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Calcium in PDB 1kwt: Rat Mannose Binding Protein A (Native, Mpd)

Protein crystallography data

The structure of Rat Mannose Binding Protein A (Native, Mpd), PDB code: 1kwt was solved by K.K.S.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 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.590, 85.370, 97.990, 90.00, 106.80, 90.00
R / Rfree (%) 19.8 / 23.4

Other elements in 1kwt:

The structure of Rat Mannose Binding Protein A (Native, Mpd) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Rat Mannose Binding Protein A (Native, Mpd) (pdb code 1kwt). 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 Binding Protein A (Native, Mpd), PDB code: 1kwt:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 1kwt

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Calcium binding site 1 out of 10 in the Rat Mannose Binding Protein A (Native, Mpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rat Mannose Binding Protein A (Native, Mpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:16.9
occ:1.00
 OD2 A:ASP194 2.4 17.1 1.0
O A:HOH626 2.4 15.2 1.0
OD2 A:ASP188 2.4 23.9 1.0
OD2 A:ASP161 2.4 17.1 1.0
O A:GLU193 2.5 16.9 1.0
OE2 A:GLU165 2.5 17.2 1.0
OE1 A:GLU165 2.5 15.9 1.0
OD1 A:ASP161 2.6 16.3 1.0
CD A:GLU165 2.9 17.2 1.0
CG A:ASP161 2.9 18.3 1.0
CG A:ASP188 3.3 23.4 1.0
C A:GLU193 3.4 17.6 1.0
CG A:ASP194 3.5 17.6 1.0
CA A:ASP194 3.8 14.8 1.0
CB A:ASP188 3.8 21.4 1.0
CA A:CA503 4.0 17.5 1.0
N A:ASP194 4.0 15.4 1.0
O A:HOH692 4.1 25.3 1.0
OD1 A:ASP188 4.2 20.0 1.0
CB A:ASP194 4.2 18.1 1.0
N A:GLU193 4.3 16.8 1.0
CG A:GLU165 4.4 17.5 1.0
CA A:ASP188 4.4 21.1 1.0
CB A:ASP161 4.4 16.2 1.0
OD1 A:ASP194 4.5 14.6 1.0
CA A:GLU193 4.5 16.4 1.0
OD1 A:ASP206 4.7 17.4 1.0
CZ A:PHE168 4.7 16.1 1.0
N A:GLY166 4.7 18.5 1.0
O A:HOH656 4.7 22.9 1.0
O A:HOH625 4.8 19.9 1.0
O A:ASP161 4.8 16.9 1.0
CA A:GLU165 4.9 17.9 1.0
C A:ASP194 5.0 15.7 1.0

Calcium binding site 2 out of 10 in 1kwt

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Calcium binding site 2 out of 10 in the Rat Mannose Binding Protein A (Native, Mpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rat Mannose Binding Protein A (Native, Mpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:21.5
occ:1.00
 OD2 A:ASP206 2.3 18.5 1.0
OE2 A:GLU193 2.4 15.9 1.0
OD1 A:ASN187 2.4 23.7 1.0
O A:ASP206 2.5 17.5 1.0
O A:HOH731 2.5 37.8 1.0
OE2 A:GLU185 2.6 26.7 1.0
OD1 A:ASN205 2.6 28.5 1.0
O A:HOH732 2.8 35.7 1.0
CG A:ASP206 3.3 18.7 1.0
CD A:GLU185 3.3 29.9 1.0
CD A:GLU193 3.4 20.3 1.0
CG A:ASN187 3.5 25.6 1.0
CG A:ASN205 3.5 27.6 1.0
OE1 A:GLU185 3.5 28.6 1.0
C A:ASP206 3.5 18.6 1.0
N A:ASP206 3.7 19.2 1.0
OE1 A:GLU193 3.8 21.0 1.0
ND2 A:ASN205 3.9 30.1 1.0
CA A:ASP206 4.0 19.2 1.0
ND2 A:ASN187 4.1 23.0 1.0
OD1 A:ASP206 4.1 17.4 1.0
N A:ASN187 4.2 22.8 1.0
CB A:ASP206 4.2 19.0 1.0
C A:ASN205 4.6 21.6 1.0
CG A:GLU193 4.6 18.3 1.0
CB A:HIS189 4.6 27.1 1.0
CG A:GLU185 4.7 23.8 1.0
N A:ILE207 4.7 16.4 1.0
CB A:ASN187 4.7 22.2 1.0
N A:ASP188 4.7 22.1 1.0
N A:HIS189 4.8 23.8 1.0
CB A:GLU193 4.8 19.1 1.0
CB A:ASN205 4.8 23.2 1.0
CA A:ASN187 4.8 22.1 1.0
CA A:ASN205 4.9 19.4 1.0

