Atomistry » Magnesium » PDB 5d1f-5d9c » 5d5g
Atomistry »
  Magnesium »
    PDB 5d1f-5d9c »
      5d5g »

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

Go back to Magnesium Binding Sites List in 5d5g
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

Go back to Magnesium Binding Sites List in 5d5g
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

Go back to Magnesium Binding Sites List in 5d5g
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

Go back to Magnesium Binding Sites List in 5d5g
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

Go back to Magnesium Binding Sites List in 5d5g
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: Mon Dec 14 20:10:10 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy