Atomistry » Calcium » PDB 1krf-1l3f » 1kwy
Atomistry »
  Calcium »
    PDB 1krf-1l3f »
      1kwy »

Calcium in PDB 1kwy: Rat Mannose Protein A Complexed with Man-A13-Man.

Protein crystallography data

The structure of Rat Mannose Protein A Complexed with Man-A13-Man., PDB code: 1kwy 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 (°) 78.860, 85.250, 98.130, 90.00, 107.34, 90.00
R / Rfree (%) 19.8 / 23.1

Other elements in 1kwy:

The structure of Rat Mannose Protein A 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 Complexed with Man-A13-Man. (pdb code 1kwy). 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 Man-A13-Man., PDB code: 1kwy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 1kwy

Go back to Calcium Binding Sites List in 1kwy
Calcium binding site 1 out of 10 in the Rat Mannose Protein A 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 Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:17.1
occ:1.00
 OD2 A:ASP161 2.3 17.0 1.0
O A:HOH626 2.4 14.7 1.0
OD2 A:ASP194 2.4 15.0 1.0
O A:GLU193 2.4 18.3 1.0
OD2 A:ASP188 2.5 19.6 1.0
OE2 A:GLU165 2.5 16.6 1.0
OE1 A:GLU165 2.6 15.7 1.0
OD1 A:ASP161 2.6 13.4 1.0
CG A:ASP161 2.8 16.3 1.0
CD A:GLU165 2.9 16.9 1.0
CG A:ASP188 3.3 19.7 1.0
C A:GLU193 3.3 18.5 1.0
CG A:ASP194 3.5 16.3 1.0
CA A:ASP194 3.7 15.8 1.0
CB A:ASP188 3.8 20.2 1.0
N A:ASP194 3.9 16.6 1.0
CA A:CA505 3.9 17.6 1.0
O A:HOH686 4.0 21.2 1.0
OD1 A:ASP188 4.2 20.3 1.0
CB A:ASP194 4.2 17.2 1.0
N A:GLU193 4.3 18.0 1.0
CB A:ASP161 4.3 15.1 1.0
CA A:ASP188 4.4 20.2 1.0
CG A:GLU165 4.4 16.3 1.0
CA A:GLU193 4.4 17.4 1.0
OD1 A:ASP194 4.5 15.5 1.0
CZ A:PHE168 4.6 13.4 1.0
N A:GLY166 4.6 18.8 1.0
O A:HOH652 4.7 18.5 1.0
O A:ASP161 4.7 18.8 1.0
O A:HOH625 4.7 21.5 1.0
OD1 A:ASP206 4.7 16.5 1.0
CA A:GLU165 4.9 17.5 1.0
C A:ASP194 5.0 16.7 1.0

Calcium binding site 2 out of 10 in 1kwy

Go back to Calcium Binding Sites List in 1kwy
Calcium binding site 2 out of 10 in the Rat Mannose Protein A 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 Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:20.3
occ:1.00
 OD2 A:ASP206 2.3 16.2 1.0
OD1 A:ASN205 2.4 17.2 1.0
OE2 A:GLU193 2.5 22.2 1.0
OD1 A:ASN187 2.5 18.2 1.0
OE2 A:GLU185 2.5 16.7 1.0
O3 A:MAN502 2.5 25.5 1.0
O A:ASP206 2.6 16.3 1.0
O4 A:MAN502 2.7 27.0 1.0
CD A:GLU185 3.3 23.3 1.0
CG A:ASP206 3.4 19.5 1.0
CG A:ASN205 3.4 18.6 1.0
C3 A:MAN502 3.4 29.1 1.0
C4 A:MAN502 3.5 27.0 1.0
CD A:GLU193 3.5 19.9 1.0
CG A:ASN187 3.5 19.7 1.0
OE1 A:GLU185 3.6 20.7 1.0
C A:ASP206 3.6 18.2 1.0
N A:ASP206 3.7 19.3 1.0
ND2 A:ASN205 3.8 17.7 1.0
OE1 A:GLU193 3.8 20.5 1.0
ND2 A:ASN187 4.0 19.3 1.0
CA A:ASP206 4.1 17.7 1.0
OD1 A:ASP206 4.1 16.5 1.0
N A:ASN187 4.2 20.5 1.0
CB A:ASP206 4.3 19.0 1.0
C A:ASN205 4.5 18.7 1.0
CB A:HIS189 4.6 28.1 1.0
CG A:GLU185 4.6 20.7 1.0
CB A:ASN205 4.7 17.5 1.0
CB A:ASN187 4.7 18.5 1.0
N A:ILE207 4.8 17.9 1.0
CG A:GLU193 4.8 20.0 1.0
N A:HIS189 4.8 22.9 1.0
N A:ASP188 4.8 19.8 1.0
C2 A:MAN502 4.8 32.2 1.0
CA A:ASN205 4.8 17.8 1.0
CA A:ASN187 4.9 20.8 1.0
C5 A:MAN502 4.9 33.2 1.0
CB A:GLU193 4.9 16.0 1.0

