 1.0
OD1 A:ASN187 2.5 18.2 1.0
OE2 A:GLU185 2.5 16.7 1.0
O3 A:MAN502 2.5 25.5 1.0
O A:ASP206 2.6 16.3 1.0
O4 A:MAN502 2.7 27.0 1.0
CD A:GLU185 3.3 23.3 1.0
CG A:ASP206 3.4 19.5 1.0
CG A:ASN205 3.4 18.6 1.0
C3 A:MAN502 3.4 29.1 1.0
C4 A:MAN502 3.5 27.0 1.0
CD A:GLU193 3.5 19.9 1.0
CG A:ASN187 3.5 19.7 1.0
OE1 A:GLU185 3.6 20.7 1.0
C A:ASP206 3.6 18.2 1.0
N A:ASP206 3.7 19.3 1.0
ND2 A:ASN205 3.8 17.7 1.0
OE1 A:GLU193 3.8 20.5 1.0
ND2 A:ASN187 4.0 19.3 1.0
CA A:ASP206 4.1 17.7 1.0
OD1 A:ASP206 4.1 16.5 1.0
N A:ASN187 4.2 20.5 1.0
CB A:ASP206 4.3 19.0 1.0
C A:ASN205 4.5 18.7 1.0
CB A:HIS189 4.6 28.1 1.0
CG A:GLU185 4.6 20.7 1.0
CB A:ASN205 4.7 17.5 1.0
CB A:ASN187 4.7 18.5 1.0
N A:ILE207 4.8 17.9 1.0
CG A:GLU193 4.8 20.0 1.0
N A:HIS189 4.8 22.9 1.0
N A:ASP188 4.8 19.8 1.0
C2 A:MAN502 4.8 32.2 1.0
CA A:ASN205 4.8 17.8 1.0
CA A:ASN187 4.9 20.8 1.0
C5 A:MAN502 4.9 33.2 1.0
CB A:GLU193 4.9 16.0 1.0

Calcium binding site 3 out of 10 in 1kwy

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Calcium binding site 3 out of 10 in the Rat Mannose Protein A Complexed with Man-A13-Man.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Rat Mannose Protein A Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:17.6
occ:1.00
 O A:HOH686 2.2 21.2 1.0
OE1 A:GLU165 2.2 15.7 1.0
OD1 A:ASP194 2.5 15.5 1.0
OD2 A:ASP194 2.6 15.0 1.0
CG A:ASP194 2.9 16.3 1.0
CD A:GLU165 3.4 16.9 1.0
CA A:CA503 3.9 17.1 1.0
CB A:GLU165 4.0 18.6 1.0
CG A:GLU165 4.1 16.3 1.0
O A:HOH687 4.2 15.9 1.0
OD2 A:ASP188 4.2 19.6 1.0
O A:ASP161 4.3 18.8 1.0
CB A:ASP194 4.4 17.2 1.0
OE2 A:GLU165 4.4 16.6 1.0
CA A:GLU165 4.5 17.5 1.0
O A:HOH685 4.5 31.1 1.0
O A:HOH620 4.6 28.6 1.0
OD2 A:ASP161 4.8 17.0 1.0
OD1 A:ASP188 4.9 20.3 1.0
CG A:ASP188 4.9 19.7 1.0
OD1 A:ASP161 4.9 13.4 1.0
N A:GLU165 5.0 16.4 1.0

Calcium binding site 4 out of 10 in 1kwy

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Calcium binding site 4 out of 10 in the Rat Mannose Protein A Complexed with Man-A13-Man.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Rat Mannose Protein A Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca606

b:77.8
occ:1.00
 O A:HOH711 2.4 29.6 1.0
O A:HOH715 2.7 33.7 1.0
O A:ASN187 4.4 22.6 1.0

