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Calcium in PDB 1kwx: Rat Mannose Protein A Complexed with B-Me-Fuc.

Protein crystallography data

The structure of Rat Mannose Protein A Complexed with B-Me-Fuc., PDB code: 1kwx 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 (°) 78.480, 85.430, 97.800, 90.00, 107.37, 90.00
R / Rfree (%) 20 / 22.9

Other elements in 1kwx:

The structure of Rat Mannose Protein A Complexed with B-Me-Fuc. 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 B-Me-Fuc. (pdb code 1kwx). 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 B-Me-Fuc., PDB code: 1kwx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 1kwx

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Calcium binding site 1 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:16.6
occ:1.00
 OD2 A:ASP188 1.9 25.3 1.0
OE1 A:GLU165 2.2 16.2 1.0
OE2 A:GLU165 2.2 15.8 1.0
OD2 A:ASP194 2.4 16.7 1.0
CD A:GLU165 2.5 16.9 1.0
O A:HOH625 2.6 14.7 1.0
O A:GLU193 2.6 14.0 1.0
OD2 A:ASP161 2.7 16.0 1.0
CG A:ASP188 2.8 24.6 1.0
OD1 A:ASP161 3.1 13.4 1.0
CG A:ASP161 3.3 16.2 1.0
CB A:ASP188 3.5 19.9 1.0
C A:GLU193 3.5 17.2 1.0
O A:HOH694 3.6 18.9 1.0
CG A:ASP194 3.6 15.0 1.0
OD1 A:ASP188 3.6 22.6 1.0
CA A:CA504 3.7 17.6 1.0
CG A:GLU165 4.1 16.2 1.0
N A:GLU193 4.1 15.2 1.0
CA A:ASP194 4.1 14.5 1.0
N A:ASP194 4.1 14.1 1.0
CA A:ASP188 4.2 21.5 1.0
CA A:GLU193 4.4 16.0 1.0
OD1 A:ASP194 4.4 12.7 1.0
CB A:ASP194 4.4 16.8 1.0
O A:HOH624 4.6 17.1 1.0
N A:GLY166 4.7 16.7 1.0
O A:HOH655 4.8 23.6 1.0
CB A:ASP161 4.8 14.4 1.0
CB A:GLU165 4.8 17.9 1.0
OD1 A:ASP206 4.9 15.5 1.0
CA A:GLU165 4.9 18.0 1.0
N A:ASP188 5.0 23.0 1.0

Calcium binding site 2 out of 10 in 1kwx

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Calcium binding site 2 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:20.2
occ:1.00
 OD1 A:ASN187 2.3 22.0 1.0
O2 A:MFB501 2.4 22.1 1.0
OD2 A:ASP206 2.4 17.8 1.0
OE2 A:GLU185 2.5 19.6 1.0
OE2 A:GLU193 2.5 21.1 1.0
OD1 A:ASN205 2.5 18.1 1.0
O3 A:MFB501 2.6 24.8 1.0
O A:ASP206 2.7 16.1 1.0
C2 A:MFB501 3.3 24.6 1.0
CD A:GLU185 3.3 20.7 1.0
C3 A:MFB501 3.3 25.1 1.0
CG A:ASN187 3.4 23.4 1.0
OE1 A:GLU185 3.4 19.1 1.0
CG A:ASP206 3.5 19.0 1.0
CD A:GLU193 3.5 19.0 1.0
CG A:ASN205 3.6 17.4 1.0
C A:ASP206 3.8 18.8 1.0
OE1 A:GLU193 3.8 19.4 1.0
ND2 A:ASN187 3.8 22.8 1.0
N A:ASP206 3.9 17.0 1.0
ND2 A:ASN205 4.0 17.6 1.0
OD1 A:ASP206 4.2 15.5 1.0
N A:ASN187 4.2 20.1 1.0
CA A:ASP206 4.2 16.6 1.0
CB A:HIS189 4.3 30.8 1.0
CB A:ASP206 4.4 14.8 1.0
CB A:ASN187 4.6 20.7 1.0
CG A:GLU185 4.6 17.9 1.0
C1 A:MFB501 4.6 27.7 1.0
C A:ASN205 4.6 17.4 1.0
C4 A:MFB501 4.7 27.9 1.0
N A:HIS189 4.7 23.9 1.0
CG A:GLU193 4.8 19.6 1.0
N A:ASP188 4.8 23.0 1.0
CA A:ASN187 4.8 22.8 1.0
CB A:ASN205 4.8 17.0 1.0
N A:ILE207 4.9 16.8 1.0
CA A:ASN205 5.0 17.5 1.0
CB A:GLU193 5.0 17.1 1.0

