Atomistry » Calcium » PDB 2m0k-2n8y » 2msb
Atomistry »
  Calcium »
    PDB 2m0k-2n8y »
      2msb »

Calcium in PDB 2msb: Structure of A C-Type Mannose-Binding Protein Complexed with An Oligosaccharide

Protein crystallography data

The structure of Structure of A C-Type Mannose-Binding Protein Complexed with An Oligosaccharide, PDB code: 2msb was solved by W.I.Weis, K.Drickamer, W.A.Hendrickson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 34.810, 85.160, 39.550, 90.00, 97.41, 90.00
R / Rfree (%) 17.4 / n/a

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of A C-Type Mannose-Binding Protein Complexed with An Oligosaccharide (pdb code 2msb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of A C-Type Mannose-Binding Protein Complexed with An Oligosaccharide, PDB code: 2msb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2msb

Go back to Calcium Binding Sites List in 2msb
Calcium binding site 1 out of 6 in the Structure of A C-Type Mannose-Binding Protein Complexed with An Oligosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A C-Type Mannose-Binding Protein Complexed with An Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:16.9
occ:1.00
 OD2 A:ASP161 2.3 16.3 1.0
O A:HOH222 2.4 15.9 1.0
O A:GLU193 2.4 14.4 1.0
OD1 A:ASP194 2.4 12.2 1.0
OE2 A:GLU165 2.5 19.4 1.0
OE1 A:GLU165 2.5 20.4 1.0
OD1 A:ASP188 2.6 25.0 1.0
OD1 A:ASP161 2.7 13.6 1.0
CD A:GLU165 2.8 19.4 1.0
CG A:ASP161 2.9 15.1 1.0
C A:GLU193 3.3 12.5 1.0
CG A:ASP188 3.4 26.3 1.0
CG A:ASP194 3.6 12.4 1.0
CA A:ASP194 3.8 13.7 1.0
CA A:CA3 3.9 21.7 1.0
CB A:ASP188 3.9 20.4 1.0
N A:ASP194 3.9 12.2 1.0
O A:HOH231 4.0 26.2 1.0
CB A:ASP194 4.2 12.4 1.0
OD2 A:ASP188 4.3 22.5 1.0
N A:GLU193 4.3 16.8 1.0
CG A:GLU165 4.3 21.2 1.0
CB A:ASP161 4.4 12.0 1.0
CA A:GLU193 4.4 16.2 1.0
CA A:ASP188 4.4 16.9 1.0
CZ A:PHE168 4.5 15.9 1.0
OD2 A:ASP194 4.5 15.8 1.0
OD2 A:ASP206 4.5 17.8 1.0
O A:HOH229 4.6 25.3 1.0
O A:ASP161 4.6 14.8 1.0
N A:GLY166 4.7 19.1 1.0
O A:HOH233 4.8 23.3 1.0
CA A:GLU165 4.9 21.8 1.0
C A:ASP194 4.9 12.3 1.0

Calcium binding site 2 out of 6 in 2msb

Go back to Calcium Binding Sites List in 2msb
Calcium binding site 2 out of 6 in the Structure of A C-Type Mannose-Binding Protein Complexed with An Oligosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A C-Type Mannose-Binding Protein Complexed with An Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:18.0
occ:1.00
 OD1 A:ASP206 2.3 19.0 1.0
OE1 A:GLU193 2.3 15.0 1.0
OD1 A:ASN205 2.4 18.1 1.0
OE1 A:GLU185 2.4 19.5 1.0
OD1 A:ASN187 2.4 19.0 1.0
O A:ASP206 2.6 14.1 1.0
CG A:ASP206 3.3 16.9 1.0
CD A:GLU185 3.4 20.9 1.0
CD A:GLU193 3.4 13.7 1.0
CG A:ASN205 3.4 14.6 1.0
CG A:ASN187 3.5 21.5 1.0
C A:ASP206 3.6 13.5 1.0
OE2 A:GLU185 3.7 19.9 1.0
N A:ASP206 3.7 15.4 1.0
OE2 A:GLU193 3.7 15.8 1.0
ND2 A:ASN205 3.7 15.8 1.0
OD2 A:ASP206 4.0 17.8 1.0
ND2 A:ASN187 4.1 24.2 1.0
CA A:ASP206 4.1 14.8 1.0
N A:ASN187 4.2 18.9 1.0
CB A:ASP206 4.3 16.1 1.0
CB A:HIS189 4.5 29.1 1.0
C A:ASN205 4.6 16.5 1.0
CG A:GLU185 4.6 15.9 1.0
CB A:ASN187 4.6 19.1 1.0
CG A:GLU193 4.7 15.6 1.0
N A:HIS189 4.7 22.8 1.0
CB A:ASN205 4.7 16.1 1.0
N A:ILE207 4.7 11.9 1.0
N A:ASP188 4.8 15.3 1.0
CA A:ASN187 4.8 20.9 1.0
CB A:GLU193 4.8 17.8 1.0
CA A:ASN205 4.9 16.4 1.0

