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Manganese in PDB 1hkd: Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside

Protein crystallography data

The structure of Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside, PDB code: 1hkd was solved by M.B.Shevtsov, I.N.Tsygannik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.95 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.793, 61.235, 136.005, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 20.9

Other elements in 1hkd:

The structure of Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside (pdb code 1hkd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside, PDB code: 1hkd:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 1hkd

Go back to Manganese Binding Sites List in 1hkd
Manganese binding site 1 out of 2 in the Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1183

b:16.7
occ:1.00
OD1 A:ASP129 2.2 12.1 1.0
O A:HOH2126 2.2 10.5 1.0
OE1 A:GLU119 2.3 14.8 1.0
O A:HOH2127 2.3 8.5 1.0
OD2 A:ASP121 2.3 13.5 1.0
NE2 A:HIS136 2.4 12.8 1.0
CD A:GLU119 3.3 15.6 1.0
CG A:ASP129 3.3 15.0 1.0
CG A:ASP121 3.3 13.1 1.0
CE1 A:HIS136 3.3 13.5 1.0
CD2 A:HIS136 3.3 13.4 1.0
OE2 A:GLU119 3.6 13.5 1.0
CB A:ASP121 3.6 13.3 1.0
OD2 A:ASP129 3.7 12.8 1.0
O A:HOH2060 3.9 10.5 1.0
OG A:SER146 4.3 17.0 1.0
CA A:CA1182 4.3 14.3 1.0
OD1 A:ASP121 4.4 11.1 1.0
CB A:ASP129 4.4 14.5 1.0
ND1 A:HIS136 4.4 12.8 1.0
CG A:HIS136 4.5 13.9 1.0
O A:ILE144 4.5 14.5 1.0
O A:HOH2084 4.5 23.7 1.0
CG A:GLU119 4.6 12.6 1.0
CD A:PRO130 4.6 18.6 1.0
NE1 A:TRP128 4.7 16.2 1.0
CD1 A:TRP128 4.7 17.5 1.0
CA A:ASP129 4.8 15.8 1.0

Manganese binding site 2 out of 2 in 1hkd

Go back to Manganese Binding Sites List in 1hkd
Manganese binding site 2 out of 2 in the Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1183

b:19.3
occ:1.00
OD1 C:ASP129 2.2 12.6 1.0
OD2 C:ASP121 2.2 15.3 1.0
OE1 C:GLU119 2.3 17.1 1.0
NE2 C:HIS136 2.3 15.8 1.0
O C:HOH2107 2.4 15.3 1.0
O C:HOH2106 2.5 12.6 1.0
CE1 C:HIS136 3.1 16.4 1.0
CG C:ASP121 3.2 16.8 1.0
CG C:ASP129 3.3 19.3 1.0
CD C:GLU119 3.3 16.6 1.0
CD2 C:HIS136 3.4 15.2 1.0
OE2 C:GLU119 3.6 18.1 1.0
CB C:ASP121 3.6 17.3 1.0
OD2 C:ASP129 3.8 16.2 1.0
O C:HOH2060 3.9 15.0 1.0
OG C:SER146 4.2 18.6 1.0
CA C:CA1182 4.2 18.5 1.0
ND1 C:HIS136 4.3 14.9 1.0
OD1 C:ASP121 4.3 17.3 1.0
O C:HOH2074 4.4 21.4 1.0
CB C:ASP129 4.4 18.2 1.0
CG C:HIS136 4.5 17.8 1.0
O C:ILE144 4.5 16.1 1.0
CG C:GLU119 4.6 13.1 1.0
CD1 C:TRP128 4.6 20.6 1.0
NE1 C:TRP128 4.7 20.7 1.0
CD C:PRO130 4.7 21.2 1.0
CA C:ASP129 4.7 19.5 1.0

Reference:

M.B.Shevtsov, I.N.Tsygannik. Structure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside To Be Published.
Page generated: Tue Dec 15 03:48:53 2020

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