Calcium binding site 3 out of 10 in 1kwx

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Calcium binding site 3 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:17.6
occ:1.00
 OE1 A:GLU165 2.1 16.2 1.0
O A:HOH694 2.3 18.9 1.0
OD2 A:ASP194 2.8 16.7 1.0
OD1 A:ASP194 2.8 12.7 1.0
CG A:ASP194 3.2 15.0 1.0
CD A:GLU165 3.3 16.9 1.0
CA A:CA502 3.7 16.6 1.0
CB A:GLU165 3.8 17.9 1.0
CG A:GLU165 3.9 16.2 1.0
OD2 A:ASP188 4.1 25.3 1.0
OE2 A:GLU165 4.3 15.8 1.0
CA A:GLU165 4.4 18.0 1.0
O A:HOH695 4.4 18.8 1.0
O A:ASP161 4.6 15.2 1.0
OD1 A:ASP188 4.6 22.6 1.0
CB A:ASP194 4.7 16.8 1.0
CG A:ASP188 4.7 24.6 1.0
OD2 A:ASP161 4.8 16.0 1.0
O A:HOH693 4.9 24.9 1.0
N A:GLU165 4.9 18.8 1.0

Calcium binding site 4 out of 10 in 1kwx

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Calcium binding site 4 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca606

b:31.0
occ:0.50
 O A:HOH721 2.4 25.8 1.0
O A:HOH730 2.6 33.5 1.0
O A:ASN187 4.4 22.4 1.0

Calcium binding site 5 out of 10 in 1kwx

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Calcium binding site 5 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:20.8
occ:1.00
 OD2 B:ASP194 2.3 19.2 1.0
O B:GLU193 2.4 18.8 1.0
O B:HOH624 2.4 18.3 1.0
OD2 B:ASP161 2.5 19.2 1.0
OE2 B:GLU165 2.5 17.9 1.0
OE1 B:GLU165 2.5 18.3 1.0
OD1 B:ASP161 2.7 17.1 1.0
OD2 B:ASP188 2.7 31.3 1.0
CD B:GLU165 2.9 18.7 1.0
CG B:ASP161 2.9 21.5 1.0
C B:GLU193 3.3 19.5 1.0
CG B:ASP194 3.4 21.4 1.0
CG B:ASP188 3.5 33.8 1.0
CA B:ASP194 3.7 20.7 1.0
CA B:CA604 3.8 22.3 1.0
N B:ASP194 3.9 16.8 1.0
O B:HOH644 3.9 19.7 1.0
CB B:ASP188 4.0 30.1 1.0
CB B:ASP194 4.1 19.9 1.0
O B:HOH623 4.2 31.4 1.0
N B:GLU193 4.3 27.9 1.0
OD1 B:ASP188 4.4 31.9 1.0
CG B:GLU165 4.4 22.7 1.0
OD1 B:ASP194 4.4 22.4 1.0
CA B:GLU193 4.4 23.6 1.0
CB B:ASP161 4.4 19.0 1.0
CA B:ASP188 4.5 33.6 1.0
CZ B:PHE168 4.6 18.9 1.0
OD1 B:ASP206 4.7 19.3 1.0
O B:ASP161 4.7 24.5 1.0
N B:GLY166 4.8 18.8 1.0
C B:ASP194 4.9 21.7 1.0
O B:HOH629 5.0 21.3 1.0

