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

Protein crystallography data

The structure of Rat Mannose Protein A Complexed with A-Me-Fuc., PDB code: 1kww 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 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.410, 85.560, 98.090, 90.00, 107.00, 90.00
R / Rfree (%) 18.9 / 22.4

Other elements in 1kww:

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

Calcium binding site 1 out of 10 in 1kww

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Calcium binding site 1 out of 10 in the Rat Mannose Protein A Complexed with A-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 A-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:14.3
occ:1.00
 O A:HOH626 2.3 11.0 1.0
OD2 A:ASP161 2.4 15.3 1.0
OD2 A:ASP188 2.4 16.5 1.0
OD2 A:ASP194 2.4 17.0 1.0
O A:GLU193 2.4 17.1 1.0
OE2 A:GLU165 2.5 14.5 1.0
OE1 A:GLU165 2.5 12.8 1.0
OD1 A:ASP161 2.7 15.1 1.0
CD A:GLU165 2.9 13.5 1.0
CG A:ASP161 2.9 16.0 1.0
CG A:ASP188 3.2 16.9 1.0
C A:GLU193 3.4 17.0 1.0
CG A:ASP194 3.6 15.6 1.0
CB A:ASP188 3.8 16.0 1.0
CA A:ASP194 3.8 14.0 1.0
N A:ASP194 4.0 15.3 1.0
CA A:CA504 4.0 13.6 1.0
O A:HOH695 4.0 25.2 1.0
OD1 A:ASP188 4.1 18.1 1.0
CB A:ASP194 4.3 17.5 1.0
N A:GLU193 4.3 14.8 1.0
CA A:ASP188 4.4 15.6 1.0
CG A:GLU165 4.4 15.5 1.0
CB A:ASP161 4.4 13.8 1.0
CA A:GLU193 4.5 15.3 1.0
OD1 A:ASP194 4.5 14.1 1.0
O A:HOH654 4.6 19.1 1.0
N A:GLY166 4.6 16.5 1.0
CZ A:PHE168 4.6 11.4 1.0
O A:HOH625 4.7 20.4 1.0
OD1 A:ASP206 4.7 15.8 1.0
O A:ASP161 4.8 13.6 1.0
CA A:GLU165 4.9 15.9 1.0
C A:ASP194 5.0 12.5 1.0

Calcium binding site 2 out of 10 in 1kww

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Calcium binding site 2 out of 10 in the Rat Mannose Protein A Complexed with A-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 A-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:17.4
occ:1.00
 OD2 A:ASP206 2.3 13.1 1.0
OD1 A:ASN187 2.4 15.8 1.0
OE2 A:GLU193 2.4 15.4 1.0
O2 A:MFU501 2.5 17.8 1.0
OD1 A:ASN205 2.5 16.5 1.0
OE2 A:GLU185 2.5 12.9 1.0
O A:ASP206 2.5 13.8 1.0
O3 A:MFU501 2.6 19.4 1.0
CG A:ASP206 3.3 16.4 1.0
C3 A:MFU501 3.3 22.0 1.0
C2 A:MFU501 3.3 19.8 1.0
CD A:GLU185 3.4 16.8 1.0
CD A:GLU193 3.4 15.2 1.0
CG A:ASN187 3.4 18.6 1.0
CG A:ASN205 3.5 16.6 1.0
C A:ASP206 3.5 13.7 1.0
N A:ASP206 3.7 14.4 1.0
OE1 A:GLU185 3.7 18.1 1.0
OE1 A:GLU193 3.8 16.6 1.0
ND2 A:ASN187 3.9 17.3 1.0
ND2 A:ASN205 3.9 13.8 1.0
CA A:ASP206 4.0 15.3 1.0
OD1 A:ASP206 4.0 15.8 1.0
N A:ASN187 4.2 17.7 1.0
CB A:ASP206 4.2 14.1 1.0
C A:ASN205 4.5 14.0 1.0
CB A:ASN187 4.6 16.4 1.0
CB A:HIS189 4.6 20.0 1.0
CG A:GLU185 4.7 13.8 1.0
CG A:GLU193 4.7 15.8 1.0
N A:ILE207 4.7 12.9 1.0
C1 A:MFU501 4.7 24.5 1.0
CB A:ASN205 4.8 15.5 1.0
N A:HIS189 4.8 17.8 1.0
C4 A:MFU501 4.8 21.9 1.0
N A:ASP188 4.8 17.4 1.0
CA A:ASN187 4.8 16.3 1.0
CB A:GLU193 4.9 16.2 1.0
CA A:ASN205 4.9 14.4 1.0
O1 A:MFU501 4.9 23.8 1.0

