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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

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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

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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

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