Calcium binding site 6 out of 10 in 1kwx

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Calcium binding site 6 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:29.2
occ:1.00
 OD2 B:ASP206 2.3 21.1 1.0
OE2 B:GLU193 2.3 24.9 1.0
OD1 B:ASN205 2.4 28.0 1.0
OD1 B:ASN187 2.5 37.9 1.0
O3 B:MFB601 2.5 34.4 1.0
O2 B:MFB601 2.6 32.3 1.0
OE2 B:GLU185 2.6 28.7 1.0
O B:ASP206 2.6 23.7 1.0
CD B:GLU193 3.3 25.8 1.0
CD B:GLU185 3.3 29.9 1.0
C3 B:MFB601 3.4 37.1 1.0
CG B:ASP206 3.4 24.8 1.0
C2 B:MFB601 3.4 36.8 1.0
CG B:ASN205 3.5 27.3 1.0
OE1 B:GLU185 3.5 25.6 1.0
CG B:ASN187 3.5 39.0 1.0
C B:ASP206 3.6 24.3 1.0
OE1 B:GLU193 3.6 31.4 1.0
N B:ASP206 3.7 24.1 1.0
ND2 B:ASN205 4.0 23.1 1.0
ND2 B:ASN187 4.1 39.2 1.0
OD1 B:ASP206 4.1 19.3 1.0
CA B:ASP206 4.1 23.2 1.0
N B:ASN187 4.3 32.6 1.0
CB B:ASP206 4.3 23.3 1.0
CB B:HIS189 4.4 39.6 1.0
C B:ASN205 4.5 26.3 1.0
CG B:GLU185 4.6 27.9 1.0
CG B:GLU193 4.7 25.1 1.0
CB B:ASN187 4.7 37.2 1.0
CB B:ASN205 4.7 26.1 1.0
N B:HIS189 4.7 37.5 1.0
N B:ILE207 4.8 24.6 1.0
C1 B:MFB601 4.8 37.1 1.0
C4 B:MFB601 4.8 35.9 1.0
N B:ASP188 4.8 32.9 1.0
CA B:ASN205 4.8 25.6 1.0
CA B:ASN187 4.9 34.8 1.0
CB B:GLU193 4.9 21.5 1.0

Calcium binding site 7 out of 10 in 1kwx

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Calcium binding site 7 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:22.3
occ:1.00
 OE1 B:GLU165 2.2 18.3 1.0
O B:HOH629 2.3 21.3 1.0
O B:HOH678 2.4 34.7 1.0
O B:HOH644 2.4 19.7 1.0
O B:HOH663 2.5 23.1 1.0
OD1 B:ASP194 2.5 22.4 1.0
OD2 B:ASP194 2.5 19.2 1.0
CG B:ASP194 2.8 21.4 1.0
CD B:GLU165 3.4 18.7 1.0
CA B:CA602 3.8 20.8 1.0
CB B:GLU165 4.1 19.6 1.0
OD2 B:ASP188 4.2 31.3 1.0
O B:ASP161 4.2 24.5 1.0
CG B:GLU165 4.2 22.7 1.0
O B:HOH703 4.3 30.1 1.0
CB B:ASP194 4.4 19.9 1.0
OE2 B:GLU165 4.4 17.9 1.0
CA B:GLU165 4.5 19.3 1.0
OD2 B:ASP161 4.6 19.2 1.0
O B:HOH664 4.7 44.2 1.0
OD1 B:ASP161 4.8 17.1 1.0
OD1 B:ASP188 4.8 31.9 1.0
O B:HOH665 4.8 40.7 1.0
CG B:ASP188 4.8 33.8 1.0
CG B:ASP161 4.9 21.5 1.0

Calcium binding site 8 out of 10 in 1kwx

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Calcium binding site 8 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:18.7
occ:1.00
 O C:GLU193 2.3 13.8 1.0
O C:HOH725 2.3 14.3 1.0
OD2 C:ASP188 2.4 18.4 1.0
OE2 C:GLU165 2.5 15.3 1.0
OD2 C:ASP194 2.5 13.4 1.0
OE1 C:GLU165 2.6 16.0 1.0
OD2 C:ASP161 2.6 19.0 1.0
OD1 C:ASP161 2.8 18.1 1.0
CD C:GLU165 2.9 17.4 1.0
CG C:ASP161 3.1 21.3 1.0
CG C:ASP188 3.2 14.8 1.0
C C:GLU193 3.3 17.2 1.0
CB C:ASP188 3.5 16.6 1.0
CG C:ASP194 3.7 18.1 1.0
CA C:ASP194 3.8 16.1 1.0
O C:HOH719 3.9 16.4 1.0
N C:ASP194 4.0 16.8 1.0
CA C:CA704 4.1 19.1 1.0
CA C:ASP188 4.2 17.7 1.0
OD1 C:ASP188 4.2 15.5 1.0
N C:GLU193 4.2 15.9 1.0
CA C:GLU193 4.3 16.4 1.0
CB C:ASP194 4.4 15.5 1.0
CG C:GLU165 4.4 17.0 1.0
OD1 C:ASP206 4.6 19.9 1.0
CZ C:PHE168 4.6 18.0 1.0
OD1 C:ASP194 4.6 17.4 1.0
CB C:ASP161 4.6 19.9 1.0
O C:HOH724 4.6 21.7 1.0
O C:HOH769 4.7 23.4 1.0
N C:GLY166 4.7 18.0 1.0
N C:ASP188 4.8 17.8 1.0
O C:ASP161 4.9 19.8 1.0
CB C:GLU193 4.9 18.7 1.0

