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Calcium in PDB 1kwz: Rat Mannose Protein A (H189V) Complexed with Man-A13-Man

Protein crystallography data

The structure of Rat Mannose Protein A (H189V) Complexed with Man-A13-Man, PDB code: 1kwz 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 (°) 79.350, 85.050, 98.160, 90.00, 106.90, 90.00
R / Rfree (%) 22.3 / 25.2

Other elements in 1kwz:

The structure of Rat Mannose Protein A (H189V) Complexed with Man-A13-Man 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 (H189V) Complexed with Man-A13-Man (pdb code 1kwz). 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 Protein A (H189V) Complexed with Man-A13-Man, PDB code: 1kwz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 1kwz

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Calcium binding site 1 out of 9 in the Rat Mannose Protein A (H189V) Complexed with Man-A13-Man


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 (H189V) Complexed with Man-A13-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:19.1
occ:1.00
 O A:HOH515 2.3 11.7 1.0
OD2 A:ASP161 2.4 17.0 1.0
O A:GLU193 2.4 20.7 1.0
OD2 A:ASP188 2.4 18.0 1.0
OD2 A:ASP194 2.5 13.7 1.0
OE2 A:GLU165 2.5 16.6 1.0
OE1 A:GLU165 2.6 13.3 1.0
OD1 A:ASP161 2.6 16.4 1.0
CG A:ASP161 2.9 21.7 1.0
CD A:GLU165 2.9 15.0 1.0
CG A:ASP188 3.3 20.0 1.0
C A:GLU193 3.3 20.4 1.0
CG A:ASP194 3.6 12.9 1.0
CA A:ASP194 3.8 15.2 1.0
CB A:ASP188 3.9 19.6 1.0
N A:ASP194 3.9 18.9 1.0
CA A:CA505 4.1 21.5 1.0
OD1 A:ASP188 4.1 17.9 1.0
N A:GLU193 4.2 18.1 1.0
CB A:ASP194 4.3 18.1 1.0
O A:HOH547 4.3 29.5 1.0
CB A:ASP161 4.4 18.0 1.0
CA A:GLU193 4.4 18.4 1.0
CG A:GLU165 4.4 16.4 1.0
CA A:ASP188 4.5 20.0 1.0
OD1 A:ASP194 4.5 13.2 1.0
CZ A:PHE168 4.5 19.2 1.0
OD1 A:ASP206 4.6 14.8 1.0
O A:HOH520 4.6 22.2 1.0
O A:HOH508 4.7 16.0 1.0
N A:GLY166 4.7 22.8 1.0
O A:ASP161 4.9 20.0 1.0

Calcium binding site 2 out of 9 in 1kwz

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Calcium binding site 2 out of 9 in the Rat Mannose Protein A (H189V) Complexed with Man-A13-Man


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 (H189V) Complexed with Man-A13-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:21.5
occ:1.00
 OD2 A:ASP206 2.3 17.2 1.0
OD1 A:ASN205 2.4 20.5 1.0
OD1 A:ASN187 2.4 23.5 1.0
OE2 A:GLU193 2.5 18.5 1.0
O A:ASP206 2.5 19.0 1.0
OE2 A:GLU185 2.6 22.3 1.0
O3 A:MAN502 2.8 30.6 1.0
O4 A:MAN502 2.9 25.7 1.0
CG A:ASP206 3.3 17.2 1.0
CD A:GLU185 3.4 26.1 1.0
CG A:ASN205 3.4 19.2 1.0
CG A:ASN187 3.4 28.1 1.0
CD A:GLU193 3.4 21.2 1.0
C A:ASP206 3.5 19.8 1.0
N A:ASP206 3.6 20.7 1.0
OE1 A:GLU185 3.6 23.0 1.0
C3 A:MAN502 3.7 31.5 1.0
C4 A:MAN502 3.8 31.2 1.0
OE1 A:GLU193 3.8 20.1 1.0
ND2 A:ASN205 3.9 17.0 1.0
ND2 A:ASN187 3.9 29.3 1.0
CA A:ASP206 4.0 18.1 1.0
OD1 A:ASP206 4.1 14.8 1.0
N A:ASN187 4.2 24.0 1.0
CB A:ASP206 4.2 18.2 1.0
C A:ASN205 4.4 18.6 1.0
CB A:ASN187 4.6 26.3 1.0
CB A:ASN205 4.7 17.1 1.0
CG A:GLU185 4.7 22.0 1.0
N A:ILE207 4.7 17.1 1.0
CG A:GLU193 4.7 18.3 1.0
N A:ASP188 4.7 23.5 1.0
CG1 A:VAL189 4.8 28.3 1.0
CG2 A:VAL189 4.8 33.8 1.0
CA A:ASN205 4.8 17.9 1.0
CA A:ASN187 4.8 23.1 1.0
CB A:GLU193 4.9 16.4 1.0
N A:VAL189 5.0 23.3 1.0

