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

Calcium in PDB 1kwx: Rat Mannose Protein A Complexed with B-Me-Fuc.

Protein crystallography data

The structure of Rat Mannose Protein A Complexed with B-Me-Fuc., PDB code: 1kwx 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 (°) 78.480, 85.430, 97.800, 90.00, 107.37, 90.00
R / Rfree (%) 20 / 22.9

Other elements in 1kwx:

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

Calcium binding site 1 out of 10 in 1kwx

Go back to Calcium Binding Sites List in 1kwx
Calcium binding site 1 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:16.6
occ:1.00
 OD2 A:ASP188 1.9 25.3 1.0
OE1 A:GLU165 2.2 16.2 1.0
OE2 A:GLU165 2.2 15.8 1.0
OD2 A:ASP194 2.4 16.7 1.0
CD A:GLU165 2.5 16.9 1.0
O A:HOH625 2.6 14.7 1.0
O A:GLU193 2.6 14.0 1.0
OD2 A:ASP161 2.7 16.0 1.0
CG A:ASP188 2.8 24.6 1.0
OD1 A:ASP161 3.1 13.4 1.0
CG A:ASP161 3.3 16.2 1.0
CB A:ASP188 3.5 19.9 1.0
C A:GLU193 3.5 17.2 1.0
O A:HOH694 3.6 18.9 1.0
CG A:ASP194 3.6 15.0 1.0
OD1 A:ASP188 3.6 22.6 1.0
CA A:CA504 3.7 17.6 1.0
CG A:GLU165 4.1 16.2 1.0
N A:GLU193 4.1 15.2 1.0
CA A:ASP194 4.1 14.5 1.0
N A:ASP194 4.1 14.1 1.0
CA A:ASP188 4.2 21.5 1.0
CA A:GLU193 4.4 16.0 1.0
OD1 A:ASP194 4.4 12.7 1.0
CB A:ASP194 4.4 16.8 1.0
O A:HOH624 4.6 17.1 1.0
N A:GLY166 4.7 16.7 1.0
O A:HOH655 4.8 23.6 1.0
CB A:ASP161 4.8 14.4 1.0
CB A:GLU165 4.8 17.9 1.0
OD1 A:ASP206 4.9 15.5 1.0
CA A:GLU165 4.9 18.0 1.0
N A:ASP188 5.0 23.0 1.0

Calcium binding site 2 out of 10 in 1kwx

Go back to Calcium Binding Sites List in 1kwx
Calcium binding site 2 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:20.2
occ:1.00
 OD1 A:ASN187 2.3 22.0 1.0
O2 A:MFB501 2.4 22.1 1.0
OD2 A:ASP206 2.4 17.8 1.0
OE2 A:GLU185 2.5 19.6 1.0
OE2 A:GLU193 2.5 21.1 1.0
OD1 A:ASN205 2.5 18.1 1.0
O3 A:MFB501 2.6 24.8 1.0
O A:ASP206 2.7 16.1 1.0
C2 A:MFB501 3.3 24.6 1.0
CD A:GLU185 3.3 20.7 1.0
C3 A:MFB501 3.3 25.1 1.0
CG A:ASN187 3.4 23.4 1.0
OE1 A:GLU185 3.4 19.1 1.0
CG A:ASP206 3.5 19.0 1.0
CD A:GLU193 3.5 19.0 1.0
CG A:ASN205 3.6 17.4 1.0
C A:ASP206 3.8 18.8 1.0
OE1 A:GLU193 3.8 19.4 1.0
ND2 A:ASN187 3.8 22.8 1.0
N A:ASP206 3.9 17.0 1.0
ND2 A:ASN205 4.0 17.6 1.0
OD1 A:ASP206 4.2 15.5 1.0
N A:ASN187 4.2 20.1 1.0
CA A:ASP206 4.2 16.6 1.0
CB A:HIS189 4.3 30.8 1.0
CB A:ASP206 4.4 14.8 1.0
CB A:ASN187 4.6 20.7 1.0
CG A:GLU185 4.6 17.9 1.0
C1 A:MFB501 4.6 27.7 1.0
C A:ASN205 4.6 17.4 1.0
C4 A:MFB501 4.7 27.9 1.0
N A:HIS189 4.7 23.9 1.0
CG A:GLU193 4.8 19.6 1.0
N A:ASP188 4.8 23.0 1.0
CA A:ASN187 4.8 22.8 1.0
CB A:ASN205 4.8 17.0 1.0
N A:ILE207 4.9 16.8 1.0
CA A:ASN205 5.0 17.5 1.0
CB A:GLU193 5.0 17.1 1.0

