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Manganese in PDB 1vln: A Triclinic Crystal Form of the Lectin Concanavalin A

Protein crystallography data

The structure of A Triclinic Crystal Form of the Lectin Concanavalin A, PDB code: 1vln was solved by P.N.Kanellopoulos, P.A.Tucker, S.J.Hamodrakas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.800, 79.300, 133.300, 97.10, 90.20, 97.50
R / Rfree (%) 20.5 / 26.5

Other elements in 1vln:

The structure of A Triclinic Crystal Form of the Lectin Concanavalin A also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the A Triclinic Crystal Form of the Lectin Concanavalin A (pdb code 1vln). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the A Triclinic Crystal Form of the Lectin Concanavalin A, PDB code: 1vln:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1vln

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Manganese binding site 1 out of 8 in the A Triclinic Crystal Form of the Lectin Concanavalin A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of A Triclinic Crystal Form of the Lectin Concanavalin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn238

b:33.7
occ:1.00
 O A:HOH241 2.1 33.1 1.0
OD2 A:ASP10 2.1 23.4 1.0
OE2 A:GLU8 2.3 26.1 1.0
OD1 A:ASP19 2.4 27.4 1.0
O A:HOH240 2.4 16.5 1.0
NE2 A:HIS24 2.4 21.6 1.0
CG A:ASP10 3.2 22.1 1.0
CG A:ASP19 3.2 29.6 1.0
CD A:GLU8 3.2 26.5 1.0
CE1 A:HIS24 3.3 20.1 1.0
CD2 A:HIS24 3.4 18.0 1.0
OE1 A:GLU8 3.4 26.0 1.0
OD2 A:ASP19 3.5 23.1 1.0
CB A:ASP10 3.5 19.0 1.0
O A:HOH242 3.9 16.6 1.0
CA A:CA239 4.1 21.5 1.0
OG A:SER34 4.2 23.2 1.0
OD1 A:ASP10 4.3 21.4 1.0
CB A:ASP19 4.4 26.4 1.0
ND1 A:HIS24 4.5 21.0 1.0
CG A:HIS24 4.5 20.9 1.0
CG A:GLU8 4.6 25.6 1.0
CA A:ASP19 4.7 29.7 1.0
O A:VAL32 4.8 23.4 1.0

Manganese binding site 2 out of 8 in 1vln

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Manganese binding site 2 out of 8 in the A Triclinic Crystal Form of the Lectin Concanavalin A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of A Triclinic Crystal Form of the Lectin Concanavalin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn238

b:39.5
occ:1.00
 O B:HOH241 1.9 36.1 1.0
OD2 B:ASP10 2.0 34.8 1.0
OE2 B:GLU8 2.1 40.0 1.0
OD1 B:ASP19 2.3 41.4 1.0
NE2 B:HIS24 2.3 29.2 1.0
O B:HOH240 2.4 18.2 1.0
CG B:ASP10 3.0 30.8 1.0
CG B:ASP19 3.2 31.6 1.0
CD B:GLU8 3.2 33.3 1.0
CE1 B:HIS24 3.3 24.3 1.0
CD2 B:HIS24 3.3 28.7 1.0
OD2 B:ASP19 3.4 31.7 1.0
CB B:ASP10 3.4 26.7 1.0
OE1 B:GLU8 3.5 31.6 1.0
CA B:CA239 4.0 28.0 1.0
OD1 B:ASP10 4.1 29.0 1.0
O B:HOH243 4.1 24.6 1.0
ND1 B:HIS24 4.4 27.0 1.0
OG B:SER34 4.4 14.5 1.0
CG B:HIS24 4.4 26.2 1.0
CB B:ASP19 4.5 28.3 1.0
CG B:GLU8 4.5 33.7 1.0
O B:VAL32 4.7 26.2 1.0
CA B:ASP19 4.8 28.4 1.0
CA B:ASP10 4.9 28.5 1.0

Manganese binding site 3 out of 8 in 1vln

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Manganese binding site 3 out of 8 in the A Triclinic Crystal Form of the Lectin Concanavalin A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of A Triclinic Crystal Form of the Lectin Concanavalin A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn238