Calcium binding site 3 out of 10 in 1kwt

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Calcium binding site 3 out of 10 in the Rat Mannose Binding Protein A (Native, Mpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Rat Mannose Binding Protein A (Native, Mpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:17.5
occ:1.00
 OE1 A:GLU165 2.3 15.9 1.0
O A:HOH692 2.3 25.3 1.0
OD1 A:ASP194 2.5 14.6 1.0
OD2 A:ASP194 2.6 17.1 1.0
CG A:ASP194 2.9 17.6 1.0
CD A:GLU165 3.5 17.2 1.0
CA A:CA501 4.0 16.9 1.0
CB A:GLU165 4.0 17.6 1.0
CG A:GLU165 4.2 17.5 1.0
O A:HOH693 4.2 16.2 1.0
OD2 A:ASP188 4.2 23.9 1.0
O A:ASP161 4.3 16.9 1.0
CB A:ASP194 4.4 18.1 1.0
CA A:GLU165 4.5 17.9 1.0
OE2 A:GLU165 4.5 17.2 1.0
O A:HOH691 4.5 21.7 1.0
O A:HOH620 4.6 26.5 1.0
OD2 A:ASP161 4.8 17.1 1.0
OD1 A:ASP161 4.9 16.3 1.0
OD1 A:ASP188 4.9 20.0 1.0
N A:GLU165 5.0 18.2 1.0
CG A:ASP188 5.0 23.4 1.0

Calcium binding site 4 out of 10 in 1kwt

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Calcium binding site 4 out of 10 in the Rat Mannose Binding Protein A (Native, Mpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Rat Mannose Binding Protein A (Native, Mpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca606

b:41.8
occ:1.00
 O A:HOH724 2.4 22.5 1.0
O A:HOH745 2.5 33.3 1.0
O A:ASN187 4.3 23.4 1.0
CD2 A:HIS189 4.8 30.4 1.0
N A:GLY190 4.8 25.1 1.0
CA A:HIS189 4.9 25.6 1.0

Calcium binding site 5 out of 10 in 1kwt

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Calcium binding site 5 out of 10 in the Rat Mannose Binding Protein A (Native, Mpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Rat Mannose Binding Protein A (Native, Mpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:23.5
occ:1.00
 O B:HOH623 2.1 24.5 1.0
OD2 B:ASP194 2.2 25.3 1.0
O B:GLU193 2.3 21.2 1.0
OD2 B:ASP161 2.4 25.8 1.0
OE1 B:GLU165 2.6 23.4 1.0
OD1 B:ASP161 2.6 20.4 1.0
OE2 B:GLU165 2.7 25.5 1.0
OD2 B:ASP188 2.8 32.6 1.0
CG B:ASP161 2.9 26.3 1.0
CD B:GLU165 3.0 26.2 1.0
C B:GLU193 3.3 24.0 1.0
CG B:ASP194 3.4 24.2 1.0
CG B:ASP188 3.5 37.3 1.0
CA B:CA603 3.6 27.1 1.0
CA B:ASP194 3.7 22.7 1.0
N B:ASP194 3.9 21.4 1.0
CB B:ASP188 3.9 35.3 1.0
O B:HOH644 4.0 23.2 1.0
CB B:ASP194 4.1 24.9 1.0
O B:HOH622 4.2 26.5 1.0
OD1 B:ASP194 4.3 24.8 1.0
CB B:ASP161 4.4 24.3 1.0
N B:GLU193 4.4 30.1 1.0
OD1 B:ASP188 4.4 33.4 1.0
CA B:GLU193 4.4 26.2 1.0
CA B:ASP188 4.4 36.8 1.0
CG B:GLU165 4.5 26.1 1.0
OD1 B:ASP206 4.6 26.5 1.0
CZ B:PHE168 4.6 22.4 1.0
O B:ASP161 4.7 29.2 1.0
O B:HOH629 4.8 26.9 1.0
C B:ASP194 4.9 22.6 1.0
N B:GLY166 4.9 24.6 1.0

