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Manganese in PDB 1v00: Erythrina Cristagalli Lectin

Protein crystallography data

The structure of Erythrina Cristagalli Lectin, PDB code: 1v00 was solved by K.Turton, R.Natesh, N.Thiyagarajan, J.A.Chaddock, K.R.Acharya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.12 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.900, 167.230, 55.130, 90.00, 97.08, 90.00
R / Rfree (%) 17.2 / 19.5

Other elements in 1v00:

The structure of Erythrina Cristagalli Lectin also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Erythrina Cristagalli Lectin (pdb code 1v00). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Erythrina Cristagalli Lectin, PDB code: 1v00:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1v00

Go back to Manganese Binding Sites List in 1v00
Manganese binding site 1 out of 4 in the Erythrina Cristagalli Lectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Erythrina Cristagalli Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1241

b:10.2
occ:1.00
OD1 A:ASP129 2.1 11.4 1.0
OE2 A:GLU127 2.2 9.3 1.0
OD1 A:ASP136 2.2 11.1 1.0
O A:HOH2296 2.2 12.2 1.0
O A:HOH2295 2.3 10.6 1.0
NE2 A:HIS142 2.3 8.0 1.0
CG A:ASP129 3.2 12.6 1.0
CG A:ASP136 3.2 11.4 1.0
CD A:GLU127 3.2 11.9 1.0
CE1 A:HIS142 3.2 13.2 1.0
CD2 A:HIS142 3.4 10.8 1.0
CB A:ASP129 3.5 9.7 1.0
OE1 A:GLU127 3.6 11.3 1.0
OD2 A:ASP136 3.7 12.3 1.0
O A:HOH2162 4.0 12.4 1.0
CA A:CA1242 4.2 10.4 1.0
OD2 A:ASP129 4.3 9.5 1.0
CB A:ASP136 4.3 12.1 1.0
O A:HOH2187 4.4 11.6 1.0
ND1 A:HIS142 4.4 10.6 1.0
O A:ILE150 4.5 12.8 1.0
CG A:HIS142 4.5 10.8 1.0
CG A:GLU127 4.5 10.9 1.0
CD A:PRO137 4.6 12.6 1.0
OG A:SER152 4.7 16.6 1.0
CA A:ASP136 4.9 12.3 1.0
NE1 A:TRP135 4.9 14.6 1.0

Manganese binding site 2 out of 4 in 1v00

Go back to Manganese Binding Sites List in 1v00
Manganese binding site 2 out of 4 in the Erythrina Cristagalli Lectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Erythrina Cristagalli Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1241

b:17.2
occ:1.00
OD2 B:ASP129 2.1 15.9 1.0
O B:HOH2222 2.1 17.4 1.0
OD1 B:ASP136 2.2 17.5 1.0
OE2 B:GLU127 2.2 13.7 1.0
NE2 B:HIS142 2.3 16.1 1.0
O B:HOH2223 2.3 15.6 1.0
CG B:ASP129 3.2 15.7 1.0
CE1 B:HIS142 3.2 17.8 1.0
CG B:ASP136 3.2 18.3 1.0
CD B:GLU127 3.3 15.5 1.0
CD2 B:HIS142 3.4 17.0 1.0
CB B:ASP129 3.5 14.7 1.0
OE1 B:GLU127 3.6 14.5 1.0
OD2 B:ASP136 3.9 17.9 1.0
O B:HOH2118 4.0 19.7 1.0
OG B:SER152 4.1 15.0 1.0
CA B:CA1242 4.3 18.6 1.0
O B:HOH2138 4.3 18.2 1.0
OD1 B:ASP129 4.3 15.9 1.0
CB B:ASP136 4.3 17.7 1.0
ND1 B:HIS142 4.4 17.1 1.0
O B:ILE150 4.5 19.4 1.0
CG B:HIS142 4.5 16.8 1.0
CG B:GLU127 4.6 14.2 1.0
CD B:PRO137 4.6 20.4 1.0
NE1 B:TRP135 4.8 18.1 1.0
CA B:ASP136 4.8 19.3 1.0
CD1 B:TRP135 4.9 19.0 1.0

