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Calcium in PDB 1kwv: Rat Mannose Binding Protein A Complexed with A-Me-Glcnac

Protein crystallography data

The structure of Rat Mannose Binding Protein A Complexed with A-Me-Glcnac, PDB code: 1kwv 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 (°) 79.000, 85.290, 98.330, 90.00, 105.60, 90.00
R / Rfree (%) 21.2 / 24.9

Other elements in 1kwv:

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

Calcium binding site 1 out of 9 in 1kwv

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Calcium binding site 1 out of 9 in the Rat Mannose Binding Protein A Complexed with A-Me-Glcnac


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 Complexed with A-Me-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:18.3
occ:1.00
 OD2 A:ASP161 2.2 18.1 1.0
O A:HOH524 2.3 20.5 1.0
OD2 A:ASP194 2.3 19.3 1.0
O A:GLU193 2.4 16.8 1.0
OE2 A:GLU165 2.5 23.5 1.0
OD2 A:ASP188 2.5 26.5 1.0
OD1 A:ASP161 2.5 20.1 1.0
OE1 A:GLU165 2.6 21.4 1.0
CG A:ASP161 2.7 20.8 1.0
CD A:GLU165 2.8 23.5 1.0
CG A:ASP188 3.3 28.3 1.0
C A:GLU193 3.4 17.9 1.0
CG A:ASP194 3.5 20.0 1.0
CA A:ASP194 3.7 16.7 1.0
CB A:ASP188 3.8 24.7 1.0
N A:ASP194 3.9 17.3 1.0
CA A:CA504 4.0 19.3 1.0
O A:HOH593 4.1 20.4 1.0
CB A:ASP194 4.2 19.1 1.0
CB A:ASP161 4.2 17.6 1.0
OD1 A:ASP188 4.2 24.9 1.0
CG A:GLU165 4.3 24.1 1.0
N A:GLU193 4.4 21.2 1.0
CA A:ASP188 4.4 26.1 1.0
OD1 A:ASP194 4.4 18.1 1.0
CA A:GLU193 4.5 20.1 1.0
CZ A:PHE168 4.6 21.8 1.0
O A:HOH555 4.7 33.6 1.0
O A:ASP161 4.7 18.2 1.0
N A:GLY166 4.7 25.4 1.0
OD1 A:ASP206 4.8 20.9 1.0
O A:HOH523 4.8 21.4 1.0
C A:ASP194 4.9 20.1 1.0
CA A:GLU165 4.9 23.8 1.0

Calcium binding site 2 out of 9 in 1kwv

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Calcium binding site 2 out of 9 in the Rat Mannose Binding Protein A Complexed with A-Me-Glcnac


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 Complexed with A-Me-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:24.2
occ:1.00
 OD2 A:ASP206 2.2 19.9 1.0
OD1 A:ASN187 2.4 27.0 1.0
OE2 A:GLU193 2.4 21.3 1.0
OD1 A:ASN205 2.5 24.1 1.0
O A:ASP206 2.5 21.5 1.0
OE2 A:GLU185 2.5 25.9 1.0
O4 A:NAG501 2.6 30.5 1.0
O3 A:NAG501 2.6 28.2 1.0
CG A:ASP206 3.3 25.9 1.0
C4 A:NAG501 3.3 31.6 1.0
CD A:GLU185 3.4 27.5 1.0
C3 A:NAG501 3.4 31.4 1.0
CD A:GLU193 3.4 21.9 1.0
CG A:ASN205 3.5 22.1 1.0
CG A:ASN187 3.5 29.5 1.0
C A:ASP206 3.6 22.0 1.0
OE1 A:GLU185 3.6 25.0 1.0
N A:ASP206 3.7 22.4 1.0
OE1 A:GLU193 3.8 25.9 1.0
ND2 A:ASN205 3.9 23.5 1.0
ND2 A:ASN187 4.0 24.8 1.0
OD1 A:ASP206 4.0 20.9 1.0
CA A:ASP206 4.0 20.7 1.0
CB A:ASP206 4.2 19.3 1.0
N A:ASN187 4.3 26.2 1.0
CB A:HIS189 4.4 36.0 1.0
C A:ASN205 4.5 22.2 1.0
CG A:GLU185 4.7 30.0 1.0
N A:ILE207 4.7 21.1 1.0
CB A:ASN187 4.7 25.7 1.0
CB A:ASN205 4.7 22.7 1.0
CG A:GLU193 4.7 22.2 1.0
N A:HIS189 4.8 31.9 1.0
C5 A:NAG501 4.8 32.6 1.0
C2 A:NAG501 4.8 34.1 1.0
CA A:ASN205 4.8 23.1 1.0
CB A:GLU193 4.9 23.3 1.0
CA A:ASN187 4.9 28.4 1.0
N A:ASP188 4.9 28.5 1.0