Calcium binding site 5 out of 10 in 1kwy

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Calcium binding site 5 out of 10 in the Rat Mannose Protein A Complexed with Man-A13-Man.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Rat Mannose Protein A Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:20.1
occ:1.00
 O B:HOH625 2.3 20.3 1.0
OD2 B:ASP194 2.3 17.9 1.0
OD2 B:ASP161 2.4 22.2 1.0
O B:GLU193 2.4 21.4 1.0
OE2 B:GLU165 2.4 17.2 1.0
OE1 B:GLU165 2.6 19.5 1.0
OD1 B:ASP161 2.7 16.5 1.0
OD2 B:ASP188 2.8 28.2 1.0
CD B:GLU165 2.9 22.8 1.0
CG B:ASP161 2.9 22.9 1.0
C B:GLU193 3.3 22.6 1.0
CG B:ASP188 3.5 28.9 1.0
CG B:ASP194 3.5 20.3 1.0
CA B:ASP194 3.7 21.5 1.0
CA B:CA605 3.8 23.9 1.0
N B:ASP194 3.9 21.6 1.0
CB B:ASP188 4.0 25.5 1.0
O B:HOH624 4.0 22.3 1.0
O B:HOH647 4.0 22.5 1.0
CB B:ASP194 4.2 21.3 1.0
OD1 B:ASP188 4.3 27.0 1.0
N B:GLU193 4.3 23.7 1.0
CG B:GLU165 4.4 22.1 1.0
CB B:ASP161 4.4 20.5 1.0
CA B:GLU193 4.4 23.8 1.0
CA B:ASP188 4.4 27.4 1.0
OD1 B:ASP194 4.4 20.8 1.0
CZ B:PHE168 4.6 18.3 1.0
OD1 B:ASP206 4.6 23.3 1.0
O B:ASP161 4.8 22.6 1.0
N B:GLY166 4.8 21.7 1.0
C B:ASP194 4.9 21.8 1.0

Calcium binding site 6 out of 10 in 1kwy

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Calcium binding site 6 out of 10 in the Rat Mannose Protein A Complexed with Man-A13-Man.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Rat Mannose Protein A Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:26.3
occ:1.00
 OE2 B:GLU193 2.2 24.8 1.0
OD2 B:ASP206 2.4 23.5 1.0
OD1 B:ASN187 2.4 31.7 1.0
O4 B:MAN602 2.4 33.5 1.0
O B:ASP206 2.5 21.0 1.0
OD1 B:ASN205 2.6 25.8 1.0
O3 B:MAN602 2.6 33.9 1.0
OE2 B:GLU185 2.6 21.9 1.0
CD B:GLU193 3.3 26.4 1.0
C3 B:MAN602 3.3 37.0 1.0
C4 B:MAN602 3.3 38.4 1.0
CG B:ASP206 3.4 24.8 1.0
CD B:GLU185 3.4 24.8 1.0
CG B:ASN205 3.5 24.4 1.0
C B:ASP206 3.5 24.2 1.0
CG B:ASN187 3.5 30.8 1.0
OE1 B:GLU185 3.6 23.6 1.0
OE1 B:GLU193 3.6 28.9 1.0
N B:ASP206 3.8 22.2 1.0
ND2 B:ASN205 3.9 23.8 1.0
CA B:ASP206 4.1 23.1 1.0
ND2 B:ASN187 4.1 32.1 1.0
OD1 B:ASP206 4.1 23.3 1.0
CB B:ASP206 4.3 23.1 1.0
N B:ASN187 4.3 26.3 1.0
CB B:HIS189 4.4 38.2 1.0
CG B:GLU193 4.6 25.2 1.0
C B:ASN205 4.6 24.4 1.0
N B:ILE207 4.6 25.3 1.0
C5 B:MAN602 4.7 39.4 1.0
CG B:GLU185 4.7 22.5 1.0
CB B:ASN187 4.7 27.0 1.0
C2 B:MAN602 4.7 39.0 1.0
N B:HIS189 4.7 32.4 1.0
CB B:GLU193 4.8 24.6 1.0
CB B:ASN205 4.8 24.5 1.0
N B:ASP188 4.8 26.8 1.0
CA B:ASN187 4.9 27.6 1.0
CA B:ASN205 4.9 24.8 1.0
CA B:ILE207 5.0 24.6 1.0

