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Manganese in PDB 3d4k: Concanavalin A Complexed to A Synthetic Analog of the Trimannoside

Protein crystallography data

The structure of Concanavalin A Complexed to A Synthetic Analog of the Trimannoside, PDB code: 3d4k was solved by R.Kadirvelraj, B.L.Foley, J.D.Dyekjaer, R.J.Woods, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.015, 63.547, 126.215, 90.00, 86.91, 90.00
R / Rfree (%) 20.5 / 23.8

Other elements in 3d4k:

The structure of Concanavalin A Complexed to A Synthetic Analog of the Trimannoside also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Concanavalin A Complexed to A Synthetic Analog of the Trimannoside (pdb code 3d4k). 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 Complexed to A Synthetic Analog of the Trimannoside, PDB code: 3d4k:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3d4k

Go back to Manganese Binding Sites List in 3d4k
Manganese binding site 1 out of 4 in the Concanavalin A Complexed to A Synthetic Analog of the Trimannoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Concanavalin A Complexed to A Synthetic Analog of the Trimannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn238

b:18.6
occ:1.00
OD2 A:ASP10 2.1 14.0 1.0
O A:HOH365 2.2 21.5 1.0
OE2 A:GLU8 2.2 17.6 1.0
O A:HOH307 2.3 20.6 1.0
NE2 A:HIS24 2.4 21.3 1.0
OD2 A:ASP19 2.5 26.9 1.0
OD1 A:ASP19 2.9 26.2 1.0
CG A:ASP19 3.0 26.0 1.0
CG A:ASP10 3.1 14.4 1.0
CD A:GLU8 3.2 18.3 1.0
CE1 A:HIS24 3.3 20.9 1.0
CD2 A:HIS24 3.4 19.7 1.0
OE1 A:GLU8 3.5 17.9 1.0
CB A:ASP10 3.5 14.8 1.0
O A:HOH250 3.9 18.4 1.0
O A:HOH753 4.1 38.8 1.0
OG A:SER34 4.2 19.0 1.0
CA A:CA239 4.2 20.1 1.0
OD1 A:ASP10 4.3 15.9 1.0
CB A:ASP19 4.3 27.8 1.0
ND1 A:HIS24 4.5 21.3 1.0
CG A:HIS24 4.5 21.2 1.0
CG A:GLU8 4.5 16.8 1.0
O A:VAL32 4.6 19.3 1.0
CA A:ASP19 4.9 28.7 1.0

Manganese binding site 2 out of 4 in 3d4k

Go back to Manganese Binding Sites List in 3d4k
Manganese binding site 2 out of 4 in the Concanavalin A Complexed to A Synthetic Analog of the Trimannoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Concanavalin A Complexed to A Synthetic Analog of the Trimannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn238

b:18.8
occ:1.00
OD2 B:ASP10 2.1 14.1 1.0
OE2 B:GLU8 2.2 16.0 1.0
O B:HOH264 2.2 17.0 1.0
O B:HOH306 2.3 20.7 1.0
OD1 B:ASP19 2.3 16.5 1.0
NE2 B:HIS24 2.4 21.4 1.0
CG B:ASP10 3.2 16.3 1.0
CG B:ASP19 3.2 21.4 1.0
CD B:GLU8 3.2 15.4 1.0
CE1 B:HIS24 3.2 20.5 1.0
CD2 B:HIS24 3.5 19.1 1.0
OE1 B:GLU8 3.6 15.5 1.0
CB B:ASP10 3.6 17.0 1.0
OD2 B:ASP19 3.6 19.9 1.0
O B:HOH257 4.0 18.8 1.0
OG B:SER34 4.2 19.7 1.0
CA B:CA239 4.2 18.3 1.0
OD1 B:ASP10 4.3 16.3 1.0
CB B:ASP19 4.4 21.7 1.0
ND1 B:HIS24 4.4 19.6 1.0
CG B:HIS24 4.5 21.7 1.0
CG B:GLU8 4.6 13.0 1.0
O B:VAL32 4.6 17.4 1.0
CA B:ASP19 4.7 24.2 1.0

Manganese binding site 3 out of 4 in 3d4k

Go back to Manganese Binding Sites List in 3d4k
Manganese binding site 3 out of 4 in the Concanavalin A Complexed to A Synthetic Analog of the Trimannoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Concanavalin A Complexed to A Synthetic Analog of the Trimannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn238

b:17.3
occ:1.00
OD2 C:ASP10 2.1 13.6 1.0
O C:HOH386 2.1 23.4 1.0
OD1 C:ASP19 2.2 19.3 1.0
OE2 C:GLU8 2.3 16.3 1.0
O C:HOH256 2.3 17.2 1.0
NE2 C:HIS24 2.4 21.7 1.0
CG C:ASP19 3.1 24.3 1.0
CG C:ASP10 3.1 16.8 1.0
CE1 C:HIS24 3.2 22.1 1.0
CD C:GLU8 3.3 16.4 1.0
CD2 C:HIS24 3.5 19.2 1.0
OD2 C:ASP19 3.6 27.7 1.0
CB C:ASP10 3.6 15.5 1.0
OE1 C:GLU8 3.6 17.1 1.0
O C:HOH281 4.0 18.9 1.0
OG C:SER34 4.1 19.5 1.0
CA C:CA239 4.2 20.0 1.0
CB C:ASP19 4.2 23.1 1.0
OD1 C:ASP10 4.2 16.0 1.0
O C:HOH710 4.3 35.5 1.0
ND1 C:HIS24 4.4 22.3 1.0
CG C:HIS24 4.5 21.4 1.0
O C:VAL32 4.6 18.3 1.0
CG C:GLU8 4.6 15.2 1.0
CA C:ASP19 4.7 25.7 1.0

Manganese binding site 4 out of 4 in 3d4k

Go back to Manganese Binding Sites List in 3d4k
Manganese binding site 4 out of 4 in the Concanavalin A Complexed to A Synthetic Analog of the Trimannoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Concanavalin A Complexed to A Synthetic Analog of the Trimannoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn238

b:16.6
occ:1.00
O D:HOH271 2.2 19.8 1.0
OD2 D:ASP10 2.2 14.8 1.0
OE2 D:GLU8 2.2 15.6 1.0
OD1 D:ASP19 2.3 20.8 1.0
NE2 D:HIS24 2.3 20.7 1.0
O D:HOH270 2.3 20.4 1.0
CG D:ASP19 3.1 22.4 1.0
CE1 D:HIS24 3.1 20.3 1.0
CG D:ASP10 3.2 17.5 1.0
CD D:GLU8 3.3 17.9 1.0
CD2 D:HIS24 3.5 17.8 1.0
OD2 D:ASP19 3.5 21.6 1.0
CB D:ASP10 3.6 16.6 1.0
OE1 D:GLU8 3.6 14.8 1.0
O D:HOH253 4.0 16.1 1.0
OG D:SER34 4.1 19.8 1.0
CA D:CA239 4.2 17.2 1.0
CB D:ASP19 4.2 22.2 1.0
O D:HOH755 4.3 41.2 1.0
ND1 D:HIS24 4.3 20.2 1.0
OD1 D:ASP10 4.3 18.4 1.0
CG D:HIS24 4.5 18.7 1.0
O D:VAL32 4.6 18.9 1.0
CG D:GLU8 4.6 16.2 1.0
CA D:ASP19 4.7 23.7 1.0

Reference:

R.Kadirvelraj, B.L.Foley, J.D.Dyekjaer, R.J.Woods. Involvement of Water in Carbohydrate-Protein Binding: Concanavalin A Revisited. J.Am.Chem.Soc. V. 130 16933 2008.
ISSN: ISSN 0002-7863
PubMed: 19053475
DOI: 10.1021/JA8039663
Page generated: Tue Dec 15 04:08:39 2020

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