Calcium binding site 3 out of 10 in 1kwy

Go back to Calcium Binding Sites List in 1kwy
Calcium binding site 3 out of 10 in the Rat Mannose Protein A 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 Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:17.6
occ:1.00
 O A:HOH686 2.2 21.2 1.0
OE1 A:GLU165 2.2 15.7 1.0
OD1 A:ASP194 2.5 15.5 1.0
OD2 A:ASP194 2.6 15.0 1.0
CG A:ASP194 2.9 16.3 1.0
CD A:GLU165 3.4 16.9 1.0
CA A:CA503 3.9 17.1 1.0
CB A:GLU165 4.0 18.6 1.0
CG A:GLU165 4.1 16.3 1.0
O A:HOH687 4.2 15.9 1.0
OD2 A:ASP188 4.2 19.6 1.0
O A:ASP161 4.3 18.8 1.0
CB A:ASP194 4.4 17.2 1.0
OE2 A:GLU165 4.4 16.6 1.0
CA A:GLU165 4.5 17.5 1.0
O A:HOH685 4.5 31.1 1.0
O A:HOH620 4.6 28.6 1.0
OD2 A:ASP161 4.8 17.0 1.0
OD1 A:ASP188 4.9 20.3 1.0
CG A:ASP188 4.9 19.7 1.0
OD1 A:ASP161 4.9 13.4 1.0
N A:GLU165 5.0 16.4 1.0

Calcium binding site 4 out of 10 in 1kwy

Go back to Calcium Binding Sites List in 1kwy
Calcium binding site 4 out of 10 in the Rat Mannose Protein A 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 Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca606

b:77.8
occ:1.00
 O A:HOH711 2.4 29.6 1.0
O A:HOH715 2.7 33.7 1.0
O A:ASN187 4.4 22.6 1.0

Calcium binding site 5 out of 10 in 1kwy

Go back to Calcium Binding Sites List in 1kwy
Calcium binding site 5 out of 10 in the Rat Mannose Protein A 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 Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:20.1
occ:1.00
 O B:HOH625 2.3 20.3 1.0
OD2 B:ASP194 2.3 17.9 1.0
OD2 B:ASP161 2.4 22.2 1.0
O B:GLU193 2.4 21.4 1.0
OE2 B:GLU165 2.4 17.2 1.0
OE1 B:GLU165 2.6 19.5 1.0
OD1 B:ASP161 2.7 16.5 1.0
OD2 B:ASP188 2.8 28.2 1.0
CD B:GLU165 2.9 22.8 1.0
CG B:ASP161 2.9 22.9 1.0
C B:GLU193 3.3 22.6 1.0
CG B:ASP188 3.5 28.9 1.0
CG B:ASP194 3.5 20.3 1.0
CA B:ASP194 3.7 21.5 1.0
CA B:CA605 3.8 23.9 1.0
N B:ASP194 3.9 21.6 1.0
CB B:ASP188 4.0 25.5 1.0
O B:HOH624 4.0 22.3 1.0
O B:HOH647 4.0 22.5 1.0
CB B:ASP194 4.2 21.3 1.0
OD1 B:ASP188 4.3 27.0 1.0
N B:GLU193 4.3 23.7 1.0
CG B:GLU165 4.4 22.1 1.0
CB B:ASP161 4.4 20.5 1.0
CA B:GLU193 4.4 23.8 1.0
CA B:ASP188 4.4 27.4 1.0
OD1 B:ASP194 4.4 20.8 1.0
CZ B:PHE168 4.6 18.3 1.0
OD1 B:ASP206 4.6 23.3 1.0
O B:ASP161 4.8 22.6 1.0
N B:GLY166 4.8 21.7 1.0
C B:ASP194 4.9 21.8 1.0