Calcium binding site 7 out of 10 in 1kwy

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Calcium binding site 7 out of 10 in the Rat Mannose Protein A Complexed with Man-A13-Man.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Rat Mannose Protein A Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca605

b:23.9
occ:1.00
 O B:HOH630 2.3 21.7 1.0
OE1 B:GLU165 2.3 19.5 1.0
O B:HOH666 2.3 26.6 1.0
O B:HOH680 2.4 26.9 1.0
OD1 B:ASP194 2.5 20.8 1.0
O B:HOH647 2.5 22.5 1.0
OD2 B:ASP194 2.5 17.9 1.0
CG B:ASP194 2.8 20.3 1.0
CD B:GLU165 3.5 22.8 1.0
CA B:CA603 3.8 20.1 1.0
O B:ASP161 4.1 22.6 1.0
OD2 B:ASP188 4.1 28.2 1.0
CB B:GLU165 4.2 20.4 1.0
O B:HOH722 4.3 35.0 1.0
CB B:ASP194 4.3 21.3 1.0
CG B:GLU165 4.3 22.1 1.0
OE2 B:GLU165 4.4 17.2 1.0
O B:HOH713 4.5 32.4 1.0
O B:HOH667 4.5 43.8 1.0
CA B:GLU165 4.6 21.7 1.0
OD2 B:ASP161 4.6 22.2 1.0
OD1 B:ASP188 4.6 27.0 1.0
OD1 B:ASP161 4.7 16.5 1.0
O B:HOH668 4.7 34.2 1.0
CG B:ASP188 4.8 28.9 1.0
CG B:ASP161 4.8 22.9 1.0
O B:HOH650 4.9 30.7 1.0

Calcium binding site 8 out of 10 in 1kwy

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Calcium binding site 8 out of 10 in the Rat Mannose Protein A Complexed with Man-A13-Man.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Rat Mannose Protein A Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:22.4
occ:1.00
 O C:HOH726 2.3 17.1 1.0
O C:GLU193 2.3 18.6 1.0
OD2 C:ASP194 2.4 16.3 1.0
OD2 C:ASP161 2.4 26.6 1.0
OD2 C:ASP188 2.5 18.3 1.0
OE1 C:GLU165 2.5 23.2 1.0
OE2 C:GLU165 2.6 23.2 1.0
OD1 C:ASP161 2.7 22.6 1.0
CG C:ASP161 2.9 26.1 1.0
CD C:GLU165 2.9 22.7 1.0
C C:GLU193 3.3 21.0 1.0
CG C:ASP188 3.4 21.3 1.0
CG C:ASP194 3.5 19.4 1.0
CA C:ASP194 3.7 19.9 1.0
CB C:ASP188 3.8 21.1 1.0
N C:ASP194 3.9 19.8 1.0
O C:HOH720 3.9 21.2 1.0
CA C:CA705 4.0 22.9 1.0
CB C:ASP194 4.2 18.6 1.0
N C:GLU193 4.3 23.1 1.0
OD1 C:ASP188 4.3 21.3 1.0
CA C:ASP188 4.3 22.1 1.0
CA C:GLU193 4.4 21.6 1.0
CB C:ASP161 4.4 25.1 1.0
CG C:GLU165 4.4 21.7 1.0
CZ C:PHE168 4.4 23.9 1.0
OD1 C:ASP194 4.5 17.3 1.0
OD1 C:ASP206 4.6 24.4 1.0
N C:GLY166 4.7 24.9 1.0
O C:HOH725 4.7 24.5 1.0
O C:HOH766 4.8 24.5 1.0
O C:ASP161 4.8 25.2 1.0
CA C:GLU165 4.9 24.7 1.0
C C:ASP194 4.9 20.3 1.0
N C:ASP188 5.0 22.8 1.0
CE1 C:PHE168 5.0 21.4 1.0

