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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

Go back to Calcium Binding Sites List in 1kwt
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: Thu Jul 11 11:31:35 2024

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