Calcium binding site 3 out of 9 in 1kwz

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Calcium binding site 3 out of 9 in the Rat Mannose Protein A (H189V) Complexed with Man-A13-Man


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 (H189V) Complexed with Man-A13-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:21.5
occ:1.00
 OE1 A:GLU165 2.3 13.3 1.0
O A:HOH547 2.3 29.5 1.0
OD1 A:ASP194 2.5 13.2 1.0
OD2 A:ASP194 2.7 13.7 1.0
CG A:ASP194 2.9 12.9 1.0
CD A:GLU165 3.4 15.0 1.0
CB A:GLU165 4.0 19.4 1.0
CA A:CA503 4.1 19.1 1.0
CG A:GLU165 4.1 16.4 1.0
O A:ASP161 4.3 20.0 1.0
O A:HOH517 4.4 23.0 1.0
OE2 A:GLU165 4.4 16.6 1.0
CB A:ASP194 4.5 18.1 1.0
CA A:GLU165 4.5 21.8 1.0
OD2 A:ASP188 4.5 18.0 1.0
O A:HOH576 4.7 41.5 1.0
O A:HOH564 4.8 26.5 1.0
OD2 A:ASP161 4.8 17.0 1.0
OD1 A:ASP161 4.9 16.4 1.0

Calcium binding site 4 out of 9 in 1kwz

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Calcium binding site 4 out of 9 in the Rat Mannose Protein A (H189V) Complexed with Man-A13-Man


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 (H189V) Complexed with Man-A13-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:24.4
occ:1.00
 O B:HOH612 2.3 18.8 1.0
OD2 B:ASP161 2.4 19.9 1.0
O B:GLU193 2.4 20.2 1.0
OD2 B:ASP194 2.5 19.1 1.0
OE2 B:GLU165 2.6 27.2 1.0
OD2 B:ASP188 2.6 26.2 1.0
OE1 B:GLU165 2.6 20.4 1.0
OD1 B:ASP161 2.6 19.8 1.0
CG B:ASP161 2.9 20.2 1.0
CD B:GLU165 2.9 26.7 1.0
C B:GLU193 3.3 25.0 1.0
CG B:ASP188 3.4 31.1 1.0
CG B:ASP194 3.6 20.5 1.0
CA B:ASP194 3.7 23.4 1.0
CA B:CA605 3.8 26.6 1.0
N B:ASP194 3.9 22.5 1.0
CB B:ASP188 3.9 28.9 1.0
O B:HOH639 4.1 28.6 1.0
O B:HOH633 4.2 29.4 1.0
CB B:ASP194 4.2 21.8 1.0
OD1 B:ASP188 4.3 27.2 1.0
N B:GLU193 4.4 29.7 1.0
CB B:ASP161 4.4 19.8 1.0
CA B:GLU193 4.4 28.5 1.0
CG B:GLU165 4.4 26.3 1.0
CZ B:PHE168 4.5 15.9 1.0
OD1 B:ASP194 4.5 28.5 1.0
OD1 B:ASP206 4.5 24.1 1.0
CA B:ASP188 4.6 31.5 1.0
O B:ASP161 4.6 21.5 1.0
N B:GLY166 4.8 23.3 1.0
O B:HOH611 4.9 26.0 1.0
C B:ASP194 4.9 23.4 1.0

Calcium binding site 5 out of 9 in 1kwz

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Calcium binding site 5 out of 9 in the Rat Mannose Protein A (H189V) Complexed with Man-A13-Man