Calcium binding site 3 out of 10 in 1kwx

Go back to Calcium Binding Sites List in 1kwx
Calcium binding site 3 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:17.6
occ:1.00
 OE1 A:GLU165 2.1 16.2 1.0
O A:HOH694 2.3 18.9 1.0
OD2 A:ASP194 2.8 16.7 1.0
OD1 A:ASP194 2.8 12.7 1.0
CG A:ASP194 3.2 15.0 1.0
CD A:GLU165 3.3 16.9 1.0
CA A:CA502 3.7 16.6 1.0
CB A:GLU165 3.8 17.9 1.0
CG A:GLU165 3.9 16.2 1.0
OD2 A:ASP188 4.1 25.3 1.0
OE2 A:GLU165 4.3 15.8 1.0
CA A:GLU165 4.4 18.0 1.0
O A:HOH695 4.4 18.8 1.0
O A:ASP161 4.6 15.2 1.0
OD1 A:ASP188 4.6 22.6 1.0
CB A:ASP194 4.7 16.8 1.0
CG A:ASP188 4.7 24.6 1.0
OD2 A:ASP161 4.8 16.0 1.0
O A:HOH693 4.9 24.9 1.0
N A:GLU165 4.9 18.8 1.0

Calcium binding site 4 out of 10 in 1kwx

Go back to Calcium Binding Sites List in 1kwx
Calcium binding site 4 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca606

b:31.0
occ:0.50
 O A:HOH721 2.4 25.8 1.0
O A:HOH730 2.6 33.5 1.0
O A:ASN187 4.4 22.4 1.0

Calcium binding site 5 out of 10 in 1kwx

Go back to Calcium Binding Sites List in 1kwx
Calcium binding site 5 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:20.8
occ:1.00
 OD2 B:ASP194 2.3 19.2 1.0
O B:GLU193 2.4 18.8 1.0
O B:HOH624 2.4 18.3 1.0
OD2 B:ASP161 2.5 19.2 1.0
OE2 B:GLU165 2.5 17.9 1.0
OE1 B:GLU165 2.5 18.3 1.0
OD1 B:ASP161 2.7 17.1 1.0
OD2 B:ASP188 2.7 31.3 1.0
CD B:GLU165 2.9 18.7 1.0
CG B:ASP161 2.9 21.5 1.0
C B:GLU193 3.3 19.5 1.0
CG B:ASP194 3.4 21.4 1.0
CG B:ASP188 3.5 33.8 1.0
CA B:ASP194 3.7 20.7 1.0
CA B:CA604 3.8 22.3 1.0
N B:ASP194 3.9 16.8 1.0
O B:HOH644 3.9 19.7 1.0
CB B:ASP188 4.0 30.1 1.0
CB B:ASP194 4.1 19.9 1.0
O B:HOH623 4.2 31.4 1.0
N B:GLU193 4.3 27.9 1.0
OD1 B:ASP188 4.4 31.9 1.0
CG B:GLU165 4.4 22.7 1.0
OD1 B:ASP194 4.4 22.4 1.0
CA B:GLU193 4.4 23.6 1.0
CB B:ASP161 4.4 19.0 1.0
CA B:ASP188 4.5 33.6 1.0
CZ B:PHE168 4.6 18.9 1.0
OD1 B:ASP206 4.7 19.3 1.0
O B:ASP161 4.7 24.5 1.0
N B:GLY166 4.8 18.8 1.0
C B:ASP194 4.9 21.7 1.0
O B:HOH629 5.0 21.3 1.0

Calcium binding site 6 out of 10 in 1kwx

Go back to Calcium Binding Sites List in 1kwx
Calcium binding site 6 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:29.2
occ:1.00
 OD2 B:ASP206 2.3 21.1 1.0
OE2 B:GLU193 2.3 24.9 1.0
OD1 B:ASN205 2.4 28.0 1.0
OD1 B:ASN187 2.5 37.9 1.0
O3 B:MFB601 2.5 34.4 1.0
O2 B:MFB601 2.6 32.3 1.0
OE2 B:GLU185 2.6 28.7 1.0
O B:ASP206 2.6 23.7 1.0
CD B:GLU193 3.3 25.8 1.0
CD B:GLU185 3.3 29.9 1.0
C3 B:MFB601 3.4 37.1 1.0
CG B:ASP206 3.4 24.8 1.0
C2 B:MFB601 3.4 36.8 1.0
CG B:ASN205 3.5 27.3 1.0
OE1 B:GLU185 3.5 25.6 1.0
CG B:ASN187 3.5 39.0 1.0
C B:ASP206 3.6 24.3 1.0
OE1 B:GLU193 3.6 31.4 1.0
N B:ASP206 3.7 24.1 1.0
ND2 B:ASN205 4.0 23.1 1.0
ND2 B:ASN187 4.1 39.2 1.0
OD1 B:ASP206 4.1 19.3 1.0
CA B:ASP206 4.1 23.2 1.0
N B:ASN187 4.3 32.6 1.0
CB B:ASP206 4.3 23.3 1.0
CB B:HIS189 4.4 39.6 1.0
C B:ASN205 4.5 26.3 1.0
CG B:GLU185 4.6 27.9 1.0
CG B:GLU193 4.7 25.1 1.0
CB B:ASN187 4.7 37.2 1.0
CB B:ASN205 4.7 26.1 1.0
N B:HIS189 4.7 37.5 1.0
N B:ILE207 4.8 24.6 1.0
C1 B:MFB601 4.8 37.1 1.0
C4 B:MFB601 4.8 35.9 1.0
N B:ASP188 4.8 32.9 1.0
CA B:ASN205 4.8 25.6 1.0
CA B:ASN187 4.9 34.8 1.0
CB B:GLU193 4.9 21.5 1.0

Calcium binding site 7 out of 10 in 1kwx

Go back to Calcium Binding Sites List in 1kwx
Calcium binding site 7 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:22.3
occ:1.00
 OE1 B:GLU165 2.2 18.3 1.0
O B:HOH629 2.3 21.3 1.0
O B:HOH678 2.4 34.7 1.0
O B:HOH644 2.4 19.7 1.0
O B:HOH663 2.5 23.1 1.0
OD1 B:ASP194 2.5 22.4 1.0
OD2 B:ASP194 2.5 19.2 1.0
CG B:ASP194 2.8 21.4 1.0
CD B:GLU165 3.4 18.7 1.0
CA B:CA602 3.8 20.8 1.0
CB B:GLU165 4.1 19.6 1.0
OD2 B:ASP188 4.2 31.3 1.0
O B:ASP161 4.2 24.5 1.0
CG B:GLU165 4.2 22.7 1.0
O B:HOH703 4.3 30.1 1.0
CB B:ASP194 4.4 19.9 1.0
OE2 B:GLU165 4.4 17.9 1.0
CA B:GLU165 4.5 19.3 1.0
OD2 B:ASP161 4.6 19.2 1.0
O B:HOH664 4.7 44.2 1.0
OD1 B:ASP161 4.8 17.1 1.0
OD1 B:ASP188 4.8 31.9 1.0
O B:HOH665 4.8 40.7 1.0
CG B:ASP188 4.8 33.8 1.0
CG B:ASP161 4.9 21.5 1.0

Calcium binding site 8 out of 10 in 1kwx

Go back to Calcium Binding Sites List in 1kwx
Calcium binding site 8 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:18.7
occ:1.00
 O C:GLU193 2.3 13.8 1.0
O C:HOH725 2.3 14.3 1.0
OD2 C:ASP188 2.4 18.4 1.0
OE2 C:GLU165 2.5 15.3 1.0
OD2 C:ASP194 2.5 13.4 1.0
OE1 C:GLU165 2.6 16.0 1.0
OD2 C:ASP161 2.6 19.0 1.0
OD1 C:ASP161 2.8 18.1 1.0
CD C:GLU165 2.9 17.4 1.0
CG C:ASP161 3.1 21.3 1.0
CG C:ASP188 3.2 14.8 1.0
C C:GLU193 3.3 17.2 1.0
CB C:ASP188 3.5 16.6 1.0
CG C:ASP194 3.7 18.1 1.0
CA C:ASP194 3.8 16.1 1.0
O C:HOH719 3.9 16.4 1.0
N C:ASP194 4.0 16.8 1.0
CA C:CA704 4.1 19.1 1.0
CA C:ASP188 4.2 17.7 1.0
OD1 C:ASP188 4.2 15.5 1.0
N C:GLU193 4.2 15.9 1.0
CA C:GLU193 4.3 16.4 1.0
CB C:ASP194 4.4 15.5 1.0
CG C:GLU165 4.4 17.0 1.0
OD1 C:ASP206 4.6 19.9 1.0
CZ C:PHE168 4.6 18.0 1.0
OD1 C:ASP194 4.6 17.4 1.0
CB C:ASP161 4.6 19.9 1.0
O C:HOH724 4.6 21.7 1.0
O C:HOH769 4.7 23.4 1.0
N C:GLY166 4.7 18.0 1.0
N C:ASP188 4.8 17.8 1.0
O C:ASP161 4.9 19.8 1.0
CB C:GLU193 4.9 18.7 1.0

