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Zinc in PDB 1x1v: Structure of Banana Lectin- Methyl-Alpha-Mannose Complex

Protein crystallography data

The structure of Structure of Banana Lectin- Methyl-Alpha-Mannose Complex, PDB code: 1x1v was solved by D.D.Singh, K.Saikrishnan, P.Kumar, A.Surolia, K.Sekar, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.92 / 2.45
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.820, 80.820, 148.000, 90.00, 90.00, 120.00
R / Rfree (%) 22.4 / 26

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Banana Lectin- Methyl-Alpha-Mannose Complex (pdb code 1x1v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Banana Lectin- Methyl-Alpha-Mannose Complex, PDB code: 1x1v:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1x1v

Go back to Zinc Binding Sites List in 1x1v
Zinc binding site 1 out of 3 in the Structure of Banana Lectin- Methyl-Alpha-Mannose Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Banana Lectin- Methyl-Alpha-Mannose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:58.3
occ:1.00
OD1 A:ASP41 2.2 47.9 1.0
ND1 A:HIS54 2.3 55.3 1.0
OD2 A:ASP41 2.3 47.3 1.0
O A:HOH449 2.5 55.0 1.0
O A:HOH448 2.6 65.3 1.0
CG A:ASP41 2.6 46.3 1.0
CG A:HIS54 2.7 54.4 1.0
CB A:HIS54 2.9 53.7 1.0
CE1 A:HIS54 3.3 55.5 1.0
CD2 A:HIS54 3.8 55.6 1.0
NE2 A:HIS54 4.0 55.2 1.0
CB A:ASP41 4.1 45.7 1.0
CE2 A:PHE32 4.2 40.3 1.0
CA A:HIS54 4.3 53.5 1.0
CZ A:PHE32 4.7 40.1 1.0
CA A:ASP41 4.9 45.5 1.0

Zinc binding site 2 out of 3 in 1x1v

Go back to Zinc Binding Sites List in 1x1v
Zinc binding site 2 out of 3 in the Structure of Banana Lectin- Methyl-Alpha-Mannose Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Banana Lectin- Methyl-Alpha-Mannose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:83.2
occ:1.00
CD2 A:HIS63 2.4 47.8 1.0
CG A:HIS63 3.0 47.1 1.0
CB A:HIS63 3.2 46.2 1.0
NE2 A:HIS63 3.5 48.1 1.0
CA A:HIS63 3.5 45.9 1.0
O A:PRO62 3.7 45.3 1.0
O4 A:MMA805 3.7 62.8 1.0
ND1 A:HIS63 4.1 48.4 1.0
CE1 A:HIS63 4.3 48.5 1.0
N A:HIS63 4.4 45.7 1.0
C A:PRO62 4.4 45.5 1.0
CE2 A:PHE104 4.6 46.4 1.0
C6 A:MMA805 4.6 63.1 1.0
C A:HIS63 4.7 45.7 1.0
C4 A:MMA805 4.9 62.7 1.0
N A:GLU64 5.0 45.9 1.0
C5 A:MMA805 5.0 62.9 1.0

Zinc binding site 3 out of 3 in 1x1v

Go back to Zinc Binding Sites List in 1x1v
Zinc binding site 3 out of 3 in the Structure of Banana Lectin- Methyl-Alpha-Mannose Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Banana Lectin- Methyl-Alpha-Mannose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn902

b:52.5
occ:1.00
OD2 B:ASP41 2.0 46.6 1.0
ND1 B:HIS54 2.1 58.0 1.0
OD1 B:ASP41 2.3 47.4 1.0
CG B:ASP41 2.5 48.0 1.0
O B:HOH450 2.9 52.1 1.0
CE1 B:HIS54 3.0 58.2 1.0
CG B:HIS54 3.1 57.9 1.0
CB B:HIS54 3.5 57.7 1.0
CA B:HIS54 3.9 58.0 1.0
CB B:ASP41 4.0 48.5 1.0
CE2 B:PHE32 4.2 50.9 1.0
NE2 B:HIS54 4.2 58.8 1.0
CD2 B:HIS54 4.2 58.2 1.0
CZ B:PHE32 4.4 50.8 1.0
O B:HOH275 4.6 59.6 1.0
N B:HIS54 4.9 58.6 1.0
CA B:ASP41 4.9 48.7 1.0
CD2 B:PHE32 4.9 50.7 1.0
C B:HIS54 4.9 57.2 1.0

Reference:

D.D.Singh, K.Saikrishnan, P.Kumar, A.Surolia, K.Sekar, M.Vijayan. Unusual Sugar Specificity of Banana Lectin From Musa Paradisiaca and Its Probable Evolutionary Origin. Crystallographic and Modelling Studies Glycobiology V. 15 1025 2005.
ISSN: ISSN 0959-6658
PubMed: 15958419
DOI: 10.1093/GLYCOB/CWI087
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