Calcium binding site 6 out of 10 in 1kwy

Go back to Calcium Binding Sites List in 1kwy
Calcium binding site 6 out of 10 in the Rat Mannose Protein A 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 Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:26.3
occ:1.00
 OE2 B:GLU193 2.2 24.8 1.0
OD2 B:ASP206 2.4 23.5 1.0
OD1 B:ASN187 2.4 31.7 1.0
O4 B:MAN602 2.4 33.5 1.0
O B:ASP206 2.5 21.0 1.0
OD1 B:ASN205 2.6 25.8 1.0
O3 B:MAN602 2.6 33.9 1.0
OE2 B:GLU185 2.6 21.9 1.0
CD B:GLU193 3.3 26.4 1.0
C3 B:MAN602 3.3 37.0 1.0
C4 B:MAN602 3.3 38.4 1.0
CG B:ASP206 3.4 24.8 1.0
CD B:GLU185 3.4 24.8 1.0
CG B:ASN205 3.5 24.4 1.0
C B:ASP206 3.5 24.2 1.0
CG B:ASN187 3.5 30.8 1.0
OE1 B:GLU185 3.6 23.6 1.0
OE1 B:GLU193 3.6 28.9 1.0
N B:ASP206 3.8 22.2 1.0
ND2 B:ASN205 3.9 23.8 1.0
CA B:ASP206 4.1 23.1 1.0
ND2 B:ASN187 4.1 32.1 1.0
OD1 B:ASP206 4.1 23.3 1.0
CB B:ASP206 4.3 23.1 1.0
N B:ASN187 4.3 26.3 1.0
CB B:HIS189 4.4 38.2 1.0
CG B:GLU193 4.6 25.2 1.0
C B:ASN205 4.6 24.4 1.0
N B:ILE207 4.6 25.3 1.0
C5 B:MAN602 4.7 39.4 1.0
CG B:GLU185 4.7 22.5 1.0
CB B:ASN187 4.7 27.0 1.0
C2 B:MAN602 4.7 39.0 1.0
N B:HIS189 4.7 32.4 1.0
CB B:GLU193 4.8 24.6 1.0
CB B:ASN205 4.8 24.5 1.0
N B:ASP188 4.8 26.8 1.0
CA B:ASN187 4.9 27.6 1.0
CA B:ASN205 4.9 24.8 1.0
CA B:ILE207 5.0 24.6 1.0

Calcium binding site 7 out of 10 in 1kwy

Go back to Calcium Binding Sites List in 1kwy
Calcium binding site 7 out of 10 in the Rat Mannose Protein A 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 Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca605

b:23.9
occ:1.00
 O B:HOH630 2.3 21.7 1.0
OE1 B:GLU165 2.3 19.5 1.0
O B:HOH666 2.3 26.6 1.0
O B:HOH680 2.4 26.9 1.0
OD1 B:ASP194 2.5 20.8 1.0
O B:HOH647 2.5 22.5 1.0
OD2 B:ASP194 2.5 17.9 1.0
CG B:ASP194 2.8 20.3 1.0
CD B:GLU165 3.5 22.8 1.0
CA B:CA603 3.8 20.1 1.0
O B:ASP161 4.1 22.6 1.0
OD2 B:ASP188 4.1 28.2 1.0
CB B:GLU165 4.2 20.4 1.0
O B:HOH722 4.3 35.0 1.0
CB B:ASP194 4.3 21.3 1.0
CG B:GLU165 4.3 22.1 1.0
OE2 B:GLU165 4.4 17.2 1.0
O B:HOH713 4.5 32.4 1.0
O B:HOH667 4.5 43.8 1.0
CA B:GLU165 4.6 21.7 1.0
OD2 B:ASP161 4.6 22.2 1.0
OD1 B:ASP188 4.6 27.0 1.0
OD1 B:ASP161 4.7 16.5 1.0
O B:HOH668 4.7 34.2 1.0
CG B:ASP188 4.8 28.9 1.0
CG B:ASP161 4.8 22.9 1.0
O B:HOH650 4.9 30.7 1.0

Calcium binding site 8 out of 10 in 1kwy

Go back to Calcium Binding Sites List in 1kwy
Calcium binding site 8 out of 10 in the Rat Mannose Protein A 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 Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:22.4
occ:1.00
 O C:HOH726 2.3 17.1 1.0
O C:GLU193 2.3 18.6 1.0
OD2 C:ASP194 2.4 16.3 1.0
OD2 C:ASP161 2.4 26.6 1.0
OD2 C:ASP188 2.5 18.3 1.0
OE1 C:GLU165 2.5 23.2 1.0
OE2 C:GLU165 2.6 23.2 1.0
OD1 C:ASP161 2.7 22.6 1.0
CG C:ASP161 2.9 26.1 1.0
CD C:GLU165 2.9 22.7 1.0
C C:GLU193 3.3 21.0 1.0
CG C:ASP188 3.4 21.3 1.0
CG C:ASP194 3.5 19.4 1.0
CA C:ASP194 3.7 19.9 1.0
CB C:ASP188 3.8 21.1 1.0
N C:ASP194 3.9 19.8 1.0
O C:HOH720 3.9 21.2 1.0
CA C:CA705 4.0 22.9 1.0
CB C:ASP194 4.2 18.6 1.0
N C:GLU193 4.3 23.1 1.0
OD1 C:ASP188 4.3 21.3 1.0
CA C:ASP188 4.3 22.1 1.0
CA C:GLU193 4.4 21.6 1.0
CB C:ASP161 4.4 25.1 1.0
CG C:GLU165 4.4 21.7 1.0
CZ C:PHE168 4.4 23.9 1.0
OD1 C:ASP194 4.5 17.3 1.0
OD1 C:ASP206 4.6 24.4 1.0
N C:GLY166 4.7 24.9 1.0
O C:HOH725 4.7 24.5 1.0
O C:HOH766 4.8 24.5 1.0
O C:ASP161 4.8 25.2 1.0
CA C:GLU165 4.9 24.7 1.0
C C:ASP194 4.9 20.3 1.0
N C:ASP188 5.0 22.8 1.0
CE1 C:PHE168 5.0 21.4 1.0

Calcium binding site 9 out of 10 in 1kwy

Go back to Calcium Binding Sites List in 1kwy
Calcium binding site 9 out of 10 in the Rat Mannose Protein A 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 Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca704

b:21.8
occ:1.00
 OD2 C:ASP206 2.1 22.7 1.0
OE2 C:GLU193 2.4 25.3 1.0
OD1 C:ASN205 2.4 23.1 1.0
OD1 C:ASN187 2.5 19.5 1.0
OE2 C:GLU185 2.5 27.6 1.0
O4 C:MAN702 2.5 31.7 1.0
O C:ASP206 2.5 20.8 1.0
O3 C:MAN702 2.7 28.5 1.0
CG C:ASP206 3.2 23.4 1.0
CD C:GLU193 3.4 23.2 1.0
CD C:GLU185 3.4 28.3 1.0
CG C:ASN205 3.4 26.3 1.0
C3 C:MAN702 3.4 35.0 1.0
C4 C:MAN702 3.4 36.8 1.0
CG C:ASN187 3.5 19.9 1.0
C C:ASP206 3.6 23.7 1.0
OE1 C:GLU185 3.6 25.3 1.0
N C:ASP206 3.7 22.6 1.0
OE1 C:GLU193 3.7 24.8 1.0
ND2 C:ASN205 3.8 24.5 1.0
CA C:ASP206 4.0 22.2 1.0
OD1 C:ASP206 4.0 24.4 1.0
ND2 C:ASN187 4.0 18.9 1.0
N C:ASN187 4.1 24.6 1.0
CB C:ASP206 4.2 22.6 1.0
C C:ASN205 4.5 25.2 1.0
CB C:HIS189 4.6 24.6 1.0
CG C:GLU193 4.7 22.5 1.0
CG C:GLU185 4.7 26.2 1.0
CB C:ASN187 4.7 23.4 1.0
CB C:ASN205 4.7 24.4 1.0
N C:ILE207 4.7 23.4 1.0
N C:HIS189 4.8 24.4 1.0
C5 C:MAN702 4.8 39.4 1.0
N C:ASP188 4.8 22.8 1.0
CA C:ASN187 4.8 23.4 1.0
CA C:ASN205 4.8 25.4 1.0
CB C:GLU193 4.8 23.5 1.0
C2 C:MAN702 4.9 38.2 1.0

Calcium binding site 10 out of 10 in 1kwy

Go back to Calcium Binding Sites List in 1kwy
Calcium binding site 10 out of 10 in the Rat Mannose Protein A 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 10 of Rat Mannose Protein A Complexed with Man-A13-Man. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca705

b:22.9
occ:1.00
 O C:HOH719 2.4 18.5 1.0
O C:HOH720 2.4 21.2 1.0
OE1 C:GLU165 2.4 23.2 1.0
OD1 C:ASP194 2.5 17.3 1.0
OD2 C:ASP194 2.6 16.3 1.0
O C:HOH742 2.6 26.4 1.0
CG C:ASP194 2.9 19.4 1.0
CD C:GLU165 3.6 22.7 1.0
CA C:CA703 4.0 22.4 1.0
CB C:GLU165 4.1 24.4 1.0
OD2 C:ASP188 4.2 18.3 1.0
CG C:GLU165 4.3 21.7 1.0
O C:HOH791 4.3 28.3 1.0
CB C:ASP194 4.4 18.6 1.0
O C:HOH768 4.4 20.5 1.0
O C:ASP161 4.4 25.2 1.0
CA C:GLU165 4.5 24.7 1.0
OE2 C:GLU165 4.6 23.2 1.0
O C:HOH767 4.6 30.1 1.0
OD2 C:ASP161 4.7 26.6 1.0
O C:HOH800 4.8 47.4 1.0
OD1 C:ASP161 4.9 22.6 1.0
CG C:ASP188 4.9 21.3 1.0
OD1 C:ASP188 4.9 21.3 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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy