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

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

Go back to Calcium Binding Sites List in 1kwv
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

Go back to Calcium Binding Sites List in 1kwv
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

Go back to Calcium Binding Sites List in 1kwv
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

Go back to Calcium Binding Sites List in 1kwv
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

Go back to Calcium Binding Sites List in 1kwv
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

Go back to Calcium Binding Sites List in 1kwv
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

Go back to Calcium Binding Sites List in 1kwv
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

Go back to Calcium Binding Sites List in 1kwv
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

Go back to Calcium Binding Sites List in 1kwv
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy