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Holmium in PDB 1msb: Structure of the Calcium-Dependent Lectin Domain From A Rat Mannose-Binding Protein Determined By Mad Phasing

Protein crystallography data

The structure of Structure of the Calcium-Dependent Lectin Domain From A Rat Mannose-Binding Protein Determined By Mad Phasing, PDB code: 1msb 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) N/A / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.400, 73.100, 45.300, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / n/a

Holmium Binding Sites:

The binding sites of Holmium atom in the Structure of the Calcium-Dependent Lectin Domain From A Rat Mannose-Binding Protein Determined By Mad Phasing (pdb code 1msb). This binding sites where shown within 5.0 Angstroms radius around Holmium atom.
In total 4 binding sites of Holmium where determined in the Structure of the Calcium-Dependent Lectin Domain From A Rat Mannose-Binding Protein Determined By Mad Phasing, PDB code: 1msb:
Jump to Holmium binding site number: 1; 2; 3; 4;

Holmium binding site 1 out of 4 in 1msb

Go back to Holmium Binding Sites List in 1msb
Holmium binding site 1 out of 4 in the Structure of the Calcium-Dependent Lectin Domain From A Rat Mannose-Binding Protein Determined By Mad Phasing


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 1 of Structure of the Calcium-Dependent Lectin Domain From A Rat Mannose-Binding Protein Determined By Mad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ho1

b:7.9
occ:1.00
O A:HOH222 2.1 4.0 1.0
OE2 A:GLU165 2.3 10.7 1.0
OD2 A:ASP188 2.3 12.6 1.0
OD2 A:ASP194 2.4 6.5 1.0
OD1 A:ASP161 2.4 10.9 1.0
OD2 A:ASP161 2.4 8.5 1.0
OE1 A:GLU165 2.5 10.1 1.0
O A:GLU193 2.5 4.3 1.0
CD A:GLU165 2.7 9.3 1.0
CG A:ASP161 2.8 10.2 1.0
CG A:ASP188 3.3 12.2 1.0
C A:GLU193 3.5 5.2 1.0
CG A:ASP194 3.5 3.1 1.0
CA A:ASP194 3.9 4.1 1.0
CB A:ASP188 4.1 9.2 1.0
OD1 A:ASP188 4.1 9.7 1.0
N A:GLU193 4.1 6.6 1.0
N A:ASP194 4.1 4.1 1.0
CB A:ASP194 4.2 2.6 1.0
O A:HOH230 4.2 26.6 1.0
CG A:GLU165 4.3 9.1 1.0
CB A:ASP161 4.3 6.7 1.0
CA A:GLU193 4.5 5.5 1.0
OD1 A:ASP194 4.5 5.4 1.0
O A:ASP161 4.5 8.5 1.0
CA A:ASP188 4.6 11.6 1.0
CZ A:PHE168 4.6 9.8 1.0
OD1 A:ASP206 4.6 5.1 1.0
N A:GLY166 4.7 12.2 1.0
CA A:GLU165 5.0 11.2 1.0

Holmium binding site 2 out of 4 in 1msb

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Holmium binding site 2 out of 4 in the Structure of the Calcium-Dependent Lectin Domain From A Rat Mannose-Binding Protein Determined By Mad Phasing


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 2 of Structure of the Calcium-Dependent Lectin Domain From A Rat Mannose-Binding Protein Determined By Mad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ho2

b:12.2
occ:1.00
O A:HOH223 2.1 15.6 1.0
OE2 A:GLU185 2.3 16.8 1.0
OD2 A:ASP206 2.3 5.5 1.0
OE2 A:GLU193 2.4 9.9 1.0
OD1 A:ASN187 2.4 11.9 1.0
OD1 A:ASN205 2.5 16.3 1.0
O A:ASP206 2.5 7.8 1.0
CD A:GLU185 3.3 18.6 1.0
CD A:GLU193 3.3 6.8 1.0
CG A:ASP206 3.4 7.9 1.0
CG A:ASN187 3.4 11.5 1.0
C A:ASP206 3.6 7.6 1.0
OE1 A:GLU185 3.6 20.9 1.0
CG A:ASN205 3.7 16.6 1.0
OE1 A:GLU193 3.7 9.3 1.0
N A:ASP206 3.8 6.5 1.0
ND2 A:ASN187 4.0 11.6 1.0
CA A:ASP206 4.1 6.8 1.0
OD1 A:ASP206 4.1 5.1 1.0
ND2 A:ASN205 4.2 21.6 1.0
N A:ASN187 4.2 11.4 1.0
CB A:ASP206 4.3 5.1 1.0
C A:ASN205 4.6 7.1 1.0
CB A:ASN187 4.6 9.9 1.0
CG A:GLU185 4.6 17.2 1.0
CG A:GLU193 4.6 4.8 1.0
N A:ILE207 4.7 6.4 1.0
CB A:GLU193 4.8 3.8 1.0
CB A:HIS189 4.8 12.6 1.0
N A:ASP188 4.8 11.6 1.0
CB A:ASN205 4.9 11.6 1.0
CA A:ASN187 4.9 10.5 1.0
N A:HIS189 4.9 12.4 1.0
CA A:ASN205 4.9 9.1 1.0

Holmium binding site 3 out of 4 in 1msb

Go back to Holmium Binding Sites List in 1msb
Holmium binding site 3 out of 4 in the Structure of the Calcium-Dependent Lectin Domain From A Rat Mannose-Binding Protein Determined By Mad Phasing


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 3 of Structure of the Calcium-Dependent Lectin Domain From A Rat Mannose-Binding Protein Determined By Mad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ho1

b:14.3
occ:1.00
O B:HOH31 2.2 13.0 1.0
OD2 B:ASP188 2.2 16.9 1.0
OE2 B:GLU165 2.4 17.9 1.0
OD2 B:ASP194 2.4 12.4 1.0
O B:GLU193 2.4 16.8 1.0
OD1 B:ASP161 2.4 13.1 1.0
OD2 B:ASP161 2.4 12.9 1.0
OE1 B:GLU165 2.6 23.5 1.0
CG B:ASP161 2.8 12.0 1.0
CD B:GLU165 2.8 20.2 1.0
CG B:ASP188 3.3 17.7 1.0
C B:GLU193 3.5 16.4 1.0
CG B:ASP194 3.6 13.4 1.0
CA B:ASP194 3.9 13.9 1.0
OD1 B:ASP188 4.1 18.1 1.0
N B:ASP194 4.1 15.5 1.0
CB B:ASP188 4.1 18.6 1.0
O B:HOH39 4.2 23.6 1.0
N B:GLU193 4.2 20.1 1.0
CB B:ASP194 4.3 12.6 1.0
CB B:ASP161 4.3 11.3 1.0
CG B:GLU165 4.4 17.1 1.0
CA B:GLU193 4.5 17.3 1.0
O B:HOH50 4.5 35.9 1.0
OD1 B:ASP194 4.5 17.3 1.0
O B:ASP161 4.5 13.9 1.0
CZ B:PHE168 4.5 9.7 1.0
OD1 B:ASP206 4.6 8.2 1.0
N B:GLY166 4.8 15.1 1.0
CA B:ASP188 4.8 20.6 1.0
CA B:GLU165 4.9 15.0 1.0

Holmium binding site 4 out of 4 in 1msb

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Holmium binding site 4 out of 4 in the Structure of the Calcium-Dependent Lectin Domain From A Rat Mannose-Binding Protein Determined By Mad Phasing


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 4 of Structure of the Calcium-Dependent Lectin Domain From A Rat Mannose-Binding Protein Determined By Mad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ho2

b:18.8
occ:1.00
O B:HOH32 1.7 36.1 1.0
OE2 B:GLU193 2.3 18.9 1.0
OD1 B:ASN187 2.3 18.1 1.0
OE2 B:GLU185 2.3 20.9 1.0
OD2 B:ASP206 2.3 12.8 1.0
OD1 B:ASN205 2.4 13.7 1.0
O B:ASP206 2.6 13.8 1.0
CD B:GLU185 3.3 21.1 1.0
CD B:GLU193 3.3 17.9 1.0
CG B:ASN187 3.3 18.9 1.0
CG B:ASP206 3.4 10.2 1.0
CG B:ASN205 3.6 11.8 1.0
C B:ASP206 3.6 13.2 1.0
OE1 B:GLU185 3.7 21.3 1.0
N B:ASP206 3.7 10.5 1.0
OE1 B:GLU193 3.7 20.8 1.0
ND2 B:ASN187 3.9 19.9 1.0
ND2 B:ASN205 4.0 11.5 1.0
CA B:ASP206 4.1 11.5 1.0
OD1 B:ASP206 4.2 8.2 1.0
CB B:ASP206 4.3 10.2 1.0
N B:ASN187 4.3 19.2 1.0
CB B:ASN187 4.5 18.6 1.0
CG B:GLU185 4.5 19.1 1.0
C B:ASN205 4.6 10.6 1.0
N B:ASP188 4.6 20.6 1.0
CG B:GLU193 4.6 16.4 1.0
N B:ILE207 4.7 14.0 1.0
CB B:ASN205 4.8 10.5 1.0
CA B:ASN187 4.8 19.4 1.0
CB B:GLU193 4.9 17.2 1.0
N B:HIS189 4.9 22.5 1.0
CA B:ASN205 4.9 10.8 1.0
CB B:HIS189 5.0 23.1 1.0

Reference:

W.I.Weis, R.Kahn, R.Fourme, K.Drickamer, W.A.Hendrickson. Structure of the Calcium-Dependent Lectin Domain From A Rat Mannose-Binding Protein Determined By Mad Phasing. Science V. 254 1608 1991.
ISSN: ISSN 0036-8075
PubMed: 1721241
Page generated: Sun Dec 13 19:18:49 2020

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