Calcium binding site 6 out of 10 in 1kwt

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Calcium binding site 6 out of 10 in the Rat Mannose Binding Protein A (Native, Mpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Rat Mannose Binding Protein A (Native, Mpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:29.1
occ:1.00
 OE2 B:GLU193 2.3 27.5 1.0
OD2 B:ASP206 2.4 27.4 1.0
O B:ASP206 2.5 24.3 1.0
O B:HOH707 2.5 29.7 1.0
OE2 B:GLU185 2.5 30.1 1.0
OD1 B:ASN205 2.6 36.8 1.0
OD1 B:ASN187 2.6 33.8 1.0
O B:HOH714 2.8 58.5 1.0
CD B:GLU193 3.3 29.8 1.0
CG B:ASP206 3.4 26.5 1.0
CD B:GLU185 3.4 31.3 1.0
C B:ASP206 3.5 26.2 1.0
CG B:ASN187 3.5 38.4 1.0
CG B:ASN205 3.6 34.3 1.0
OE1 B:GLU193 3.6 31.1 1.0
N B:ASP206 3.7 24.7 1.0
OE1 B:GLU185 3.7 31.1 1.0
ND2 B:ASN205 4.0 36.2 1.0
ND2 B:ASN187 4.0 37.3 1.0
CA B:ASP206 4.0 25.1 1.0
OD1 B:ASP206 4.2 26.5 1.0
N B:ASN187 4.2 33.9 1.0
CB B:ASP206 4.3 25.3 1.0
C B:ASN205 4.6 28.3 1.0
CG B:GLU193 4.6 29.0 1.0
CB B:HIS189 4.6 47.4 1.0
N B:ILE207 4.6 26.1 1.0
CB B:ASN187 4.7 35.5 1.0
N B:ASP188 4.7 36.9 1.0
CG B:GLU185 4.8 31.8 1.0
N B:HIS189 4.8 42.1 1.0
CB B:GLU193 4.8 28.2 1.0
CB B:ASN205 4.8 32.0 1.0
CA B:ASN187 4.9 35.0 1.0
CA B:ASN205 4.9 28.4 1.0
CA B:ILE207 4.9 26.2 1.0

Calcium binding site 7 out of 10 in 1kwt

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Calcium binding site 7 out of 10 in the Rat Mannose Binding Protein A (Native, Mpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Rat Mannose Binding Protein A (Native, Mpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:27.1
occ:1.00
 O B:HOH687 2.2 34.4 1.0
OE1 B:GLU165 2.3 23.4 1.0
O B:HOH666 2.4 31.9 1.0
O B:HOH629 2.4 26.9 1.0
OD2 B:ASP194 2.5 25.3 1.0
O B:HOH644 2.5 23.2 1.0
OD1 B:ASP194 2.6 24.8 1.0
CG B:ASP194 2.8 24.2 1.0
CD B:GLU165 3.6 26.2 1.0
CA B:CA601 3.6 23.5 1.0
OD2 B:ASP188 4.0 32.6 1.0
O B:ASP161 4.2 29.2 1.0
CB B:GLU165 4.3 25.9 1.0
CB B:ASP194 4.4 24.9 1.0
O B:HOH737 4.4 37.5 1.0
CG B:GLU165 4.4 26.1 1.0
OD2 B:ASP161 4.4 25.8 1.0
OE2 B:GLU165 4.5 25.5 1.0
CA B:GLU165 4.6 24.9 1.0
OD1 B:ASP161 4.6 20.4 1.0
CG B:ASP188 4.6 37.3 1.0
OD1 B:ASP188 4.6 33.4 1.0
CG B:ASP161 4.7 26.3 1.0
O B:HOH647 5.0 36.1 1.0

Calcium binding site 8 out of 10 in 1kwt

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Calcium binding site 8 out of 10 in the Rat Mannose Binding Protein A (Native, Mpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Rat Mannose Binding Protein A (Native, Mpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca701

b:19.9
occ:1.00
 O C:HOH724 2.3 13.6 1.0
O C:GLU193 2.3 18.9 1.0
OD2 C:ASP161 2.4 24.6 1.0
OD2 C:ASP194 2.4 18.0 1.0
OE2 C:GLU165 2.5 16.8 1.0
OD2 C:ASP188 2.5 18.4 1.0
OE1 C:GLU165 2.6 17.3 1.0
OD1 C:ASP161 2.7 20.9 1.0
CD C:GLU165 2.9 19.9 1.0
CG C:ASP161 2.9 23.3 1.0
C C:GLU193 3.4 18.8 1.0
CG C:ASP188 3.4 18.8 1.0
CG C:ASP194 3.6 20.9 1.0
CB C:ASP188 3.8 16.6 1.0
CA C:ASP194 3.8 18.2 1.0
O C:HOH718 3.9 18.4 1.0
N C:ASP194 4.0 20.2 1.0
CA C:CA703 4.0 20.4 1.0
CB C:ASP194 4.3 20.2 1.0
CA C:ASP188 4.4 19.9 1.0
OD1 C:ASP188 4.4 19.1 1.0
CG C:GLU165 4.4 18.4 1.0
CB C:ASP161 4.4 21.9 1.0
N C:GLU193 4.4 18.8 1.0
CZ C:PHE168 4.5 18.5 1.0
CA C:GLU193 4.5 20.3 1.0
OD1 C:ASP194 4.5 16.4 1.0
N C:GLY166 4.6 21.6 1.0
OD1 C:ASP206 4.6 17.3 1.0
O C:HOH723 4.7 21.5 1.0
O C:HOH768 4.7 23.8 1.0
O C:ASP161 4.8 21.2 1.0
O C:HOH717 4.9 18.0 1.0
CA C:GLU165 4.9 21.3 1.0
N C:ASP188 5.0 19.6 1.0
C C:ASP194 5.0 20.3 1.0