Calcium binding site 3 out of 6 in 2msb

Go back to Calcium Binding Sites List in 2msb
Calcium binding site 3 out of 6 in the Structure of A C-Type Mannose-Binding Protein Complexed with An Oligosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of A C-Type Mannose-Binding Protein Complexed with An Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:21.7
occ:1.00
 OE1 A:GLU165 2.2 20.4 1.0
O A:HOH231 2.3 26.2 1.0
O A:HOH241 2.3 28.1 1.0
OD1 A:ASP194 2.4 12.2 1.0
O A:HOH242 2.5 21.1 1.0
O A:HOH240 2.5 21.2 1.0
OD2 A:ASP194 2.5 15.8 1.0
CG A:ASP194 2.8 12.4 1.0
CD A:GLU165 3.4 19.4 1.0
CA A:CA1 3.9 16.9 1.0
CG A:GLU165 4.1 21.2 1.0
CB A:GLU165 4.1 21.2 1.0
O A:HOH245 4.2 28.0 0.8
O A:ASP161 4.2 14.8 1.0
OD1 A:ASP188 4.3 25.0 1.0
CB A:ASP194 4.4 12.4 1.0
O A:HOH284 4.4 40.4 1.0
O A:HOH263 4.4 34.1 0.7
OE2 A:GLU165 4.4 19.4 1.0
O A:HOH239 4.6 29.7 1.0
CA A:GLU165 4.7 21.8 1.0
O A:HOH307 4.7 44.5 0.9
O A:HOH257 4.8 33.7 0.8
OD2 A:ASP161 4.8 16.3 1.0
OD2 A:ASP188 4.8 22.5 1.0
CG A:ASP188 4.9 26.3 1.0
OD1 A:ASP161 4.9 13.6 1.0

Calcium binding site 4 out of 6 in 2msb

Go back to Calcium Binding Sites List in 2msb
Calcium binding site 4 out of 6 in the Structure of A C-Type Mannose-Binding Protein Complexed with An Oligosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of A C-Type Mannose-Binding Protein Complexed with An Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1

b:14.2
occ:1.00
 OD1 B:ASP194 2.3 13.8 1.0
O B:GLU193 2.4 10.7 1.0
O B:HOH223 2.4 14.3 1.0
OD2 B:ASP161 2.5 14.0 1.0
OD1 B:ASP188 2.5 14.8 1.0
OE1 B:GLU165 2.5 13.3 1.0
OE2 B:GLU165 2.5 15.3 1.0
OD1 B:ASP161 2.7 10.6 1.0
CD B:GLU165 2.9 13.4 1.0
CG B:ASP161 2.9 14.2 1.0
C B:GLU193 3.4 11.0 1.0
CG B:ASP188 3.4 18.6 1.0
CG B:ASP194 3.5 16.5 1.0
CA B:ASP194 3.8 11.6 1.0
CA B:CA222 3.9 11.5 1.0
CB B:ASP188 3.9 13.5 1.0
N B:ASP194 4.0 8.9 1.0
O B:HOH235 4.0 17.2 1.0
CB B:ASP194 4.2 11.8 1.0
N B:GLU193 4.3 11.3 1.0
OD2 B:ASP188 4.3 16.8 1.0
CG B:GLU165 4.4 11.6 1.0
CA B:ASP188 4.4 15.3 1.0
OD2 B:ASP194 4.4 15.0 1.0
CA B:GLU193 4.4 11.3 1.0
CB B:ASP161 4.4 9.0 1.0
O B:HOH230 4.5 23.7 1.0
OD2 B:ASP206 4.5 12.7 1.0
CZ B:PHE168 4.7 17.1 1.0
N B:GLY166 4.7 14.9 1.0
O B:ASP161 4.8 14.0 1.0
O B:HOH239 4.8 20.6 0.8
C B:ASP194 4.9 13.1 1.0
O B:HOH233 5.0 13.3 1.0