Calcium binding site 9 out of 10 in 1kwx

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Calcium binding site 9 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:19.9
occ:1.00
 OD2 C:ASP206 2.2 18.3 1.0
OE2 C:GLU193 2.3 21.2 1.0
OD1 C:ASN187 2.3 14.9 1.0
OE2 C:GLU185 2.6 20.5 1.0
O C:ASP206 2.6 16.6 1.0
O3 C:MFB701 2.6 20.5 1.0
O2 C:MFB701 2.7 22.1 1.0
OD1 C:ASN205 2.7 17.5 1.0
CG C:ASP206 3.2 21.0 1.0
CD C:GLU193 3.3 19.9 1.0
CG C:ASN187 3.4 20.0 1.0
C3 C:MFB701 3.4 23.3 1.0
CD C:GLU185 3.5 21.6 1.0
C2 C:MFB701 3.5 21.9 1.0
OE1 C:GLU193 3.6 19.6 1.0
C C:ASP206 3.6 18.2 1.0
CG C:ASN205 3.7 23.4 1.0
OE1 C:GLU185 3.8 19.6 1.0
N C:ASP206 3.8 18.9 1.0
ND2 C:ASN187 3.9 14.3 1.0
OD1 C:ASP206 3.9 19.9 1.0
N C:ASN187 4.0 18.8 1.0
ND2 C:ASN205 4.1 19.2 1.0
CA C:ASP206 4.1 17.9 1.0
CB C:ASP206 4.2 15.1 1.0
CB C:HIS189 4.3 19.9 1.0
CB C:ASN187 4.6 16.6 1.0
N C:HIS189 4.6 21.3 1.0
CG C:GLU193 4.6 18.7 1.0
N C:ASP188 4.6 17.8 1.0
C C:ASN205 4.6 21.1 1.0
CA C:ASN187 4.7 18.2 1.0
CG C:GLU185 4.7 16.8 1.0
N C:ILE207 4.8 19.0 1.0
CB C:GLU193 4.8 18.7 1.0
C4 C:MFB701 4.8 23.5 1.0
C1 C:MFB701 4.9 24.1 1.0
CB C:ASN205 4.9 19.9 1.0
CA C:PRO186 5.0 19.2 1.0
C C:ASN187 5.0 19.0 1.0
C C:PRO186 5.0 19.8 1.0
CA C:ASN205 5.0 21.1 1.0

Calcium binding site 10 out of 10 in 1kwx

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Calcium binding site 10 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca704

b:19.1
occ:1.00
 O C:HOH718 2.4 16.4 1.0
OE1 C:GLU165 2.4 16.0 1.0
O C:HOH719 2.5 16.4 1.0
O C:HOH741 2.5 21.5 1.0
OD1 C:ASP194 2.5 17.4 1.0
OD2 C:ASP194 2.6 13.4 1.0
CG C:ASP194 2.9 18.1 1.0
CD C:GLU165 3.6 17.4 1.0
CA C:CA702 4.1 18.7 1.0
O C:HOH799 4.2 27.4 1.0
CB C:GLU165 4.2 17.9 1.0
OD2 C:ASP188 4.2 18.4 1.0
O C:HOH771 4.2 19.2 1.0
CG C:GLU165 4.3 17.0 1.0
O C:ASP161 4.4 19.8 1.0
CB C:ASP194 4.4 15.5 1.0
O C:HOH798 4.5 57.4 1.0
OE2 C:GLU165 4.5 15.3 1.0
CA C:GLU165 4.6 20.3 1.0
O C:HOH770 4.7 24.9 1.0
O C:HOH811 4.7 35.9 1.0
CG C:ASP188 4.9 14.8 1.0
OD2 C:ASP161 4.9 19.0 1.0
OD1 C:ASP188 4.9 15.5 1.0
OD1 C:ASP161 5.0 18.1 1.0
O C:HOH720 5.0 23.5 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 11:32:03 2024

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