Calcium binding site 3 out of 10 in 1kww

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Calcium binding site 3 out of 10 in the Rat Mannose Protein A Complexed with A-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 A-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:13.6
occ:1.00
 O A:HOH695 2.3 25.2 1.0
OE1 A:GLU165 2.3 12.8 1.0
OD1 A:ASP194 2.5 14.1 1.0
OD2 A:ASP194 2.6 17.0 1.0
CG A:ASP194 2.9 15.6 1.0
CD A:GLU165 3.5 13.5 1.0
CA A:CA502 4.0 14.3 1.0
CB A:GLU165 4.0 15.7 1.0
CG A:GLU165 4.1 15.5 1.0
OD2 A:ASP188 4.2 16.5 1.0
O A:HOH696 4.3 16.4 1.0
O A:ASP161 4.4 13.6 1.0
CB A:ASP194 4.4 17.5 1.0
CA A:GLU165 4.4 15.9 1.0
OE2 A:GLU165 4.5 14.5 1.0
O A:HOH694 4.6 24.8 1.0
O A:HOH620 4.6 23.8 1.0
OD1 A:ASP188 4.9 18.1 1.0
OD2 A:ASP161 4.9 15.3 1.0
N A:GLU165 4.9 17.9 1.0
CG A:ASP188 4.9 16.9 1.0

Calcium binding site 4 out of 10 in 1kww

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Calcium binding site 4 out of 10 in the Rat Mannose Protein A Complexed with A-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 A-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca606

b:29.4
occ:1.00
 O A:HOH738 2.5 23.2 1.0
O A:HOH727 2.5 21.2 1.0
O A:ASN187 4.3 16.9 1.0
CD2 A:HIS189 4.6 22.3 1.0
N A:GLY190 4.9 20.8 1.0

Calcium binding site 5 out of 10 in 1kww

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Calcium binding site 5 out of 10 in the Rat Mannose Protein A Complexed with A-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 A-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:17.6
occ:1.00
 O B:HOH624 2.2 17.9 1.0
OD2 B:ASP194 2.3 15.4 1.0
OD2 B:ASP161 2.4 15.3 1.0
O B:GLU193 2.4 18.2 1.0
OE2 B:GLU165 2.5 18.6 1.0
OE1 B:GLU165 2.6 16.9 1.0
OD1 B:ASP161 2.6 15.3 1.0
CG B:ASP161 2.8 18.5 1.0
CD B:GLU165 2.9 18.9 1.0
OD2 B:ASP188 2.9 25.6 1.0
C B:GLU193 3.3 20.6 1.0
CG B:ASP194 3.4 17.6 1.0
CG B:ASP188 3.5 28.4 1.0
CA B:ASP194 3.6 19.0 1.0
CA B:CA604 3.7 20.4 1.0
N B:ASP194 3.9 18.6 1.0
O B:HOH645 3.9 19.6 1.0
CB B:ASP188 4.0 23.8 1.0
CB B:ASP194 4.1 18.3 1.0
O B:HOH623 4.1 21.8 1.0
OD1 B:ASP188 4.3 25.4 1.0
OD1 B:ASP194 4.3 18.5 1.0
N B:GLU193 4.3 22.4 1.0
CB B:ASP161 4.4 20.4 1.0
CA B:GLU193 4.4 21.9 1.0
CG B:GLU165 4.4 20.2 1.0
CA B:ASP188 4.5 26.7 1.0
OD1 B:ASP206 4.6 20.4 1.0
CZ B:PHE168 4.6 17.9 1.0
O B:ASP161 4.7 20.1 1.0
O B:HOH629 4.8 20.3 1.0
N B:GLY166 4.8 17.4 1.0
C B:ASP194 4.9 19.2 1.0