Calcium binding site 3 out of 9 in 1kwv

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Calcium binding site 3 out of 9 in the Rat Mannose Binding Protein A Complexed with A-Me-Glcnac


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 Complexed with A-Me-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:19.3
occ:1.00
 OE1 A:GLU165 2.2 21.4 1.0
O A:HOH593 2.3 20.4 1.0
OD1 A:ASP194 2.4 18.1 1.0
OD2 A:ASP194 2.6 19.3 1.0
CG A:ASP194 2.8 20.0 1.0
CD A:GLU165 3.4 23.5 1.0
CA A:CA502 4.0 18.3 1.0
CB A:GLU165 4.1 24.6 1.0
CG A:GLU165 4.1 24.1 1.0
OD2 A:ASP188 4.2 26.5 1.0
O A:ASP161 4.3 18.2 1.0
O A:HOH594 4.3 19.2 1.0
CB A:ASP194 4.4 19.1 1.0
O A:HOH592 4.4 23.7 1.0
OE2 A:GLU165 4.4 23.5 1.0
CA A:GLU165 4.5 23.8 1.0
O A:HOH518 4.5 35.4 1.0
O A:HOH608 4.7 51.0 1.0
OD2 A:ASP161 4.7 18.1 1.0
OD1 A:ASP188 4.9 24.9 1.0
CG A:ASP188 4.9 28.3 1.0
OD1 A:ASP161 5.0 20.1 1.0

Calcium binding site 4 out of 9 in 1kwv

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Calcium binding site 4 out of 9 in the Rat Mannose Binding Protein A Complexed with A-Me-Glcnac


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 Complexed with A-Me-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:33.4
occ:1.00
 O B:HOH624 2.1 34.0 1.0
OD2 B:ASP194 2.2 36.3 1.0
O B:GLU193 2.3 27.9 1.0
OD2 B:ASP161 2.4 32.8 1.0
OD2 B:ASP188 2.5 39.3 1.0
OE1 B:GLU165 2.6 33.4 1.0
OD1 B:ASP161 2.7 31.4 1.0
OE2 B:GLU165 2.8 39.6 1.0
CG B:ASP161 2.9 34.8 1.0
CD B:GLU165 3.0 38.9 1.0
C B:GLU193 3.3 33.8 1.0
CG B:ASP194 3.3 38.6 1.0
CG B:ASP188 3.4 42.5 1.0
CA B:CA604 3.5 45.8 1.0
CA B:ASP194 3.7 33.5 1.0
CB B:ASP188 3.8 40.1 1.0
N B:ASP194 3.9 32.0 1.0
O B:HOH645 3.9 34.8 1.0
CB B:ASP194 4.1 36.1 1.0
OD1 B:ASP194 4.3 38.1 1.0
O B:HOH623 4.3 34.2 1.0
N B:GLU193 4.3 41.3 1.0
OD1 B:ASP188 4.4 40.5 1.0
CA B:GLU193 4.4 36.5 1.0
CB B:ASP161 4.4 35.1 1.0
CZ B:PHE168 4.4 33.6 1.0
CA B:ASP188 4.4 42.3 1.0
CG B:GLU165 4.5 43.1 1.0
OD1 B:ASP206 4.6 26.8 1.0
O B:ASP161 4.8 39.8 1.0
O B:HOH630 4.9 38.4 1.0
C B:ASP194 4.9 33.8 1.0

Calcium binding site 5 out of 9 in 1kwv

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Calcium binding site 5 out of 9 in the Rat Mannose Binding Protein A Complexed with A-Me-Glcnac


