Zinc in PDB 8qmg: Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets.

The structure of Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets., PDB code: 8qmg was solved by Y.Bloch, S.N.Savvides, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.23 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.506, 145.973, 82.054, 90, 95.95, 90
R / Rfree (%)	20.8 / 24.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets. (pdb code 8qmg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets., PDB code: 8qmg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in the Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:51.0 occ:1.00 NE2 A:HIS115 2.0 54.6 1.0 OE2 A:GLU123 2.1 35.8 1.0 O A:HOH403 2.4 38.7 1.0 CE1 A:HIS115 2.8 47.0 1.0 HE1 A:HIS115 2.8 56.4 1.0 O A:HOH391 2.9 34.2 1.0 O A:HOH325 3.1 46.5 1.0 CD A:GLU123 3.1 34.7 1.0 CD2 A:HIS115 3.1 43.3 1.0 HG3 A:GLU123 3.1 40.6 1.0 HH22 A:ARG163 3.2 40.8 1.0 HD2 A:HIS115 3.4 52.0 1.0 HE2 A:TYR62 3.4 38.3 1.0 CG A:GLU123 3.5 33.8 1.0 HG2 A:GLU123 3.6 40.6 1.0 CE2 A:TYR62 3.7 31.9 1.0 NH2 A:ARG163 3.9 34.0 1.0 HD2 A:TYR62 3.9 37.4 1.0 ND1 A:HIS115 3.9 49.5 1.0 HH21 A:ARG163 4.0 40.8 1.0 CD2 A:TYR62 4.0 31.2 1.0 CG A:HIS115 4.1 44.2 1.0 OE1 A:GLU123 4.2 32.9 1.0 CZ A:TYR62 4.5 32.6 1.0 HH A:TYR62 4.6 43.8 1.0 HD1 A:HIS115 4.7 59.3 1.0 HH12 A:ARG163 4.9 39.2 1.0 OH A:TYR62 4.9 36.5 1.0 CB A:GLU123 5.0 31.8 1.0 CG A:TYR62 5.0 30.2 1.0

Zinc binding site 2 out of 24 in the Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:38.4 occ:1.00 NE2 B:HIS115 2.1 30.8 1.0 O B:HOH397 2.2 29.1 1.0 NE2 H:HIS115 2.2 32.7 1.0 O H:HOH290 2.9 33.6 1.0 CE1 B:HIS115 3.0 31.4 1.0 CD2 B:HIS115 3.1 30.1 1.0 CD2 H:HIS115 3.1 33.2 1.0 HD2 H:HIS115 3.2 39.8 1.0 HE1 B:HIS115 3.2 37.7 1.0 CE1 H:HIS115 3.2 37.2 1.0 HD2 B:HIS115 3.2 36.1 1.0 HE1 H:HIS115 3.5 44.6 1.0 HA B:ARG117 3.7 38.7 1.0 HA H:ARG117 3.8 41.8 1.0 O B:LEU116 4.1 30.1 1.0 ND1 B:HIS115 4.1 31.2 1.0 CG B:HIS115 4.2 30.5 1.0 O H:LEU116 4.2 33.2 1.0 CG H:HIS115 4.3 34.4 1.0 ND1 H:HIS115 4.3 36.5 1.0 H B:SER118 4.5 47.8 1.0 O B:HOH406 4.5 37.6 1.0 CA B:ARG117 4.6 32.2 1.0 H H:SER118 4.6 42.9 1.0 CA H:ARG117 4.7 34.8 1.0 HD1 B:HIS115 4.9 37.4 1.0 N B:SER118 4.9 39.9 1.0 C B:LEU116 5.0 29.8 1.0