Calcium binding site 6 out of 10 in 1kww

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Calcium binding site 6 out of 10 in the Rat Mannose Protein A Complexed with A-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 A-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:23.9
occ:1.00
 OE2 B:GLU193 2.3 22.4 1.0
OD2 B:ASP206 2.4 19.2 1.0
OD1 B:ASN187 2.4 26.9 1.0
O B:ASP206 2.5 21.6 1.0
O3 B:MFU601 2.5 27.7 1.0
O2 B:MFU601 2.5 27.5 1.0
OD1 B:ASN205 2.6 23.2 1.0
OE2 B:GLU185 2.6 22.1 1.0
C3 B:MFU601 3.2 28.1 1.0
CD B:GLU193 3.3 23.1 1.0
C2 B:MFU601 3.3 27.9 1.0
CG B:ASP206 3.4 20.1 1.0
CD B:GLU185 3.5 21.1 1.0
CG B:ASN205 3.5 23.5 1.0
C B:ASP206 3.5 20.1 1.0
CG B:ASN187 3.6 29.9 1.0
OE1 B:GLU193 3.6 24.4 1.0
OE1 B:GLU185 3.7 22.3 1.0
N B:ASP206 3.7 20.0 1.0
ND2 B:ASN205 3.9 20.5 1.0
CA B:ASP206 4.1 19.5 1.0
OD1 B:ASP206 4.1 20.4 1.0
ND2 B:ASN187 4.2 30.6 1.0
N B:ASN187 4.3 24.4 1.0
CB B:ASP206 4.3 19.2 1.0
CB B:HIS189 4.5 38.0 1.0
C B:ASN205 4.5 22.1 1.0
CG B:GLU193 4.6 23.0 1.0
N B:ILE207 4.6 21.0 1.0
N B:HIS189 4.7 31.1 1.0
C4 B:MFU601 4.7 28.1 1.0
CB B:ASN187 4.7 28.3 1.0
C1 B:MFU601 4.7 27.7 1.0
CG B:GLU185 4.7 22.9 1.0
N B:ASP188 4.7 23.2 1.0
CB B:ASN205 4.8 22.4 1.0
CA B:ASN205 4.8 22.0 1.0
CA B:ASN187 4.9 26.0 1.0
CB B:GLU193 4.9 19.4 1.0
O1 B:MFU601 4.9 28.2 1.0

Calcium binding site 7 out of 10 in 1kww

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Calcium binding site 7 out of 10 in the Rat Mannose Protein A Complexed with A-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 A-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:20.4
occ:1.00
 OE1 B:GLU165 2.2 16.9 1.0
O B:HOH645 2.3 19.6 1.0
O B:HOH629 2.3 20.3 1.0
O B:HOH665 2.4 22.9 1.0
OD1 B:ASP194 2.5 18.5 1.0
OD2 B:ASP194 2.5 15.4 1.0
O B:HOH684 2.7 33.6 1.0
CG B:ASP194 2.8 17.6 1.0
CD B:GLU165 3.5 18.9 1.0
CA B:CA602 3.7 17.6 1.0
OD2 B:ASP188 4.2 25.6 1.0
O B:ASP161 4.2 20.1 1.0
CG B:GLU165 4.3 20.2 1.0
O B:HOH666 4.3 42.5 1.0
CB B:GLU165 4.3 16.9 1.0
O B:HOH710 4.3 29.9 1.0
CB B:ASP194 4.3 18.3 1.0
OE2 B:GLU165 4.4 18.6 1.0
O B:HOH721 4.5 39.7 1.0
OD2 B:ASP161 4.6 15.3 1.0
OD1 B:ASP188 4.6 25.4 1.0
CA B:GLU165 4.6 18.0 1.0
OD1 B:ASP161 4.7 15.3 1.0
CG B:ASP188 4.8 28.4 1.0
CG B:ASP161 4.9 18.5 1.0
O B:HOH648 4.9 32.2 1.0
O B:HOH667 4.9 32.1 1.0

Calcium binding site 8 out of 10 in 1kww

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Calcium binding site 8 out of 10 in the Rat Mannose Protein A Complexed with A-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 A-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:17.8
occ:1.00
 O C:HOH725 2.2 12.8 1.0
OD2 C:ASP161 2.3 19.0 1.0
O C:GLU193 2.4 16.2 1.0
OD2 C:ASP194 2.4 13.3 1.0
OE2 C:GLU165 2.4 16.9 1.0
OE1 C:GLU165 2.6 15.7 1.0
OD2 C:ASP188 2.6 17.3 1.0
OD1 C:ASP161 2.7 17.3 1.0
CD C:GLU165 2.8 16.1 1.0
CG C:ASP161 2.9 21.1 1.0
C C:GLU193 3.3 18.2 1.0
CG C:ASP188 3.4 19.7 1.0
CG C:ASP194 3.6 16.9 1.0
CA C:ASP194 3.8 17.0 1.0
CB C:ASP188 3.8 17.8 1.0
N C:ASP194 3.9 16.8 1.0
O C:HOH719 3.9 18.6 1.0
CA C:CA704 3.9 17.4 1.0
CB C:ASP194 4.2 16.5 1.0
N C:GLU193 4.3 17.3 1.0
CG C:GLU165 4.3 16.5 1.0
CB C:ASP161 4.4 19.4 1.0
CA C:ASP188 4.4 17.7 1.0
CA C:GLU193 4.4 18.0 1.0
CZ C:PHE168 4.4 18.9 1.0
OD1 C:ASP188 4.5 18.0 1.0
OD1 C:ASP194 4.5 16.1 1.0
N C:GLY166 4.6 22.3 1.0
OD1 C:ASP206 4.6 20.1 1.0
O C:HOH724 4.7 18.9 1.0
O C:HOH770 4.7 21.5 1.0
O C:ASP161 4.9 21.3 1.0
CA C:GLU165 4.9 20.8 1.0
C C:ASP194 4.9 17.2 1.0
O C:HOH718 5.0 15.8 1.0