Manganese binding site 3 out of 4 in 1v00

Go back to Manganese Binding Sites List in 1v00
Manganese binding site 3 out of 4 in the Erythrina Cristagalli Lectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Erythrina Cristagalli Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1241

b:11.2
occ:1.00
OD1 C:ASP136 2.1 12.3 1.0
OD2 C:ASP129 2.1 12.2 1.0
OE2 C:GLU127 2.2 13.0 1.0
O C:HOH2329 2.2 11.5 1.0
O C:HOH2330 2.3 10.0 1.0
NE2 C:HIS142 2.4 11.5 1.0
CG C:ASP136 3.2 15.6 1.0
CG C:ASP129 3.2 13.3 1.0
CD C:GLU127 3.2 12.4 1.0
CE1 C:HIS142 3.2 11.9 1.0
CD2 C:HIS142 3.4 11.5 1.0
CB C:ASP129 3.5 12.1 1.0
OE1 C:GLU127 3.5 11.4 1.0
OD2 C:ASP136 3.7 15.1 1.0
O C:HOH2196 4.0 12.3 1.0
OG C:SER152 4.2 13.4 1.0
CA C:CA1242 4.2 11.0 1.0
CB C:ASP136 4.3 13.7 1.0
OD1 C:ASP129 4.3 10.6 1.0
O C:HOH2228 4.4 13.5 1.0
ND1 C:HIS142 4.4 11.6 1.0
O C:ILE150 4.4 14.8 1.0
CG C:HIS142 4.5 10.1 1.0
CG C:GLU127 4.6 10.6 1.0
CD C:PRO137 4.7 15.7 1.0
NE1 C:TRP135 4.8 13.9 1.0
CA C:ASP136 4.9 14.1 1.0
CD1 C:TRP135 5.0 13.4 1.0

Manganese binding site 4 out of 4 in 1v00

Go back to Manganese Binding Sites List in 1v00
Manganese binding site 4 out of 4 in the Erythrina Cristagalli Lectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Erythrina Cristagalli Lectin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1241

b:12.3
occ:1.00
OD2 D:ASP129 2.1 12.8 1.0
OD1 D:ASP136 2.2 14.1 1.0
O D:HOH2270 2.2 12.2 1.0
OE2 D:GLU127 2.2 13.7 1.0
O D:HOH2269 2.3 13.8 1.0
NE2 D:HIS142 2.3 11.6 1.0
CE1 D:HIS142 3.2 13.0 1.0
CG D:ASP129 3.2 11.9 1.0
CG D:ASP136 3.2 13.9 1.0
CD D:GLU127 3.2 15.2 1.0
CD2 D:HIS142 3.4 11.3 1.0
CB D:ASP129 3.5 11.2 1.0
OE1 D:GLU127 3.6 13.3 1.0
OD2 D:ASP136 3.7 15.8 1.0
O D:HOH2149 4.0 15.4 1.0
CA D:CA1242 4.1 12.8 1.0
OG D:SER152 4.2 14.0 1.0
CB D:ASP136 4.3 13.8 1.0
OD1 D:ASP129 4.3 12.5 1.0
ND1 D:HIS142 4.3 12.1 1.0
O D:HOH2169 4.4 16.4 1.0
CG D:HIS142 4.5 11.8 1.0
CG D:GLU127 4.5 11.9 1.0
O D:ILE150 4.5 17.1 1.0
CD D:PRO137 4.7 14.2 1.0
NE1 D:TRP135 4.8 16.3 1.0
CA D:ASP136 4.9 14.6 1.0
CD1 D:TRP135 4.9 15.9 1.0

Reference:

K.Turton, R.Natesh, N.Thiyagarajan, J.A.Chaddock, K.R.Acharya. Crystal Structures of Erythrina Cristagalli Lectin with Bound N-Linked Oligosaccharide and Lactose Glycobiology V. 14 923 2004.
ISSN: ISSN 0959-6658
PubMed: 15201215
DOI: 10.1093/GLYCOB/CWH114
Page generated: Tue Dec 15 03:56:41 2020

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