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Magnesium in PDB 5d5g: Structure of Colocasia Esculenta Agglutinin

Protein crystallography data

The structure of Structure of Colocasia Esculenta Agglutinin, PDB code: 5d5g was solved by H.Biswas, R.Chattopadhyaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.99 / 1.74
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 122.012, 47.198, 82.251, 90.00, 90.00, 90.00
R / Rfree (%) 34.4 / 42.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Colocasia Esculenta Agglutinin (pdb code 5d5g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of Colocasia Esculenta Agglutinin, PDB code: 5d5g:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5d5g

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Magnesium binding site 1 out of 5 in the Structure of Colocasia Esculenta Agglutinin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Colocasia Esculenta Agglutinin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:9.3
occ:1.00
 O B:GLY102 1.8 5.7 1.0
O A:PRO98 1.9 12.7 1.0
N B:GLY102 2.2 12.2 1.0
C B:GLY102 2.4 10.5 1.0
CA A:GLY97 2.4 13.0 1.0
C A:GLY97 2.5 6.8 1.0
CA B:GLY102 2.7 10.4 1.0
C A:PRO98 2.8 7.4 1.0
N A:PRO98 2.9 4.0 1.0
O A:GLY97 3.1 10.2 1.0
CA A:PRO98 3.3 10.2 1.0
N A:GLY97 3.3 18.3 1.0
C B:TYR101 3.4 12.6 1.0
N B:PRO103 3.7 9.3 1.0
O B:HOH313 3.7 7.6 1.0
CD A:PRO98 3.9 7.7 1.0
CA B:TYR101 3.9 12.4 1.0
N A:SER99 3.9 8.1 1.0
CG2 A:VAL100 4.2 7.4 1.0
C A:PHE96 4.3 15.3 1.0
CA A:SER99 4.4 10.1 1.0
CG A:PRO98 4.4 7.4 1.0
CD B:PRO103 4.5 7.6 1.0
O B:TYR101 4.5 11.2 1.0
CB A:PRO98 4.5 8.1 1.0
C A:SER99 4.7 18.8 1.0
N A:VAL100 4.7 24.4 1.0
CB B:TYR101 4.7 11.5 1.0
O A:PHE96 4.8 14.6 1.0
CE2 B:TYR88 4.8 9.1 1.0
CA B:PRO103 4.8 13.1 1.0
O B:PRO103 5.0 16.9 1.0

Magnesium binding site 2 out of 5 in 5d5g

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Magnesium binding site 2 out of 5 in the Structure of Colocasia Esculenta Agglutinin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Colocasia Esculenta Agglutinin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:14.1
occ:1.00
 N A:ALA85 1.9 15.6 1.0
O A:LEU6 1.9 11.6 1.0
CA A:ALA85 2.5 8.8 1.0
CB A:ALA85 2.5 8.7 1.0
O A:ALA85 2.5 14.2 1.0
C A:LEU6 2.8 13.8 1.0
C A:ALA85 2.9 14.9 1.0
C A:ALA84 3.0 18.3 1.0
N A:LEU6 3.1 13.0 1.0
CB A:LEU6 3.1 8.5 1.0
CA A:LEU6 3.1 8.3 1.0
CA A:ALA84 3.4 15.9 0.4
CD2 A:LEU55 3.6 10.7 1.0
CG A:LEU6 3.8 9.2 1.0
N A:LEU7 4.0 12.9 1.0
O A:ALA84 4.1 21.1 1.0
N A:VAL86 4.2 14.3 1.0
CD2 A:LEU6 4.3 5.9 1.0
C A:TYR5 4.3 8.2 1.0
CB A:ALA84 4.4 15.8 1.0
N A:ALA84 4.5 17.0 1.0
CA A:LEU7 4.6 12.6 1.0
CG A:LEU55 4.7 10.2 1.0
CA A:TYR5 4.8 13.4 1.0
O A:TYR83 5.0 15.7 1.0

Magnesium binding site 3 out of 5 in 5d5g

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Magnesium binding site 3 out of 5 in the Structure of Colocasia Esculenta Agglutinin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Colocasia Esculenta Agglutinin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:12.3
occ:1.00
 C B:ASN6 1.9 6.8 1.0
O B:THR22 2.0 3.2 1.0
N B:ASN7 2.1 6.6 1.0
O B:ASN6 2.2 10.6 1.0
CA B:ASN7 2.3 9.9 1.0
CB B:ASN7 2.6 11.5 1.0
CB B:ASN6 2.8 7.4 0.1
CA B:ASN6 2.9 5.2 1.0
C B:THR22 3.0 7.2 1.0
N B:THR22 3.2 9.6 1.0
CA B:THR22 3.6 7.8 1.0
CG B:ASN7 3.7 7.9 1.0
C B:ASN7 3.8 11.1 1.0
OD1 B:ASN7 4.1 6.1 1.0
N B:ASN6 4.1 7.2 1.0
CB B:THR22 4.1 7.9 0.5
CG B:ASN6 4.1 7.5 0.3
N B:ALA23 4.2 3.7 1.0
C B:LEU21 4.3 12.5 1.0
ND2 B:ASN6 4.5 9.1 0.8
N B:LEU8 4.5 11.3 1.0
CA B:ALA23 4.6 9.3 1.0
CA B:LEU21 4.6 7.5 1.0
O B:ASN7 4.6 13.1 1.0
O B:HOH306 4.7 4.9 1.0
ND2 B:ASN7 4.7 4.6 1.0
O B:THR5 4.7 15.8 1.0
OG1 B:THR22 4.7 6.4 0.4
CB B:ALA23 4.7 16.3 1.0
CB B:LEU21 4.8 15.3 0.7
C B:THR5 4.8 9.8 1.0

Magnesium binding site 4 out of 5 in 5d5g

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Magnesium binding site 4 out of 5 in the Structure of Colocasia Esculenta Agglutinin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Colocasia Esculenta Agglutinin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:14.4
occ:1.00
 O B:VAL89 1.9 7.4 1.0
O B:VAL99 2.0 5.2 1.0
CA B:ILE100 2.3 9.4 1.0
CA B:LEU90 2.4 11.1 1.0
C B:VAL89 2.7 12.2 1.0
C B:VAL99 2.7 10.1 1.0
N B:TYR101 2.8 11.2 1.0
C B:ILE100 2.9 13.0 1.0
N B:ILE100 2.9 5.6 1.0
N B:LEU90 2.9 11.6 1.0
N B:ILE91 3.0 10.8 1.0
C B:LEU90 3.1 15.9 1.0
CD1 B:TYR101 3.5 14.4 1.0
CB B:ILE100 3.5 10.2 1.0
CB B:LEU90 3.6 6.2 1.0
CG2 B:ILE100 3.9 7.8 1.0
O B:ILE100 3.9 16.2 1.0
CG1 B:ILE100 4.0 12.1 1.0
CA B:TYR101 4.1 12.4 1.0
CA B:VAL89 4.2 10.8 1.0
CD1 B:LEU90 4.2 5.8 0.7
O B:LEU90 4.2 20.7 1.0
CA B:VAL99 4.2 9.6 1.0
CE1 B:TYR101 4.2 16.4 1.0
CG B:TYR101 4.3 15.6 1.0
CB B:TYR101 4.3 11.5 1.0
CA B:ILE91 4.4 10.4 1.0
CG B:LEU90 4.4 7.5 0.7
CB B:ILE91 4.6 14.4 0.6
N B:VAL89 4.6 10.6 1.0
CG1 B:ILE91 4.6 6.6 0.6
CG1 B:VAL89 4.7 11.5 1.0
N B:VAL99 4.7 4.8 1.0
O B:TYR101 4.8 11.2 1.0
CB B:VAL99 4.9 10.2 0.3
CB B:VAL89 4.9 15.5 1.0
O B:ILE91 4.9 12.7 1.0
C B:TYR101 5.0 12.6 1.0

Magnesium binding site 5 out of 5 in 5d5g

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Magnesium binding site 5 out of 5 in the Structure of Colocasia Esculenta Agglutinin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Colocasia Esculenta Agglutinin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:17.4
occ:1.00
 O B:ILE91 1.8 12.7 1.0
O B:PHE97 2.1 15.4 1.0
CA B:ALA98 2.3 12.9 1.0
C B:ILE91 2.6 16.9 1.0
CA B:LEU92 2.8 11.6 1.0
C B:PHE97 2.8 20.0 1.0
N B:ARG93 2.9 24.7 1.0
N B:VAL99 2.9 4.8 1.0
N B:ALA98 3.0 20.9 1.0
C B:ALA98 3.1 15.7 1.0
N B:LEU92 3.1 15.6 1.0
CG B:ARG93 3.3 19.5 1.0
C B:LEU92 3.3 26.3 1.0
CA B:ILE91 3.9 10.4 1.0
CB B:LEU92 4.0 14.1 1.0
CA B:ARG93 4.1 24.9 1.0
CB B:ARG93 4.2 23.1 1.0
CG2 B:ILE91 4.2 9.4 0.5
CA B:VAL99 4.2 9.6 1.0
CB B:ILE91 4.3 14.4 0.6
O B:ALA98 4.3 11.1 1.0
CA B:PHE97 4.3 20.7 1.0
CD1 B:LEU92 4.3 16.1 1.0
N B:ILE91 4.3 10.8 1.0
CD B:ARG93 4.4 13.1 1.0
CD1 B:LEU90 4.5 5.8 0.7
O B:VAL99 4.5 5.2 1.0
O B:LEU92 4.5 23.6 1.0
CG2 B:VAL99 4.6 13.8 0.3
CG B:LEU92 4.7 15.5 1.0
CB B:VAL99 4.7 10.2 0.3
CB B:PHE97 4.7 20.3 1.0
N B:PHE97 4.8 21.5 1.0
C B:VAL99 4.9 10.1 1.0

Reference:

R.Chattopadhyaya, H.Biswas, A.Sarkar. Crystal Structure Colocasia Esculenta Tuber Agglutinin at 1.74A Resolution and Its Quaternary Interactions J Glycobio V. 6 00126 2017.
ISSN: ISSN 2168-958X
DOI: 10.4172/2168-958X.1000126
Page generated: Sun Sep 29 02:31:16 2024

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