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Manganese in PDB 1vam: Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside

Protein crystallography data

The structure of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside, PDB code: 1vam 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 / 2.75
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 135.190, 155.380, 71.250, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 26

Other elements in 1vam:

The structure of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside (pdb code 1vam). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside, PDB code: 1vam:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1vam

Go back to Manganese Binding Sites List in 1vam
Manganese binding site 1 out of 4 in the Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn238

b:33.1
occ:1.00
NE2 A:HIS24 2.2 28.8 1.0
O A:HOH248 2.3 39.1 1.0
OE2 A:GLU8 2.3 35.0 1.0
OD2 A:ASP10 2.3 24.1 1.0
O A:HOH247 2.4 31.4 1.0
OD1 A:ASP19 2.4 45.4 1.0
CD2 A:HIS24 3.2 31.2 1.0
CD A:GLU8 3.2 32.3 1.0
CG A:ASP19 3.2 43.6 1.0
CE1 A:HIS24 3.3 29.6 1.0
CG A:ASP10 3.3 25.2 1.0
OE1 A:GLU8 3.4 30.1 1.0
OD2 A:ASP19 3.5 45.1 1.0
CB A:ASP10 3.6 21.6 1.0
O A:HOH249 3.8 26.0 1.0
OG A:SER34 4.2 28.9 1.0
CA A:CA239 4.4 34.3 1.0
CG A:HIS24 4.4 27.9 1.0
OD1 A:ASP10 4.4 24.8 1.0
ND1 A:HIS24 4.4 30.4 1.0
CB A:ASP19 4.5 42.2 1.0
CG A:GLU8 4.6 29.1 1.0
CA A:ASP19 4.7 44.6 1.0
O A:VAL32 4.8 37.1 1.0

Manganese binding site 2 out of 4 in 1vam

Go back to Manganese Binding Sites List in 1vam
Manganese binding site 2 out of 4 in the Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn238

b:34.6
occ:1.00
O B:HOH246 2.1 44.2 1.0
OD2 B:ASP10 2.1 18.6 1.0
OD1 B:ASP19 2.1 36.9 1.0
O B:HOH245 2.2 23.1 1.0
OE2 B:GLU8 2.3 41.2 1.0
NE2 B:HIS24 2.7 29.8 1.0
CG B:ASP10 3.2 20.3 1.0
CG B:ASP19 3.2 34.1 1.0
CD B:GLU8 3.3 38.6 1.0
CE1 B:HIS24 3.3 26.3 1.0
CB B:ASP10 3.5 20.0 1.0
OE1 B:GLU8 3.6 34.4 1.0
OD2 B:ASP19 3.7 31.0 1.0
CD2 B:HIS24 3.8 27.8 1.0
O B:HOH248 3.9 30.3 1.0
CA B:CA239 4.1 30.1 1.0
OG B:SER34 4.2 24.1 1.0
OD1 B:ASP10 4.3 21.4 1.0
CB B:ASP19 4.4 31.1 1.0
ND1 B:HIS24 4.5 26.3 1.0
CA B:ASP19 4.6 37.9 1.0
CG B:GLU8 4.6 32.6 1.0
O B:VAL32 4.7 31.1 1.0
CG B:HIS24 4.8 26.4 1.0

Manganese binding site 3 out of 4 in 1vam

Go back to Manganese Binding Sites List in 1vam
Manganese binding site 3 out of 4 in the Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn238

b:27.9
occ:1.00
O C:HOH246 2.0 25.8 1.0
O C:HOH245 2.1 38.0 1.0
OD2 C:ASP10 2.2 36.8 1.0
NE2 C:HIS24 2.2 22.9 1.0
OE2 C:GLU8 2.4 31.2 1.0
OD1 C:ASP19 2.6 31.7 1.0
CE1 C:HIS24 3.1 21.2 1.0
CG C:ASP10 3.2 37.1 1.0
CD2 C:HIS24 3.4 23.9 1.0
CD C:GLU8 3.4 26.8 1.0
CG C:ASP19 3.4 27.9 1.0
OD2 C:ASP19 3.6 28.7 1.0
CB C:ASP10 3.6 30.1 1.0
OE1 C:GLU8 3.6 24.8 1.0
O C:HOH247 4.1 23.1 1.0
CA C:CA239 4.2 24.3 1.0
ND1 C:HIS24 4.3 25.7 1.0
OD1 C:ASP10 4.4 36.1 1.0
OG C:SER34 4.4 20.7 1.0
CG C:HIS24 4.4 27.9 1.0
CG C:GLU8 4.8 23.9 1.0
CB C:ASP19 4.8 26.8 1.0
O C:VAL32 4.8 33.2 1.0

Manganese binding site 4 out of 4 in 1vam

Go back to Manganese Binding Sites List in 1vam
Manganese binding site 4 out of 4 in the Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn238

b:42.6
occ:1.00
OD2 D:ASP10 2.1 32.9 1.0
OD1 D:ASP19 2.1 41.6 1.0
O D:HOH247 2.2 34.2 1.0
NE2 D:HIS24 2.2 34.9 1.0
OE2 D:GLU8 2.3 38.6 1.0
O D:HOH243 2.4 49.1 1.0
CG D:ASP10 3.1 31.1 1.0
CG D:ASP19 3.1 42.3 1.0
CE1 D:HIS24 3.1 32.8 1.0
CD2 D:HIS24 3.3 36.3 1.0
CD D:GLU8 3.3 37.0 1.0
CB D:ASP10 3.3 31.5 1.0
OD2 D:ASP19 3.6 35.1 1.0
OE1 D:GLU8 3.6 38.6 1.0
O D:HOH246 4.0 34.9 1.0
OG D:SER34 4.1 42.0 1.0
OD1 D:ASP10 4.2 31.9 1.0
CA D:CA239 4.2 36.4 1.0
ND1 D:HIS24 4.3 35.7 1.0
CB D:ASP19 4.3 41.9 1.0
CG D:HIS24 4.4 36.6 1.0
CA D:ASP19 4.6 45.5 1.0
CG D:GLU8 4.7 30.8 1.0
O D:VAL32 4.8 42.0 1.0
CA D:ASP10 4.9 27.2 1.0

Reference:

P.N.Kanellopoulos, K.Pavlou, A.Perrakis, B.Agianian, C.E.Vorgias, C.Mavrommatis, M.Soufi, P.A.Tucker, S.J.Hamodrakas. The Crystal Structure of the Complexes of Concanavalin A with 4'-Nitrophenyl-Alpha-D-Mannopyranoside and 4'-Nitrophenyl-Alpha-D-Glucopyranoside. J.Struct.Biol. V. 116 345 1996.
ISSN: ISSN 1047-8477
PubMed: 8812993
DOI: 10.1006/JSBI.1996.0052
Page generated: Tue Dec 15 03:56:56 2020

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