b:41.2
occ:1.00
 OE2 C:GLU8 2.1 37.9 1.0
OD1 C:ASP19 2.2 32.6 1.0
O C:HOH240 2.2 27.6 1.0
OD2 C:ASP10 2.2 35.6 1.0
NE2 C:HIS24 2.4 28.1 1.0
CG C:ASP19 3.1 27.8 1.0
CD C:GLU8 3.2 33.7 1.0
CG C:ASP10 3.4 35.0 1.0
CE1 C:HIS24 3.4 24.8 1.0
CD2 C:HIS24 3.4 29.0 1.0
OD2 C:ASP19 3.5 27.6 1.0
OE1 C:GLU8 3.6 37.0 1.0
CB C:ASP10 3.8 26.8 1.0
O C:HOH242 4.2 21.3 1.0
CA C:CA239 4.3 24.6 1.0
CB C:ASP19 4.3 26.2 1.0
OG C:SER34 4.3 29.5 1.0
OD1 C:ASP10 4.4 38.5 1.0
CG C:GLU8 4.5 28.7 1.0
ND1 C:HIS24 4.5 28.8 1.0
CA C:ASP19 4.5 26.1 1.0
CG C:HIS24 4.5 27.1 1.0
O C:HOH241 4.6 38.6 1.0
O C:VAL32 4.8 31.8 1.0
CD C:PRO20 5.0 30.5 1.0

Manganese binding site 4 out of 8 in 1vln

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Manganese binding site 4 out of 8 in the A Triclinic Crystal Form of the Lectin Concanavalin A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of A Triclinic Crystal Form of the Lectin Concanavalin A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn238

b:38.5
occ:1.00
 OD2 D:ASP10 2.0 28.5 1.0
O D:HOH241 2.2 24.3 1.0
OD1 D:ASP19 2.3 23.6 1.0
NE2 D:HIS24 2.3 26.0 1.0
O D:HOH240 2.4 38.1 1.0
OE2 D:GLU8 2.5 32.5 1.0
CG D:ASP10 3.0 27.4 1.0
CG D:ASP19 3.0 27.4 1.0
CE1 D:HIS24 3.1 24.4 1.0
OD2 D:ASP19 3.3 31.9 1.0
CD D:GLU8 3.4 27.9 1.0
CD2 D:HIS24 3.4 25.9 1.0
CB D:ASP10 3.5 20.6 1.0
OE1 D:GLU8 3.6 25.8 1.0
OD1 D:ASP10 3.9 29.0 1.0
O D:HOH242 4.0 21.6 1.0
CA D:CA239 4.1 25.2 1.0
ND1 D:HIS24 4.3 20.6 1.0
CB D:ASP19 4.3 24.1 1.0
OG D:SER34 4.4 17.9 1.0
CG D:HIS24 4.5 24.5 1.0
CA D:ASP19 4.7 26.0 1.0
CG D:GLU8 4.8 26.7 1.0
O D:VAL32 4.8 22.1 1.0
CA D:ASP10 5.0 19.0 1.0

Manganese binding site 5 out of 8 in 1vln

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Manganese binding site 5 out of 8 in the A Triclinic Crystal Form of the Lectin Concanavalin A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of A Triclinic Crystal Form of the Lectin Concanavalin A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn238

b:30.8
occ:1.00
 O E:HOH241 2.0 30.2 1.0
O E:HOH240 2.2 23.8 1.0
OD2 E:ASP10 2.2 26.3 1.0
NE2 E:HIS24 2.2 22.3 1.0
OE2 E:GLU8 2.3 32.5 1.0
OD1 E:ASP19 2.4 28.3 1.0
CD2 E:HIS24 3.2 21.6 1.0
CG E:ASP10 3.2 28.0 1.0
CE1 E:HIS24 3.2 18.6 1.0
CD E:GLU8 3.2 29.6 1.0
CG E:ASP19 3.3 28.8 1.0
OE1 E:GLU8 3.5 28.5 1.0
CB E:ASP10 3.5 23.8 1.0
OD2 E:ASP19 3.6 24.7 1.0
O E:HOH243 4.0 21.0 1.0
CA E:CA239 4.1 26.8 1.0
OG E:SER34 4.2 26.9 1.0
OD1 E:ASP10 4.3 28.6 1.0
ND1 E:HIS24 4.4 20.6 1.0
CG E:HIS24 4.4 18.4 1.0
CB E:ASP19 4.6 26.8 1.0
O E:VAL32 4.6 25.4 1.0
CG E:GLU8 4.6 23.2 1.0
CA E:ASP19 4.9 30.1 1.0