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 (H189V) Complexed with Man-A13-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:32.2
occ:1.00
 OD2 B:ASP206 2.4 20.6 1.0
OE2 B:GLU185 2.4 28.0 1.0
OE2 B:GLU193 2.5 26.6 1.0
OD1 B:ASN187 2.5 35.5 1.0
OD1 B:ASN205 2.5 27.6 1.0
O3 B:MAN602 2.5 38.9 1.0
O B:ASP206 2.6 23.1 1.0
O4 B:MAN602 2.6 36.8 1.0
CD B:GLU185 3.3 29.1 1.0
C3 B:MAN602 3.3 43.8 1.0
CG B:ASP206 3.4 24.6 1.0
C4 B:MAN602 3.4 44.2 1.0
CD B:GLU193 3.4 28.6 1.0
OE1 B:GLU185 3.5 26.2 1.0
CG B:ASN205 3.5 28.3 1.0
CG B:ASN187 3.5 35.1 1.0
C B:ASP206 3.6 25.4 1.0
N B:ASP206 3.7 21.4 1.0
OE1 B:GLU193 3.8 27.7 1.0
ND2 B:ASN205 3.9 26.1 1.0
ND2 B:ASN187 4.1 30.9 1.0
CA B:ASP206 4.1 23.7 1.0
OD1 B:ASP206 4.1 24.1 1.0
N B:ASN187 4.2 29.8 1.0
CB B:ASP206 4.3 25.4 1.0
CG2 B:VAL189 4.4 39.4 1.0
C B:ASN205 4.5 25.1 1.0
CG B:GLU185 4.6 28.2 1.0
CB B:ASN187 4.7 32.3 1.0
N B:ASP188 4.7 29.6 1.0
CB B:ASN205 4.7 28.4 1.0
CG B:GLU193 4.7 30.4 1.0
C2 B:MAN602 4.8 47.1 1.0
N B:ILE207 4.8 23.6 1.0
C5 B:MAN602 4.8 46.0 1.0
CA B:ASN205 4.8 27.0 1.0
CA B:ASN187 4.8 31.2 1.0
CB B:GLU193 4.9 28.9 1.0

Calcium binding site 6 out of 9 in 1kwz

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Calcium binding site 6 out of 9 in the Rat Mannose Protein A (H189V) Complexed with Man-A13-Man


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 (H189V) Complexed with Man-A13-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca605

b:26.6
occ:1.00
 O B:HOH611 2.3 26.0 1.0
OE1 B:GLU165 2.3 20.4 1.0
O B:HOH618 2.3 23.1 1.0
O B:HOH639 2.5 28.6 1.0
OD2 B:ASP194 2.5 19.1 1.0
O B:HOH647 2.5 39.5 1.0
OD1 B:ASP194 2.6 28.5 1.0
CG B:ASP194 2.9 20.5 1.0
CD B:GLU165 3.5 26.7 1.0
CA B:CA603 3.8 24.4 1.0
O B:ASP161 4.0 21.5 1.0
OD2 B:ASP188 4.1 26.2 1.0
CB B:GLU165 4.2 21.7 1.0
CG B:GLU165 4.3 26.3 1.0
O B:HOH629 4.4 28.5 1.0
CB B:ASP194 4.5 21.8 1.0
OE2 B:GLU165 4.5 27.2 1.0
CA B:GLU165 4.5 22.1 1.0
OD2 B:ASP161 4.5 19.9 1.0
OD1 B:ASP188 4.7 27.2 1.0
OD1 B:ASP161 4.7 19.8 1.0
O B:HOH641 4.7 33.4 1.0
CG B:ASP188 4.8 31.1 1.0
O B:HOH657 4.8 35.9 1.0
CG B:ASP161 4.8 20.2 1.0

Calcium binding site 7 out of 9 in 1kwz

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Calcium binding site 7 out of 9 in the Rat Mannose Protein A (H189V) Complexed with Man-A13-Man


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 (H189V) Complexed with Man-A13-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:22.6
occ:1.00
 O C:GLU193 2.2 22.9 1.0
O C:HOH708 2.3 16.3 1.0
OD2 C:ASP194 2.4 22.9 1.0
OD2 C:ASP188 2.4 22.9 1.0
OE1 C:GLU165 2.6 19.9 1.0
OD2 C:ASP161 2.6 22.1 1.0
OE2 C:GLU165 2.7 20.4 1.0
OD1 C:ASP161 2.7 23.2 1.0
CD C:GLU165 3.0 21.9 1.0
CG C:ASP161 3.0 25.5 1.0
C C:GLU193 3.2 20.7 1.0
CG C:ASP188 3.3 22.2 1.0
CG C:ASP194 3.5 25.0 1.0
CA C:ASP194 3.6 22.1 1.0
N C:ASP194 3.7 21.2 1.0
CB C:ASP188 3.8 23.7 1.0
CA C:CA705 3.9 20.7 1.0
O C:HOH707 3.9 23.2 1.0
CB C:ASP194 4.1 23.3 1.0
N C:GLU193 4.2 21.8 1.0
OD1 C:ASP188 4.3 18.1 1.0
CA C:GLU193 4.3 21.9 1.0
CZ C:PHE168 4.5 26.4 1.0
CG C:GLU165 4.5 21.9 1.0
CA C:ASP188 4.5 22.2 1.0
OD1 C:ASP194 4.5 23.9 1.0
CB C:ASP161 4.5 23.6 1.0
O C:HOH718 4.6 27.1 1.0
OD1 C:ASP206 4.6 27.9 1.0
O C:HOH735 4.7 25.6 1.0
N C:GLY166 4.8 29.0 1.0
C C:ASP194 4.8 21.9 1.0
O C:ASP161 4.9 25.9 1.0
CB C:GLU193 4.9 23.9 1.0
O C:HOH709 4.9 21.4 1.0