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 Complexed with A-Me-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:33.4
occ:1.00
 OE2 B:GLU193 2.2 37.3 1.0
OD2 B:ASP206 2.3 27.6 1.0
OD1 B:ASN187 2.4 39.5 1.0
OE2 B:GLU185 2.5 31.4 1.0
O B:ASP206 2.5 30.8 1.0
OD1 B:ASN205 2.6 38.5 1.0
O3 B:NAG601 2.7 49.4 1.0
O4 B:NAG601 2.7 45.3 1.0
CD B:GLU193 3.3 39.6 1.0
CG B:ASP206 3.3 34.5 1.0
CD B:GLU185 3.4 31.9 1.0
CG B:ASN187 3.5 45.2 1.0
C4 B:NAG601 3.5 50.5 1.0
C3 B:NAG601 3.5 51.5 1.0
C B:ASP206 3.5 32.8 1.0
CG B:ASN205 3.6 37.4 1.0
OE1 B:GLU185 3.6 30.9 1.0
OE1 B:GLU193 3.7 40.5 1.0
N B:ASP206 3.7 33.1 1.0
ND2 B:ASN187 4.0 44.8 1.0
OD1 B:ASP206 4.0 26.8 1.0
ND2 B:ASN205 4.0 37.6 1.0
CA B:ASP206 4.0 32.2 1.0
CB B:ASP206 4.2 31.4 1.0
N B:ASN187 4.2 38.5 1.0
CB B:HIS189 4.4 54.2 1.0
C B:ASN205 4.5 35.1 1.0
CG B:GLU193 4.6 38.2 1.0
N B:HIS189 4.6 48.0 1.0
N B:ASP188 4.6 40.1 1.0
CB B:ASN187 4.6 41.0 1.0
N B:ILE207 4.7 31.0 1.0
CG B:GLU185 4.7 33.2 1.0
CB B:GLU193 4.7 37.1 1.0
CB B:ASN205 4.8 35.5 1.0
CA B:ASN187 4.8 39.8 1.0
C2 B:NAG601 4.9 52.1 1.0
CA B:ASN205 4.9 35.4 1.0
C5 B:NAG601 4.9 52.4 1.0
C B:ASN187 5.0 40.2 1.0

Calcium binding site 6 out of 9 in 1kwv

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Calcium binding site 6 out of 9 in the Rat Mannose Binding Protein A Complexed with A-Me-Glcnac


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 Complexed with A-Me-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:45.8
occ:1.00
 O B:HOH685 2.1 34.9 1.0
OE1 B:GLU165 2.4 33.4 1.0
O B:HOH630 2.5 38.4 1.0
OD2 B:ASP194 2.6 36.3 1.0
OD1 B:ASP194 2.6 38.1 1.0
O B:HOH645 2.6 34.8 1.0
CG B:ASP194 2.9 38.6 1.0
CA B:CA602 3.5 33.4 1.0
CD B:GLU165 3.6 38.9 1.0
OD2 B:ASP188 3.9 39.3 1.0
O B:ASP161 4.0 39.8 1.0
OD2 B:ASP161 4.1 32.8 1.0
CB B:GLU165 4.2 43.4 1.0
CG B:GLU165 4.3 43.1 1.0
CB B:ASP194 4.4 36.1 1.0
O B:HOH666 4.4 58.0 1.0
CA B:GLU165 4.5 41.2 1.0
OE2 B:GLU165 4.5 39.6 1.0
CG B:ASP161 4.6 34.8 1.0
CG B:ASP188 4.6 42.5 1.0
OD1 B:ASP161 4.6 31.4 1.0
OD1 B:ASP188 4.7 40.5 1.0
C B:ASP161 4.9 41.4 1.0
O B:HOH648 4.9 57.2 1.0
N B:GLU165 5.0 42.1 1.0

Calcium binding site 7 out of 9 in 1kwv

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Calcium binding site 7 out of 9 in the Rat Mannose Binding Protein A Complexed with A-Me-Glcnac


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 Complexed with A-Me-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:23.1
occ:1.00
 O C:GLU193 2.3 18.9 1.0
O C:HOH726 2.4 14.9 1.0
OD2 C:ASP161 2.4 21.9 1.0
OD2 C:ASP194 2.4 19.3 1.0
OE1 C:GLU165 2.5 21.0 1.0
OD2 C:ASP188 2.5 25.2 1.0
OE2 C:GLU165 2.6 23.5 1.0
OD1 C:ASP161 2.7 21.5 1.0
CD C:GLU165 2.9 25.1 1.0
CG C:ASP161 2.9 23.8 1.0
C C:GLU193 3.3 22.3 1.0
CG C:ASP188 3.4 23.2 1.0
CG C:ASP194 3.6 20.7 1.0
CB C:ASP188 3.8 22.0 1.0
CA C:ASP194 3.8 21.6 1.0
CA C:CA704 4.0 22.8 1.0
N C:ASP194 4.0 21.8 1.0
O C:HOH720 4.0 19.7 1.0
CB C:ASP194 4.3 21.1 1.0
OD1 C:ASP188 4.3 24.2 1.0
CA C:ASP188 4.4 23.5 1.0
CG C:GLU165 4.4 24.0 1.0
N C:GLU193 4.4 22.3 1.0
CB C:ASP161 4.4 23.8 1.0
CA C:GLU193 4.4 23.5 1.0
CZ C:PHE168 4.5 20.0 1.0
OD1 C:ASP194 4.5 19.7 1.0
N C:GLY166 4.6 27.0 1.0
OD1 C:ASP206 4.6 23.7 1.0
O C:HOH768 4.6 28.9 1.0
O C:HOH725 4.7 26.8 1.0
O C:ASP161 4.7 27.0 1.0
CA C:GLU165 4.9 27.5 1.0
O C:HOH719 5.0 22.0 1.0
C C:ASP194 5.0 22.0 1.0