Calcium binding site 5 out of 6 in 2msb

Go back to Calcium Binding Sites List in 2msb
Calcium binding site 5 out of 6 in the Structure of A C-Type Mannose-Binding Protein Complexed with An Oligosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of A C-Type Mannose-Binding Protein Complexed with An Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:17.3
occ:1.00
 OE1 B:GLU193 2.3 16.4 1.0
OD1 B:ASP206 2.4 16.7 1.0
OD1 B:ASN205 2.4 15.3 1.0
O B:ASP206 2.5 15.8 1.0
O3 B:MAN9 2.5 27.3 1.0
OD1 B:ASN187 2.5 18.6 1.0
O4 B:MAN9 2.5 20.3 1.0
OE1 B:GLU185 2.7 24.1 1.0
C4 B:MAN9 3.3 25.3 1.0
C3 B:MAN9 3.3 25.4 1.0
CD B:GLU193 3.3 12.4 1.0
CG B:ASN205 3.4 11.8 1.0
CG B:ASP206 3.4 13.7 1.0
CG B:ASN187 3.4 23.1 1.0
CD B:GLU185 3.5 22.7 1.0
C B:ASP206 3.5 17.6 1.0
OE2 B:GLU193 3.7 17.8 1.0
N B:ASP206 3.7 15.0 1.0
OE2 B:GLU185 3.8 23.2 1.0
ND2 B:ASN205 3.8 18.6 1.0
ND2 B:ASN187 4.0 22.2 1.0
CA B:ASP206 4.1 16.2 1.0
OD2 B:ASP206 4.2 12.7 1.0
N B:ASN187 4.2 19.8 1.0
CB B:ASP206 4.3 15.4 1.0
C B:ASN205 4.5 15.8 1.0
CB B:HIS189 4.6 23.7 1.0
CG B:GLU193 4.6 11.9 1.0
N B:ILE207 4.6 15.2 1.0
CB B:ASN187 4.6 22.5 1.0
C2 B:MAN9 4.7 29.4 1.0
CB B:ASN205 4.7 17.8 1.0
C5 B:MAN9 4.7 29.4 1.0
CG B:GLU185 4.7 21.3 1.0
N B:ASP188 4.7 15.5 1.0
N B:HIS189 4.7 18.2 1.0
CB B:GLU193 4.8 12.0 1.0
CA B:ASN187 4.8 20.4 1.0
CA B:ASN205 4.8 14.2 1.0
O2 B:MAN9 5.0 32.1 1.0
CA B:ILE207 5.0 14.5 1.0

Calcium binding site 6 out of 6 in 2msb

Go back to Calcium Binding Sites List in 2msb
Calcium binding site 6 out of 6 in the Structure of A C-Type Mannose-Binding Protein Complexed with An Oligosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of A C-Type Mannose-Binding Protein Complexed with An Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca222

b:11.5
occ:1.00
 O B:HOH235 2.2 17.2 1.0
O B:HOH237 2.3 21.0 1.0
OE1 B:GLU165 2.3 13.3 1.0
O B:HOH232 2.4 18.8 1.0
O B:HOH233 2.4 13.3 1.0
OD2 B:ASP194 2.5 15.0 1.0
OD1 B:ASP194 2.6 13.8 1.0
CG B:ASP194 2.9 16.5 1.0
CD B:GLU165 3.5 13.4 1.0
CA B:CA1 3.9 14.2 1.0
O B:HOH265 4.0 24.4 0.6
CB B:GLU165 4.1 15.0 1.0
CG B:GLU165 4.1 11.6 1.0
OD1 B:ASP188 4.2 14.8 1.0
O B:HOH290 4.2 29.6 0.6
O B:HOH245 4.3 30.2 0.9
O B:ASP161 4.3 14.0 1.0
CB B:ASP194 4.4 11.8 1.0
OE2 B:GLU165 4.4 15.3 1.0
O B:HOH279 4.5 34.8 1.0
CA B:GLU165 4.5 12.4 1.0
O B:HOH326 4.6 36.7 0.8
O B:HOH234 4.7 13.3 1.0
OD1 B:ASP161 4.8 10.6 1.0
OD2 B:ASP188 4.9 16.8 1.0
CG B:ASP188 4.9 18.6 1.0
OD2 B:ASP161 4.9 14.0 1.0

Reference:

W.I.Weis, K.Drickamer, W.A.Hendrickson. Structure of A C-Type Mannose-Binding Protein Complexed with An Oligosaccharide. Nature V. 360 127 1992.
ISSN: ISSN 0028-0836
PubMed: 1436090
DOI: 10.1038/360127A0
Page generated: Fri Jul 12 14:22:07 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