Calcium binding site 8 out of 9 in 1kwz

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Calcium binding site 8 out of 9 in the Rat Mannose Protein A (H189V) Complexed with Man-A13-Man


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 (H189V) Complexed with Man-A13-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca704

b:25.7
occ:1.00
 OD2 C:ASP206 2.1 20.2 1.0
OD1 C:ASN187 2.4 23.3 1.0
OE2 C:GLU193 2.4 21.7 1.0
OD1 C:ASN205 2.5 26.1 1.0
OE2 C:GLU185 2.5 26.4 1.0
O C:ASP206 2.5 23.1 1.0
O3 C:MAN702 2.7 33.4 1.0
O4 C:MAN702 2.8 36.1 1.0
CG C:ASP206 3.2 23.6 1.0
CD C:GLU193 3.3 22.0 1.0
CD C:GLU185 3.3 30.1 1.0
CG C:ASN187 3.5 24.1 1.0
CG C:ASN205 3.5 32.7 1.0
C4 C:MAN702 3.5 39.9 1.0
C3 C:MAN702 3.6 40.4 1.0
C C:ASP206 3.6 24.1 1.0
OE1 C:GLU185 3.6 28.7 1.0
OE1 C:GLU193 3.6 24.0 1.0
N C:ASP206 3.7 25.8 1.0
ND2 C:ASN205 4.0 28.7 1.0
ND2 C:ASN187 4.0 26.1 1.0
OD1 C:ASP206 4.0 27.9 1.0
CA C:ASP206 4.0 23.9 1.0
N C:ASN187 4.1 26.9 1.0
CB C:ASP206 4.2 23.0 1.0
CG1 C:VAL189 4.5 33.1 1.0
C C:ASN205 4.5 28.4 1.0
N C:ASP188 4.6 23.0 1.0
CG C:GLU185 4.6 29.7 1.0
CG C:GLU193 4.6 22.4 1.0
CB C:ASN187 4.7 25.7 1.0
N C:ILE207 4.7 21.9 1.0
CB C:GLU193 4.8 23.9 1.0
CB C:ASN205 4.8 30.2 1.0
CA C:ASN187 4.8 24.8 1.0
N C:VAL189 4.9 24.6 1.0
CA C:ASN205 4.9 30.5 1.0
CG2 C:VAL189 4.9 31.6 1.0
C2 C:MAN702 4.9 43.0 1.0
C5 C:MAN702 5.0 43.1 1.0
CB C:GLU185 5.0 32.0 1.0

Calcium binding site 9 out of 9 in 1kwz

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Calcium binding site 9 out of 9 in the Rat Mannose Protein A (H189V) Complexed with Man-A13-Man


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 (H189V) Complexed with Man-A13-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca705

b:20.7
occ:1.00
 O C:HOH707 2.2 23.2 1.0
O C:HOH709 2.4 21.4 1.0
OE1 C:GLU165 2.4 19.9 1.0
O C:HOH711 2.4 23.7 1.0
OD1 C:ASP194 2.5 23.9 1.0
OD2 C:ASP194 2.5 22.9 1.0
CG C:ASP194 2.9 25.0 1.0
CD C:GLU165 3.6 21.9 1.0
CA C:CA703 3.9 22.6 1.0
OD2 C:ASP188 4.2 22.9 1.0
CB C:GLU165 4.2 23.8 1.0
O C:HOH715 4.3 21.9 1.0
CG C:GLU165 4.3 21.9 1.0
CB C:ASP194 4.4 23.3 1.0
O C:ASP161 4.6 25.9 1.0
OE2 C:GLU165 4.6 20.4 1.0
O C:HOH720 4.6 32.1 1.0
CA C:GLU165 4.7 27.3 1.0
O C:HOH726 4.7 31.2 1.0
OD1 C:ASP188 4.9 18.1 1.0
CG C:ASP188 4.9 22.2 1.0
OD2 C:ASP161 4.9 22.1 1.0
O C:HOH772 4.9 45.5 1.0
OD1 C:ASP161 4.9 23.2 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 11:37:01 2024

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