Calcium binding site 8 out of 9 in 1kwv

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Calcium binding site 8 out of 9 in the Rat Mannose Binding Protein A Complexed with A-Me-Glcnac


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 Complexed with A-Me-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:23.7
occ:1.00
 OD2 C:ASP206 2.2 24.1 1.0
OE2 C:GLU193 2.3 25.5 1.0
O3 C:NAG701 2.5 22.7 1.0
OD1 C:ASN205 2.5 21.0 1.0
O C:ASP206 2.5 19.2 1.0
OD1 C:ASN187 2.6 24.0 1.0
O4 C:NAG701 2.6 27.8 1.0
OE2 C:GLU185 2.6 28.8 1.0
CG C:ASP206 3.3 23.7 1.0
CD C:GLU193 3.3 24.7 1.0
C3 C:NAG701 3.3 31.2 1.0
C4 C:NAG701 3.4 28.5 1.0
CG C:ASN205 3.4 27.2 1.0
CD C:GLU185 3.5 32.6 1.0
C C:ASP206 3.6 22.5 1.0
CG C:ASN187 3.6 24.9 1.0
OE1 C:GLU193 3.7 24.2 1.0
OE1 C:GLU185 3.7 32.0 1.0
N C:ASP206 3.8 24.2 1.0
ND2 C:ASN205 3.8 22.6 1.0
OD1 C:ASP206 4.0 23.7 1.0
ND2 C:ASN187 4.0 21.5 1.0
CA C:ASP206 4.1 23.6 1.0
CB C:ASP206 4.3 23.3 1.0
N C:ASN187 4.3 22.1 1.0
CB C:HIS189 4.4 25.7 1.0
C C:ASN205 4.5 26.6 1.0
CG C:GLU193 4.6 24.1 1.0
N C:HIS189 4.7 27.0 1.0
N C:ILE207 4.7 21.5 1.0
C2 C:NAG701 4.7 33.6 1.0
CB C:ASN205 4.7 25.4 1.0
C5 C:NAG701 4.8 36.0 1.0
CG C:GLU185 4.8 28.6 1.0
N C:ASP188 4.8 22.6 1.0
CB C:GLU193 4.8 25.4 1.0
CB C:ASN187 4.8 23.6 1.0
CA C:ASN205 4.9 25.3 1.0
CA C:ASN187 5.0 23.0 1.0

Calcium binding site 9 out of 9 in 1kwv

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Calcium binding site 9 out of 9 in the Rat Mannose Binding Protein A Complexed with A-Me-Glcnac


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 Complexed with A-Me-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca704

b:22.8
occ:1.00
 O C:HOH720 2.3 19.7 1.0
O C:HOH744 2.4 28.8 1.0
O C:HOH719 2.4 22.0 1.0
OE1 C:GLU165 2.4 21.0 1.0
OD1 C:ASP194 2.5 19.7 1.0
OD2 C:ASP194 2.6 19.3 1.0
CG C:ASP194 2.9 20.7 1.0
CD C:GLU165 3.6 25.1 1.0
CA C:CA702 4.0 23.1 1.0
CB C:GLU165 4.1 23.3 1.0
OD2 C:ASP188 4.1 25.2 1.0
O C:HOH802 4.3 29.4 1.0
CG C:GLU165 4.3 24.0 1.0
O C:ASP161 4.4 27.0 1.0
CB C:ASP194 4.4 21.1 1.0
O C:HOH771 4.4 23.6 1.0
CA C:GLU165 4.6 27.5 1.0
OE2 C:GLU165 4.6 23.5 1.0
O C:HOH819 4.6 35.6 1.0
OD2 C:ASP161 4.8 21.9 1.0
O C:HOH801 4.8 65.4 1.0
OD1 C:ASP188 4.9 24.2 1.0
CG C:ASP188 4.9 23.2 1.0
O C:HOH721 4.9 24.2 1.0
O C:HOH770 4.9 35.4 1.0
OD1 C:ASP161 5.0 21.5 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 11:31:47 2024

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