Calcium binding site 9 out of 10 in 1kwx

Go back to Calcium Binding Sites List in 1kwx
Calcium binding site 9 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:19.9
occ:1.00
 OD2 C:ASP206 2.2 18.3 1.0
OE2 C:GLU193 2.3 21.2 1.0
OD1 C:ASN187 2.3 14.9 1.0
OE2 C:GLU185 2.6 20.5 1.0
O C:ASP206 2.6 16.6 1.0
O3 C:MFB701 2.6 20.5 1.0
O2 C:MFB701 2.7 22.1 1.0
OD1 C:ASN205 2.7 17.5 1.0
CG C:ASP206 3.2 21.0 1.0
CD C:GLU193 3.3 19.9 1.0
CG C:ASN187 3.4 20.0 1.0
C3 C:MFB701 3.4 23.3 1.0
CD C:GLU185 3.5 21.6 1.0
C2 C:MFB701 3.5 21.9 1.0
OE1 C:GLU193 3.6 19.6 1.0
C C:ASP206 3.6 18.2 1.0
CG C:ASN205 3.7 23.4 1.0
OE1 C:GLU185 3.8 19.6 1.0
N C:ASP206 3.8 18.9 1.0
ND2 C:ASN187 3.9 14.3 1.0
OD1 C:ASP206 3.9 19.9 1.0
N C:ASN187 4.0 18.8 1.0
ND2 C:ASN205 4.1 19.2 1.0
CA C:ASP206 4.1 17.9 1.0
CB C:ASP206 4.2 15.1 1.0
CB C:HIS189 4.3 19.9 1.0
CB C:ASN187 4.6 16.6 1.0
N C:HIS189 4.6 21.3 1.0
CG C:GLU193 4.6 18.7 1.0
N C:ASP188 4.6 17.8 1.0
C C:ASN205 4.6 21.1 1.0
CA C:ASN187 4.7 18.2 1.0
CG C:GLU185 4.7 16.8 1.0
N C:ILE207 4.8 19.0 1.0
CB C:GLU193 4.8 18.7 1.0
C4 C:MFB701 4.8 23.5 1.0
C1 C:MFB701 4.9 24.1 1.0
CB C:ASN205 4.9 19.9 1.0
CA C:PRO186 5.0 19.2 1.0
C C:ASN187 5.0 19.0 1.0
C C:PRO186 5.0 19.8 1.0
CA C:ASN205 5.0 21.1 1.0

Calcium binding site 10 out of 10 in 1kwx

Go back to Calcium Binding Sites List in 1kwx
Calcium binding site 10 out of 10 in the Rat Mannose Protein A Complexed with B-Me-Fuc.


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 B-Me-Fuc. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca704

b:19.1
occ:1.00
 O C:HOH718 2.4 16.4 1.0
OE1 C:GLU165 2.4 16.0 1.0
O C:HOH719 2.5 16.4 1.0
O C:HOH741 2.5 21.5 1.0
OD1 C:ASP194 2.5 17.4 1.0
OD2 C:ASP194 2.6 13.4 1.0
CG C:ASP194 2.9 18.1 1.0
CD C:GLU165 3.6 17.4 1.0
CA C:CA702 4.1 18.7 1.0
O C:HOH799 4.2 27.4 1.0
CB C:GLU165 4.2 17.9 1.0
OD2 C:ASP188 4.2 18.4 1.0
O C:HOH771 4.2 19.2 1.0
CG C:GLU165 4.3 17.0 1.0
O C:ASP161 4.4 19.8 1.0
CB C:ASP194 4.4 15.5 1.0
O C:HOH798 4.5 57.4 1.0
OE2 C:GLU165 4.5 15.3 1.0
CA C:GLU165 4.6 20.3 1.0
O C:HOH770 4.7 24.9 1.0
O C:HOH811 4.7 35.9 1.0
CG C:ASP188 4.9 14.8 1.0
OD2 C:ASP161 4.9 19.0 1.0
OD1 C:ASP188 4.9 15.5 1.0
OD1 C:ASP161 5.0 18.1 1.0
O C:HOH720 5.0 23.5 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 11:32:03 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy