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Magnesium in PDB 2z48: Crystal Structure of Hemolytic Lectin Cel-III Complexed with Galnac

Protein crystallography data

The structure of Crystal Structure of Hemolytic Lectin Cel-III Complexed with Galnac, PDB code: 2z48 was solved by T.Hatakeyama, H.Unno, S.Eto, H.Hidemura, T.Uchida, Y.Kouzuma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.96 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 52.637, 65.169, 66.675, 85.30, 73.55, 89.94
R / Rfree (%) 18.5 / 21.8

Other elements in 2z48:

The structure of Crystal Structure of Hemolytic Lectin Cel-III Complexed with Galnac also contains other interesting chemical elements:

Calcium (Ca) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hemolytic Lectin Cel-III Complexed with Galnac (pdb code 2z48). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Hemolytic Lectin Cel-III Complexed with Galnac, PDB code: 2z48:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2z48

Go back to Magnesium Binding Sites List in 2z48
Magnesium binding site 1 out of 4 in the Crystal Structure of Hemolytic Lectin Cel-III Complexed with Galnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Hemolytic Lectin Cel-III Complexed with Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1111

b:23.5
occ:1.00
 OD1 A:ASN32 2.2 26.8 1.0
O A:HOH1273 2.3 34.2 1.0
O A:ILE33 2.3 19.1 1.0
OD1 A:ASN72 2.4 25.0 1.0
O A:ILE131 2.4 19.9 1.0
O A:VAL73 2.6 20.3 1.0
CG A:ASN32 3.1 24.6 1.0
CG A:ASN72 3.3 25.1 1.0
ND2 A:ASN32 3.4 27.0 1.0
C A:ILE33 3.4 19.7 1.0
N A:ILE33 3.4 20.6 1.0
C A:ILE131 3.5 18.8 1.0
N A:ILE131 3.7 19.4 1.0
ND2 A:ASN72 3.7 24.1 1.0
C A:VAL73 3.7 21.9 1.0
N A:VAL73 3.8 23.2 1.0
CA A:ILE33 3.9 20.0 1.0
CA A:ILE131 4.0 18.2 1.0
O A:HOH1292 4.1 24.9 1.0
CA A:VAL73 4.3 21.6 1.0
CB A:ILE33 4.3 20.1 1.0
CB A:ASN32 4.4 21.8 1.0
CB A:ILE131 4.4 17.9 1.0
C A:ASN32 4.4 21.1 1.0
N A:ALA34 4.6 19.2 1.0
CA A:ASN32 4.6 22.0 1.0
CB A:ASN72 4.7 25.4 1.0
N A:GLY132 4.7 18.7 1.0
C A:ASP130 4.7 19.8 1.0
C A:ASN72 4.7 24.5 1.0
N A:MET74 4.8 21.7 1.0
CB A:VAL73 4.8 21.7 1.0
CA A:ASN72 4.9 25.5 1.0
CB A:ASP130 4.9 22.3 1.0
CA A:ASP130 5.0 21.3 1.0

Magnesium binding site 2 out of 4 in 2z48

Go back to Magnesium Binding Sites List in 2z48
Magnesium binding site 2 out of 4 in the Crystal Structure of Hemolytic Lectin Cel-III Complexed with Galnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Hemolytic Lectin Cel-III Complexed with Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1112

b:15.0
occ:1.00
 OD1 A:ASN218 2.3 15.1 1.0
OD1 A:ASN177 2.4 12.8 1.0
O A:VAL266 2.4 12.1 1.0
O A:VAL178 2.4 12.3 1.0
O A:VAL219 2.5 12.2 1.0
OD1 A:ASP265 2.6 15.1 1.0
CG A:ASN177 3.3 14.4 1.0
CG A:ASN218 3.3 15.1 1.0
C A:VAL266 3.5 13.2 1.0
C A:VAL178 3.5 12.8 1.0
ND2 A:ASN177 3.5 14.0 1.0
C A:VAL219 3.6 12.1 1.0
N A:VAL219 3.6 12.0 1.0
N A:VAL266 3.6 13.9 1.0
N A:VAL178 3.6 12.5 1.0
CG A:ASP265 3.6 17.0 1.0
ND2 A:ASN218 3.8 20.7 1.0
CA A:VAL266 4.0 12.9 1.0
CA A:VAL178 4.1 13.4 1.0
CA A:VAL219 4.1 11.4 1.0
OD2 A:ASP265 4.2 19.1 1.0
O A:HOH1437 4.2 18.9 1.0
O A:HOH1306 4.3 25.1 1.0
CB A:VAL266 4.3 12.1 1.0
O A:HOH1484 4.5 26.5 1.0
CB A:VAL178 4.5 13.2 1.0
C A:ASN218 4.5 12.8 1.0
CB A:VAL219 4.6 11.7 1.0
CB A:ASN218 4.6 13.5 1.0
CB A:ASN177 4.6 14.6 1.0
C A:ASN177 4.6 14.1 1.0
N A:LEU179 4.7 12.6 1.0
N A:GLY267 4.7 11.5 1.0
C A:ASP265 4.7 14.2 1.0
CA A:ASN218 4.7 12.8 1.0
N A:GLY220 4.7 12.2 1.0
CB A:ASP265 4.8 14.8 1.0
CA A:ASN177 4.8 14.6 1.0
CA A:ASP265 5.0 14.7 1.0

Magnesium binding site 3 out of 4 in 2z48

Go back to Magnesium Binding Sites List in 2z48
Magnesium binding site 3 out of 4 in the Crystal Structure of Hemolytic Lectin Cel-III Complexed with Galnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Hemolytic Lectin Cel-III Complexed with Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1211

b:28.3
occ:1.00
 OD1 B:ASN72 2.2 25.1 1.0
O B:ILE131 2.3 20.1 1.0
OD1 B:ASN32 2.3 26.7 1.0
O B:HOH2286 2.4 32.3 1.0
O B:ILE33 2.5 18.9 1.0
O B:VAL73 2.6 19.9 1.0
CG B:ASN72 3.2 25.3 1.0
CG B:ASN32 3.2 24.6 1.0
C B:ILE131 3.4 18.9 1.0
ND2 B:ASN32 3.5 26.9 1.0
C B:ILE33 3.5 19.6 1.0
ND2 B:ASN72 3.5 24.1 1.0
N B:ILE33 3.5 20.7 1.0
N B:ILE131 3.7 19.5 1.0
N B:VAL73 3.7 23.1 1.0
C B:VAL73 3.7 21.4 1.0
CA B:ILE131 4.0 18.5 1.0
CA B:ILE33 4.0 19.9 1.0
CA B:VAL73 4.2 21.5 1.0
O B:HOH2119 4.3 26.3 1.0
CB B:ILE33 4.4 20.2 1.0
CB B:ILE131 4.4 18.2 1.0
CB B:ASN72 4.5 25.7 1.0
CB B:ASN32 4.5 21.6 1.0
N B:GLY132 4.5 19.2 1.0
C B:ASN32 4.5 21.0 1.0
C B:ASN72 4.6 24.4 1.0
N B:ALA34 4.7 19.4 1.0
CA B:ASN32 4.7 22.0 1.0
CA B:ASN72 4.7 25.4 1.0
C B:ASP130 4.7 20.1 1.0
CB B:VAL73 4.8 21.5 1.0
N B:MET74 4.8 21.7 1.0
CB B:ASP130 4.9 22.4 1.0
CA B:ASP130 5.0 21.3 1.0
CA B:GLY132 5.0 19.4 1.0

Magnesium binding site 4 out of 4 in 2z48

Go back to Magnesium Binding Sites List in 2z48
Magnesium binding site 4 out of 4 in the Crystal Structure of Hemolytic Lectin Cel-III Complexed with Galnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Hemolytic Lectin Cel-III Complexed with Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1212

b:16.2
occ:1.00
 O B:VAL178 2.3 13.1 1.0
O B:VAL266 2.4 12.6 1.0
OD1 B:ASN218 2.4 15.7 1.0
OD1 B:ASN177 2.4 12.4 1.0
O B:VAL219 2.5 12.9 1.0
OD1 B:ASP265 2.5 15.4 1.0
CG B:ASN177 3.2 14.7 1.0
CG B:ASN218 3.4 15.4 1.0
C B:VAL266 3.4 13.4 1.0
C B:VAL178 3.5 13.2 1.0
ND2 B:ASN177 3.5 14.4 1.0
C B:VAL219 3.6 12.8 1.0
N B:VAL266 3.6 14.2 1.0
CG B:ASP265 3.6 17.4 1.0
N B:VAL178 3.6 13.1 1.0
N B:VAL219 3.6 12.5 1.0
ND2 B:ASN218 3.8 21.2 1.0
CA B:VAL266 3.9 13.3 1.0
CA B:VAL178 4.1 13.7 1.0
CA B:VAL219 4.1 11.8 1.0
OD2 B:ASP265 4.2 19.8 1.0
O B:HOH2208 4.2 19.2 1.0
CB B:VAL266 4.3 12.5 1.0
O B:HOH2097 4.4 26.0 1.0
CB B:VAL178 4.5 13.6 1.0
O B:HOH2233 4.5 22.0 1.0
C B:ASN218 4.5 13.1 1.0
CB B:VAL219 4.6 12.0 1.0
CB B:ASN177 4.6 14.6 1.0
C B:ASN177 4.6 14.3 1.0
N B:LEU179 4.6 13.4 1.0
N B:GLY267 4.6 11.8 1.0
CB B:ASN218 4.6 13.9 1.0
C B:ASP265 4.7 14.4 1.0
N B:GLY220 4.7 12.6 1.0
CA B:ASN218 4.7 13.2 1.0
CB B:ASP265 4.8 14.8 1.0
CA B:ASN177 4.8 14.5 1.0
CA B:ASP265 4.9 14.8 1.0
CA B:LEU179 5.0 14.1 1.0

Reference:

T.Hatakeyama, H.Unno, Y.Kouzuma, T.Uchida, S.Eto, H.Hidemura, N.Kato, M.Yonekura, M.Kusunoki. C-Type Lectin-Like Carbohydrate-Recognition of the Hemolytic Lectin Cel-III Containing Ricin-Type Beta-Trefoil Folds J.Biol.Chem. V. 282 37826 2007.
ISSN: ISSN 0021-9258
PubMed: 17977832
DOI: 10.1074/JBC.M705604200
Page generated: Mon Dec 14 07:49:48 2020

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