Calcium binding site 9 out of 10 in 1kwt

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Calcium binding site 9 out of 10 in the Rat Mannose Binding Protein A (Native, Mpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Rat Mannose Binding Protein A (Native, Mpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:22.4
occ:1.00
 OD2 C:ASP206 2.2 18.0 1.0
O C:HOH811 2.3 28.1 1.0
OE2 C:GLU193 2.3 22.1 1.0
O C:ASP206 2.5 19.5 1.0
OD1 C:ASN187 2.5 19.0 1.0
OD1 C:ASN205 2.6 32.9 1.0
O C:HOH819 2.7 25.7 1.0
OE2 C:GLU185 2.8 32.3 1.0
CG C:ASP206 3.3 20.4 1.0
CD C:GLU193 3.3 22.6 1.0
CG C:ASN205 3.4 34.0 1.0
CD C:GLU185 3.5 31.1 1.0
C C:ASP206 3.5 22.2 1.0
CG C:ASN187 3.6 23.5 1.0
OE1 C:GLU193 3.7 22.8 1.0
OE1 C:GLU185 3.7 29.9 1.0
N C:ASP206 3.7 24.1 1.0
ND2 C:ASN205 3.8 34.5 1.0
OD1 C:ASP206 4.0 17.3 1.0
CA C:ASP206 4.0 21.6 1.0
ND2 C:ASN187 4.1 22.9 1.0
CB C:ASP206 4.2 19.3 1.0
N C:ASN187 4.2 22.2 1.0
CB C:HIS189 4.5 23.6 1.0
C C:ASN205 4.6 26.4 1.0
CG C:GLU193 4.6 19.4 1.0
N C:ILE207 4.6 21.1 1.0
O C:HOH746 4.7 45.4 1.0
N C:HIS189 4.7 21.9 1.0
CB C:GLU193 4.7 19.6 1.0
CG C:GLU185 4.8 28.1 1.0
CB C:ASN205 4.8 30.3 1.0
N C:ASP188 4.8 19.6 1.0
CB C:ASN187 4.8 21.6 1.0
CA C:ASN205 4.9 27.7 1.0
CA C:ASN187 4.9 21.1 1.0

Calcium binding site 10 out of 10 in 1kwt

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Calcium binding site 10 out of 10 in the Rat Mannose Binding Protein A (Native, Mpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Rat Mannose Binding Protein A (Native, Mpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:20.4
occ:1.00
 O C:HOH717 2.3 18.0 1.0
OE1 C:GLU165 2.4 17.3 1.0
O C:HOH742 2.5 17.7 1.0
O C:HOH718 2.5 18.4 1.0
OD1 C:ASP194 2.5 16.4 1.0
OD2 C:ASP194 2.6 18.0 1.0
CG C:ASP194 2.9 20.9 1.0
CD C:GLU165 3.6 19.9 1.0
CA C:CA701 4.0 19.9 1.0
CB C:GLU165 4.1 18.9 1.0
OD2 C:ASP188 4.2 18.4 1.0
O C:HOH796 4.2 22.1 1.0
CG C:GLU165 4.3 18.4 1.0
O C:HOH770 4.3 19.5 1.0
O C:ASP161 4.4 21.2 1.0
CB C:ASP194 4.4 20.2 1.0
OE2 C:GLU165 4.5 16.8 1.0
CA C:GLU165 4.5 21.3 1.0
O C:HOH810 4.7 39.5 1.0
O C:HOH769 4.7 27.6 1.0
OD2 C:ASP161 4.8 24.6 1.0
OD1 C:ASP161 4.9 20.9 1.0
CG C:ASP188 4.9 18.8 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: Sat Dec 12 03:04:18 2020

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