Zinc binding site 3 out of 24 in the Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:41.5 occ:1.00 OE2 B:GLU138 1.9 41.5 1.0 OE2 B:GLU49 2.0 38.7 1.0 OD2 C:ASP10 2.1 46.5 1.0 O C:HOH342 2.1 33.1 1.0 HG2 B:GLU138 2.7 43.5 1.0 CD B:GLU138 2.7 39.9 1.0 CG C:ASP10 2.7 43.3 1.0 OD1 C:ASP10 2.8 44.8 1.0 O B:HOH301 2.8 42.0 1.0 CD B:GLU49 3.0 36.1 1.0 HE3 B:LYS47 3.0 47.0 1.0 HG2 B:GLU49 3.2 40.3 1.0 CG B:GLU138 3.2 36.3 1.0 CG B:GLU49 3.6 33.6 1.0 HE C:ARG9 3.7 62.6 1.0 OE1 B:GLU138 3.7 38.4 1.0 HG3 B:GLU138 3.7 43.5 1.0 CE B:LYS47 3.9 39.2 1.0 HG3 C:ARG9 3.9 55.6 1.0 HZ2 B:LYS47 3.9 51.8 1.0 OE1 B:GLU49 3.9 34.2 1.0 HG3 B:GLU49 3.9 40.3 1.0 HZ1 B:LYS47 4.1 51.8 1.0 HG2 B:LYS47 4.1 41.2 1.0 NZ B:LYS47 4.2 43.1 1.0 HD2 C:ARG9 4.2 60.0 1.0 CB C:ASP10 4.2 39.8 1.0 HB3 B:GLU138 4.2 39.4 1.0 CB B:GLU138 4.4 32.8 1.0 NE C:ARG9 4.4 52.2 1.0 HD2 B:LYS47 4.4 43.2 1.0 HA C:ASP10 4.5 47.6 1.0 HE2 B:LYS47 4.5 47.0 1.0 HB3 C:ASP10 4.5 47.8 1.0 CD C:ARG9 4.6 50.0 1.0 CD B:LYS47 4.6 36.0 1.0 CG C:ARG9 4.7 46.4 1.0 HB2 C:ASP10 4.8 47.8 1.0 HA B:GLU49 4.8 39.0 1.0 CA C:ASP10 4.8 39.7 1.0 CG B:LYS47 4.9 34.3 1.0 CB B:GLU49 4.9 33.7 1.0 HB2 B:GLU138 4.9 39.4 1.0

Zinc binding site 4 out of 24 in the Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:59.5 occ:1.00 OE2 B:GLU140 2.3 36.8 1.0 HH21 B:ARG82 2.7 42.5 0.5 O B:HOH383 2.7 30.6 1.0 O B:HOH321 2.8 34.9 1.0 HG21 B:VAL87 3.1 37.7 1.0 CD B:GLU140 3.1 32.1 1.0 OE1 B:GLU140 3.2 31.2 1.0 NH2 B:ARG82 3.3 35.4 0.5 HE B:ARG82 3.5 40.2 0.5 HG11 B:VAL87 3.6 42.1 1.0 HH22 B:ARG82 3.8 42.5 0.5 HG13 B:VAL84 3.8 42.0 1.0 CG2 B:VAL87 3.9 31.4 1.0 NE B:ARG82 4.0 33.5 0.5 CZ B:ARG82 4.0 34.9 0.5 HA B:VAL84 4.0 38.6 1.0 HG23 B:VAL87 4.1 37.7 1.0 HB B:VAL87 4.1 39.8 1.0 HG22 B:VAL84 4.2 37.8 1.0 CB B:VAL87 4.4 33.1 1.0 CG1 B:VAL87 4.4 35.1 1.0 CG B:GLU140 4.5 29.4 1.0 O B:HOH344 4.5 33.1 1.0 HG22 B:VAL87 4.6 37.7 1.0 HH B:TYR45 4.7 38.7 1.0 HG2 B:GLU140 4.7 35.4 1.0 CG1 B:VAL84 4.7 35.0 1.0 HG3 B:GLU140 4.8 35.4 1.0 HG3 B:ARG82 4.8 36.0 0.5 HG12 B:VAL87 4.9 42.1 1.0 CA B:VAL84 4.9 32.2 1.0 O B:VAL84 4.9 32.4 1.0

Zinc binding site 5 out of 24 in the Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:102.8 occ:1.00 OE1 B:GLU73 2.1 49.8 1.0 O B:HOH375 2.5 49.0 1.0 O B:HOH351 2.7 56.1 1.0 CD B:GLU73 3.0 49.1 1.0 O B:HOH403 3.2 62.8 1.0 OE2 B:GLU73 3.2 45.7 1.0 HA B:GLU73 3.9 47.8 1.0 HG21 B:THR150 3.9 51.7 1.0 O B:HOH339 4.4 40.2 1.0 CG B:GLU73 4.4 41.1 1.0 HB3 B:GLU73 4.5 47.8 1.0 OE1 B:GLU75 4.5 40.3 1.0 CA B:GLU73 4.7 39.8 1.0 HG22 B:THR150 4.7 51.7 1.0 CB B:GLU73 4.8 39.8 1.0 CG2 B:THR150 4.8 43.0 1.0 HG2 B:GLU73 4.9 49.3 1.0 O B:HOH356 4.9 40.7 1.0 HG3 B:GLU73 5.0 49.3 1.0