Calcium binding site 9 out of 10 in 1kwy

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Calcium binding site 9 out of 10 in the Rat Mannose Protein A Complexed with Man-A13-Man.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Rat Mannose Protein A Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca704

b:21.8
occ:1.00
 OD2 C:ASP206 2.1 22.7 1.0
OE2 C:GLU193 2.4 25.3 1.0
OD1 C:ASN205 2.4 23.1 1.0
OD1 C:ASN187 2.5 19.5 1.0
OE2 C:GLU185 2.5 27.6 1.0
O4 C:MAN702 2.5 31.7 1.0
O C:ASP206 2.5 20.8 1.0
O3 C:MAN702 2.7 28.5 1.0
CG C:ASP206 3.2 23.4 1.0
CD C:GLU193 3.4 23.2 1.0
CD C:GLU185 3.4 28.3 1.0
CG C:ASN205 3.4 26.3 1.0
C3 C:MAN702 3.4 35.0 1.0
C4 C:MAN702 3.4 36.8 1.0
CG C:ASN187 3.5 19.9 1.0
C C:ASP206 3.6 23.7 1.0
OE1 C:GLU185 3.6 25.3 1.0
N C:ASP206 3.7 22.6 1.0
OE1 C:GLU193 3.7 24.8 1.0
ND2 C:ASN205 3.8 24.5 1.0
CA C:ASP206 4.0 22.2 1.0
OD1 C:ASP206 4.0 24.4 1.0
ND2 C:ASN187 4.0 18.9 1.0
N C:ASN187 4.1 24.6 1.0
CB C:ASP206 4.2 22.6 1.0
C C:ASN205 4.5 25.2 1.0
CB C:HIS189 4.6 24.6 1.0
CG C:GLU193 4.7 22.5 1.0
CG C:GLU185 4.7 26.2 1.0
CB C:ASN187 4.7 23.4 1.0
CB C:ASN205 4.7 24.4 1.0
N C:ILE207 4.7 23.4 1.0
N C:HIS189 4.8 24.4 1.0
C5 C:MAN702 4.8 39.4 1.0
N C:ASP188 4.8 22.8 1.0
CA C:ASN187 4.8 23.4 1.0
CA C:ASN205 4.8 25.4 1.0
CB C:GLU193 4.8 23.5 1.0
C2 C:MAN702 4.9 38.2 1.0

Calcium binding site 10 out of 10 in 1kwy

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Calcium binding site 10 out of 10 in the Rat Mannose Protein A Complexed with Man-A13-Man.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Rat Mannose Protein A Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca705

b:22.9
occ:1.00
 O C:HOH719 2.4 18.5 1.0
O C:HOH720 2.4 21.2 1.0
OE1 C:GLU165 2.4 23.2 1.0
OD1 C:ASP194 2.5 17.3 1.0
OD2 C:ASP194 2.6 16.3 1.0
O C:HOH742 2.6 26.4 1.0
CG C:ASP194 2.9 19.4 1.0
CD C:GLU165 3.6 22.7 1.0
CA C:CA703 4.0 22.4 1.0
CB C:GLU165 4.1 24.4 1.0
OD2 C:ASP188 4.2 18.3 1.0
CG C:GLU165 4.3 21.7 1.0
O C:HOH791 4.3 28.3 1.0
CB C:ASP194 4.4 18.6 1.0
O C:HOH768 4.4 20.5 1.0
O C:ASP161 4.4 25.2 1.0
CA C:GLU165 4.5 24.7 1.0
OE2 C:GLU165 4.6 23.2 1.0
O C:HOH767 4.6 30.1 1.0
OD2 C:ASP161 4.7 26.6 1.0
O C:HOH800 4.8 47.4 1.0
OD1 C:ASP161 4.9 22.6 1.0
CG C:ASP188 4.9 21.3 1.0
OD1 C:ASP188 4.9 21.3 1.0

Reference:

K.K.Ng, A.R.Kolatkar, S.Park-Snyder, H.Feinberg, D.A.Clark, K.Drickamer, W.I.Weis. Orientation of Bound Ligands in Mannose-Binding Proteins. Implications For Multivalent Ligand Recognition. J.Biol.Chem. V. 277 16088 2002.
ISSN: ISSN 0021-9258
PubMed: 11850428
DOI: 10.1074/JBC.M200493200
Page generated: Thu Jul 11 11:37:01 2024

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