Calcium binding site 9 out of 10 in 1kww

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Calcium binding site 9 out of 10 in the Rat Mannose Protein A Complexed with A-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 A-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:17.8
occ:1.00
 OD2 C:ASP206 2.2 18.7 1.0
OE2 C:GLU193 2.3 20.5 1.0
OD1 C:ASN205 2.4 17.9 1.0
OD1 C:ASN187 2.4 18.4 1.0
O C:ASP206 2.4 18.5 1.0
OE2 C:GLU185 2.5 20.7 1.0
O3 C:MFU701 2.5 22.5 1.0
O2 C:MFU701 2.6 22.6 1.0
CG C:ASP206 3.2 20.6 1.0
C3 C:MFU701 3.3 25.5 1.0
CD C:GLU193 3.3 21.8 1.0
C2 C:MFU701 3.4 24.6 1.0
CG C:ASN205 3.4 19.7 1.0
CD C:GLU185 3.4 25.1 1.0
C C:ASP206 3.4 18.9 1.0
CG C:ASN187 3.5 20.6 1.0
N C:ASP206 3.6 19.6 1.0
OE1 C:GLU185 3.7 23.8 1.0
OE1 C:GLU193 3.7 19.8 1.0
ND2 C:ASN205 3.8 18.1 1.0
CA C:ASP206 3.9 18.7 1.0
OD1 C:ASP206 4.0 20.1 1.0
ND2 C:ASN187 4.1 18.5 1.0
CB C:ASP206 4.2 17.1 1.0
N C:ASN187 4.2 21.0 1.0
C C:ASN205 4.4 21.1 1.0
N C:ILE207 4.6 18.1 1.0
CB C:HIS189 4.6 20.8 1.0
CG C:GLU193 4.6 18.0 1.0
CB C:ASN205 4.7 20.3 1.0
CB C:ASN187 4.7 20.0 1.0
CG C:GLU185 4.7 23.2 1.0
C4 C:MFU701 4.7 25.6 1.0
C1 C:MFU701 4.8 28.1 1.0
N C:HIS189 4.8 20.5 1.0
N C:ASP188 4.8 18.1 1.0
CA C:ASN205 4.8 21.9 1.0
CB C:GLU193 4.8 19.6 1.0
CA C:ASN187 4.8 19.2 1.0
O1 C:MFU701 5.0 26.2 1.0
CA C:ILE207 5.0 17.4 1.0

Calcium binding site 10 out of 10 in 1kww

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Calcium binding site 10 out of 10 in the Rat Mannose Protein A Complexed with A-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 A-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca704

b:17.4
occ:1.00
 O C:HOH718 2.3 15.8 1.0
OE1 C:GLU165 2.3 15.7 1.0
OD1 C:ASP194 2.4 16.1 1.0
O C:HOH719 2.4 18.6 1.0
OD2 C:ASP194 2.5 13.3 1.0
O C:HOH743 2.6 22.8 1.0
CG C:ASP194 2.8 16.9 1.0
CD C:GLU165 3.5 16.1 1.0
CA C:CA702 3.9 17.8 1.0
OD2 C:ASP188 4.1 17.3 1.0
CB C:GLU165 4.2 19.1 1.0
O C:HOH803 4.2 23.1 1.0
O C:HOH772 4.2 21.6 1.0
CG C:GLU165 4.2 16.5 1.0
CB C:ASP194 4.3 16.5 1.0
O C:ASP161 4.4 21.3 1.0
OE2 C:GLU165 4.4 16.9 1.0
O C:HOH802 4.5 29.8 1.0
CA C:GLU165 4.6 20.8 1.0
OD2 C:ASP161 4.7 19.0 1.0
O C:HOH771 4.7 28.3 1.0
OD1 C:ASP161 4.8 17.3 1.0
O C:HOH816 4.8 38.2 1.0
CG C:ASP188 5.0 19.7 1.0
CG C:ASP161 5.0 21.1 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 11:32:00 2024

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