Zinc binding site 6 out of 24 in the Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:32.3 occ:1.00 NE2 E:HIS115 2.1 32.4 1.0 NE2 C:HIS115 2.3 31.5 1.0 O C:HOH390 2.4 30.4 1.0 O C:HOH397 2.9 29.4 1.0 CD2 E:HIS115 3.1 32.8 1.0 CE1 E:HIS115 3.1 33.0 1.0 CD2 C:HIS115 3.2 31.6 1.0 HD2 E:HIS115 3.2 39.3 1.0 HD2 C:HIS115 3.3 38.0 1.0 CE1 C:HIS115 3.3 33.2 1.0 HE1 E:HIS115 3.3 39.6 1.0 HE1 C:HIS115 3.5 39.9 1.0 HA C:ARG117 3.7 40.2 1.0 HA E:ARG117 3.7 38.8 1.0 ND1 E:HIS115 4.2 33.5 1.0 CG E:HIS115 4.2 33.2 1.0 O C:LEU116 4.3 32.4 1.0 O E:LEU116 4.3 30.9 1.0 CG C:HIS115 4.4 32.1 1.0 ND1 C:HIS115 4.4 33.1 1.0 H E:SER118 4.4 39.4 1.0 H C:SER118 4.6 44.8 1.0 CA E:ARG117 4.7 32.4 1.0 CA C:ARG117 4.7 33.5 1.0 N E:SER118 4.9 32.8 1.0

Zinc binding site 7 out of 24 in the Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:38.9 occ:1.00 OE2 C:GLU138 1.9 40.3 1.0 OE2 C:GLU49 2.0 36.0 1.0 OD1 B:ASP10 2.0 38.3 1.0 O C:HOH378 2.2 26.3 1.0 HG2 C:GLU138 2.7 41.4 1.0 CG B:ASP10 2.8 33.1 1.0 HG2 C:GLU49 2.8 41.3 1.0 CD C:GLU138 2.9 36.5 1.0 CD C:GLU49 2.9 36.8 1.0 OD2 B:ASP10 2.9 30.4 1.0 CG C:GLU138 3.2 34.5 1.0 CG C:GLU49 3.3 34.4 1.0 HE B:ARG9 3.3 59.0 1.0 HE3 C:LYS47 3.4 44.8 1.0 HG3 C:GLU49 3.5 41.3 1.0 HZ2 C:LYS47 3.6 46.1 1.0 HG3 C:GLU138 3.7 41.4 1.0 HG3 B:ARG9 3.7 45.2 1.0 HD2 B:ARG9 3.8 51.9 1.0 OE1 C:GLU49 3.9 37.2 1.0 OE1 C:GLU138 4.0 37.1 1.0 HZ1 C:LYS47 4.0 46.1 1.0 NE B:ARG9 4.1 49.1 1.0 NZ C:LYS47 4.1 38.5 1.0 CB B:ASP10 4.1 36.5 1.0 CE C:LYS47 4.2 37.3 1.0 CD B:ARG9 4.3 43.2 1.0 HA B:ASP10 4.3 37.8 1.0 HG2 C:LYS47 4.4 44.0 1.0 HB3 B:ASP10 4.4 43.8 1.0 CG B:ARG9 4.4 37.6 1.0 HB3 C:GLU138 4.5 39.0 1.0 CB C:GLU138 4.5 32.5 1.0 HD2 C:LYS47 4.6 42.4 1.0 CB C:GLU49 4.7 36.0 1.0 CA B:ASP10 4.7 31.5 1.0 HA C:GLU49 4.7 39.2 1.0 HB2 B:ASP10 4.8 43.8 1.0 CD C:LYS47 4.8 35.4 1.0 HE2 C:LYS47 4.9 44.8 1.0 HZ3 C:LYS47 4.9 46.1 1.0 HH21 B:ARG9 5.0 68.8 1.0 HG2 B:ARG9 5.0 45.2 1.0 N B:ASP10 5.0 32.2 1.0 N C:GLU49 5.0 31.2 1.0