Manganese binding site 6 out of 8 in 1vln

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Manganese binding site 6 out of 8 in the A Triclinic Crystal Form of the Lectin Concanavalin A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of A Triclinic Crystal Form of the Lectin Concanavalin A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn238

b:34.6
occ:1.00
 NE2 F:HIS24 2.2 31.2 1.0
OD2 F:ASP10 2.2 21.3 1.0
OE2 F:GLU8 2.3 29.8 1.0
O F:HOH241 2.3 27.8 1.0
OD1 F:ASP19 2.5 27.9 1.0
O F:HOH240 2.6 24.7 1.0
CE1 F:HIS24 3.1 28.2 1.0
CG F:ASP19 3.2 28.7 1.0
CD2 F:HIS24 3.2 29.7 1.0
CG F:ASP10 3.3 25.1 1.0
CD F:GLU8 3.3 24.2 1.0
OD2 F:ASP19 3.4 25.8 1.0
CB F:ASP10 3.6 21.9 1.0
OE1 F:GLU8 3.6 27.1 1.0
O F:HOH242 4.1 19.1 1.0
CA F:CA239 4.2 26.3 1.0
ND1 F:HIS24 4.2 31.6 1.0
CG F:HIS24 4.3 31.1 1.0
OD1 F:ASP10 4.4 25.0 1.0
CB F:ASP19 4.4 30.4 1.0
OG F:SER34 4.6 17.4 1.0
CG F:GLU8 4.6 24.0 1.0
O F:VAL32 4.7 26.1 1.0
CA F:ASP19 4.8 30.4 1.0

Manganese binding site 7 out of 8 in 1vln

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Manganese binding site 7 out of 8 in the A Triclinic Crystal Form of the Lectin Concanavalin A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of A Triclinic Crystal Form of the Lectin Concanavalin A within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn238

b:38.3
occ:1.00
 OD2 G:ASP10 2.0 22.7 1.0
O G:HOH240 2.2 26.0 1.0
OE2 G:GLU8 2.2 29.6 1.0
NE2 G:HIS24 2.3 25.9 1.0
O G:HOH241 2.3 29.6 1.0
OD1 G:ASP19 2.4 31.7 1.0
CG G:ASP10 3.0 22.8 1.0
CD G:GLU8 3.2 30.5 1.0
CG G:ASP19 3.2 33.3 1.0
CE1 G:HIS24 3.2 21.6 1.0
CD2 G:HIS24 3.3 28.9 1.0
OE1 G:GLU8 3.4 32.3 1.0
OD2 G:ASP19 3.4 34.6 1.0
CB G:ASP10 3.4 17.2 1.0
O G:HOH242 3.9 23.7 1.0
OD1 G:ASP10 4.2 25.1 1.0
CA G:CA239 4.2 26.8 1.0
OG G:SER34 4.3 24.3 1.0
ND1 G:HIS24 4.4 27.6 1.0
CG G:HIS24 4.4 25.4 1.0
CB G:ASP19 4.5 25.1 1.0
CG G:GLU8 4.6 21.1 1.0
O G:VAL32 4.8 27.7 1.0
CA G:ASP19 4.8 30.0 1.0
CA G:ASP10 5.0 21.1 1.0

Manganese binding site 8 out of 8 in 1vln

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Manganese binding site 8 out of 8 in the A Triclinic Crystal Form of the Lectin Concanavalin A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of A Triclinic Crystal Form of the Lectin Concanavalin A within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn238

b:40.3
occ:1.00
 O H:HOH241 1.9 26.9 1.0
OD1 H:ASP19 2.2 38.6 1.0
OD2 H:ASP10 2.3 37.5 1.0
OE2 H:GLU8 2.3 28.0 1.0
NE2 H:HIS24 2.3 23.4 1.0
O H:HOH240 2.4 28.6 1.0
CG H:ASP19 3.1 33.6 1.0
CE1 H:HIS24 3.2 21.0 1.0
CG H:ASP10 3.2 35.7 1.0
CD H:GLU8 3.3 28.2 1.0
OD2 H:ASP19 3.3 37.1 1.0
CD2 H:HIS24 3.4 24.4 1.0
CB H:ASP10 3.5 30.6 1.0
OE1 H:GLU8 3.7 31.6 1.0
O H:HOH243 4.0 24.2 1.0
CA H:CA239 4.2 29.7 1.0
ND1 H:HIS24 4.3 22.8 1.0
OD1 H:ASP10 4.3 38.1 1.0
CB H:ASP19 4.4 31.1 1.0
CG H:HIS24 4.5 18.3 1.0
OG H:SER34 4.5 27.1 1.0
CG H:GLU8 4.6 25.7 1.0
CA H:ASP19 4.7 28.5 1.0
O H:VAL32 4.8 30.1 1.0
CD H:PRO20 4.9 30.6 1.0

Reference:

P.N.Kanellopoulos, P.A.Tucker, K.Pavlou, B.Agianian, S.J.Hamodrakas. A Triclinic Crystal Form of the Lectin Concanavalin A J.Struct.Biol. V. 117 16 1996.
ISSN: ISSN 1047-8477
PubMed: 8812975
DOI: 10.1006/JSBI.1996.0065
Page generated: Sat Oct 5 12:49:38 2024

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