Zinc binding site 8 out of 24 in the Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn203 b:52.4 occ:1.00 O C:HOH391 2.2 43.9 1.0 OE2 C:GLU140 2.2 40.3 1.0 O C:HOH377 2.5 38.7 1.0 O C:HOH403 2.6 40.9 1.0 O C:HOH385 2.7 34.9 1.0 CD C:GLU140 2.9 36.2 1.0 OE1 C:GLU140 2.9 35.8 1.0 HG21 C:VAL87 3.1 45.5 1.0 HG11 C:VAL87 3.9 47.9 1.0 O C:HOH381 3.9 38.3 1.0 HA C:VAL84 3.9 41.6 1.0 HG13 C:VAL84 3.9 41.0 1.0 CG2 C:VAL87 4.0 37.9 1.0 HG22 C:VAL84 4.1 40.2 1.0 HG23 C:VAL87 4.1 45.5 1.0 HB C:VAL87 4.2 47.6 1.0 CG C:GLU140 4.3 33.7 1.0 CB C:VAL87 4.5 39.7 1.0 HG3 C:GLU140 4.6 40.4 1.0 HG2 C:GLU140 4.6 40.4 1.0 CG1 C:VAL87 4.7 39.9 1.0 O C:HOH369 4.7 34.4 1.0 HG22 C:VAL87 4.7 45.5 1.0 HH C:TYR45 4.7 44.0 1.0 O C:VAL84 4.8 36.0 1.0 CA C:VAL84 4.8 34.7 1.0 CG1 C:VAL84 4.8 34.1 1.0 CG2 C:VAL84 5.0 33.5 1.0

Zinc binding site 9 out of 24 in the Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:98.5 occ:1.00 OE2 D:GLU140 2.6 37.6 1.0 O D:HOH373 2.9 32.5 1.0 HG21 D:VAL87 3.0 44.4 1.0 OE1 D:GLU140 3.1 35.4 1.0 CD D:GLU140 3.1 36.1 1.0 HH21 D:ARG82 3.1 47.7 1.0 O D:HOH337 3.3 39.5 1.0 HG13 D:VAL84 3.5 41.2 1.0 NH2 D:ARG82 3.8 39.7 1.0 HG22 D:VAL84 3.8 40.5 1.0 HE D:ARG82 3.8 45.6 1.0 CG2 D:VAL87 4.0 37.0 1.0 HA D:VAL84 4.0 39.1 1.0 HG23 D:VAL87 4.2 44.4 1.0 HH22 D:ARG82 4.2 47.7 1.0 HG11 D:VAL87 4.2 43.5 1.0 CG1 D:VAL84 4.3 34.4 1.0 NE D:ARG82 4.4 38.0 1.0 HH D:TYR45 4.4 38.1 1.0 CZ D:ARG82 4.4 39.2 1.0 CG D:GLU140 4.5 33.3 1.0 HG11 D:VAL84 4.5 41.2 1.0 HG22 D:VAL87 4.5 44.4 1.0 HG2 D:GLU140 4.5 40.0 1.0 HB D:VAL87 4.6 43.9 1.0 CG2 D:VAL84 4.7 33.8 1.0 CB D:VAL87 4.8 36.6 1.0 CA D:VAL84 4.8 32.6 1.0 CB D:VAL84 4.8 33.5 1.0 O D:VAL84 4.9 33.6 1.0 O D:HOH345 4.9 37.5 1.0 CG1 D:VAL87 4.9 36.2 1.0

Zinc binding site 10 out of 24 in the Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:52.4 occ:1.00 NE2 D:HIS115 1.9 71.3 1.0 OE2 D:GLU123 1.9 35.9 1.0 O D:HOH377 2.5 34.0 1.0 O D:HOH372 2.6 36.2 1.0 CE1 D:HIS115 2.6 56.5 1.0 HE1 D:HIS115 2.8 67.8 1.0 CD2 D:HIS115 2.9 68.4 1.0 CD D:GLU123 3.0 34.6 1.0 HG3 D:GLU123 3.0 42.1 1.0 HD2 D:HIS115 3.3 82.1 1.0 HH22 D:ARG163 3.3 38.0 1.0 CG D:GLU123 3.4 35.1 1.0 HG2 D:GLU123 3.5 42.1 1.0 HE2 D:TYR62 3.5 39.5 1.0 ND1 D:HIS115 3.7 51.3 1.0 CE2 D:TYR62 3.8 32.9 1.0 CG D:HIS115 3.9 54.6 1.0 HD2 D:TYR62 4.0 38.3 1.0 CD2 D:TYR62 4.0 31.9 1.0 NH2 D:ARG163 4.1 31.7 1.0 OE1 D:GLU123 4.1 31.5 1.0 HH21 D:ARG163 4.2 38.0 1.0 CZ D:TYR62 4.5 31.4 1.0 HH D:TYR62 4.6 39.6 1.0 CB D:GLU123 4.8 32.6 1.0 HH12 D:ARG163 4.9 36.2 1.0 HB2 D:GLU123 4.9 39.1 1.0 OH D:TYR62 4.9 33.0 1.0 CG D:TYR62 5.0 31.3 1.0

Y.Bloch, S.N.Savvides. Tobacco Lectin Nictaba in Apo State Including I and Eu Sad Datasets. To Be Published.