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Zinc in PDB 6obg: Ricin A Chain Bound to Vhh Antibody V8E6

Enzymatic activity of Ricin A Chain Bound to Vhh Antibody V8E6

All present enzymatic activity of Ricin A Chain Bound to Vhh Antibody V8E6:
3.2.2.22;

Protein crystallography data

The structure of Ricin A Chain Bound to Vhh Antibody V8E6, PDB code: 6obg was solved by M.J.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.74 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.795, 77.885, 92.597, 90.00, 98.95, 90.00
R / Rfree (%) 18.9 / 21.8

Other elements in 6obg:

The structure of Ricin A Chain Bound to Vhh Antibody V8E6 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Ricin A Chain Bound to Vhh Antibody V8E6 (pdb code 6obg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Ricin A Chain Bound to Vhh Antibody V8E6, PDB code: 6obg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 6obg

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Zinc binding site 1 out of 9 in the Ricin A Chain Bound to Vhh Antibody V8E6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ricin A Chain Bound to Vhh Antibody V8E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:30.4
occ:0.80
 NE2 A:HIS65 2.0 51.6 1.0
CE1 A:HIS65 2.8 43.8 1.0
O A:HOH481 3.1 46.9 1.0
CD2 A:HIS65 3.1 46.5 1.0
ND1 A:HIS65 4.0 42.5 1.0
N A:GLY15 4.0 36.4 1.0
CG A:HIS65 4.1 45.4 1.0
CA A:GLY15 4.7 40.5 1.0
C A:ALA14 4.7 34.6 1.0
CA A:ALA14 4.8 44.1 1.0

Zinc binding site 2 out of 9 in 6obg

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Zinc binding site 2 out of 9 in the Ricin A Chain Bound to Vhh Antibody V8E6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ricin A Chain Bound to Vhh Antibody V8E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:48.3
occ:0.66
 O A:HOH507 2.0 49.2 1.0
O A:HOH525 2.0 56.5 1.0
O A:HOH423 2.1 52.3 1.0
O A:HOH533 2.2 58.2 1.0
NE2 A:HIS94 2.2 66.1 1.0
O A:HOH458 2.2 50.2 1.0
O A:HOH542 2.7 60.0 1.0
CD2 A:HIS94 3.0 55.6 1.0
CE1 A:HIS94 3.3 65.2 1.0
CG A:HIS94 4.2 55.0 1.0
ND1 A:HIS94 4.3 53.6 1.0
O A:PRO95 4.4 54.6 1.0

Zinc binding site 3 out of 9 in 6obg

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Zinc binding site 3 out of 9 in the Ricin A Chain Bound to Vhh Antibody V8E6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ricin A Chain Bound to Vhh Antibody V8E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:68.6
occ:0.74
 OE1 A:GLU67 2.2 75.7 1.0
O A:HOH536 2.4 70.8 1.0
OE2 A:GLU67 2.4 81.5 1.0
CD A:GLU67 2.6 75.1 1.0
CG A:GLU67 3.9 67.0 1.0

Zinc binding site 4 out of 9 in 6obg

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Zinc binding site 4 out of 9 in the Ricin A Chain Bound to Vhh Antibody V8E6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ricin A Chain Bound to Vhh Antibody V8E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:35.8
occ:0.59
 O A:HOH451 1.9 45.5 1.0
ND1 A:HIS40 2.1 69.0 1.0
CE1 A:HIS40 3.0 62.6 1.0
CG A:HIS40 3.1 56.7 1.0
CB A:HIS40 3.5 44.3 1.0
CA A:HIS40 3.6 46.3 1.0
O A:HOH492 4.0 41.8 1.0
NE2 A:HIS40 4.1 58.6 1.0
CD2 A:HIS40 4.2 63.6 1.0
N A:HIS40 4.2 40.1 1.0
O A:HOH405 4.5 51.0 1.0
C A:HIS40 4.8 38.8 1.0

Zinc binding site 5 out of 9 in 6obg

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Zinc binding site 5 out of 9 in the Ricin A Chain Bound to Vhh Antibody V8E6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Ricin A Chain Bound to Vhh Antibody V8E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:49.5
occ:0.93
 O B:HOH485 2.1 56.1 1.0
ND1 B:HIS40 2.2 72.1 1.0
O B:HOH481 2.2 65.5 1.0
CE1 B:HIS40 3.0 59.1 1.0
CG B:HIS40 3.1 56.2 1.0
CB B:HIS40 3.5 42.5 1.0
CA B:HIS40 3.8 49.8 1.0
NE2 B:HIS40 4.1 57.3 1.0
CD2 B:HIS40 4.2 53.6 1.0
N B:HIS40 4.6 39.8 1.0
O B:HOH403 4.6 54.9 1.0
C B:HIS40 4.9 49.7 1.0

Zinc binding site 6 out of 9 in 6obg

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Zinc binding site 6 out of 9 in the Ricin A Chain Bound to Vhh Antibody V8E6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Ricin A Chain Bound to Vhh Antibody V8E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:50.1
occ:0.91
 NE2 B:HIS65 2.1 74.1 1.0
CE1 B:HIS65 2.7 66.7 1.0
O B:HOH451 3.0 59.4 1.0
CD2 B:HIS65 3.3 67.6 1.0
N B:GLY15 3.8 58.8 1.0
ND1 B:HIS65 4.0 63.3 1.0
CG B:HIS65 4.2 69.4 1.0
CA B:GLY15 4.5 56.0 1.0
CA B:ALA14 4.6 62.2 1.0
C B:ALA14 4.6 61.9 1.0
O B:THR13 4.9 55.5 1.0

Zinc binding site 7 out of 9 in 6obg

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Zinc binding site 7 out of 9 in the Ricin A Chain Bound to Vhh Antibody V8E6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Ricin A Chain Bound to Vhh Antibody V8E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:71.5
occ:1.00
 OD1 B:ASP244 2.3 80.3 1.0
OD2 B:ASP244 2.4 81.4 1.0
O B:HOH418 2.5 65.9 1.0
OG B:SER246 2.6 71.0 1.0
CG B:ASP244 2.7 76.8 1.0
CB B:SER246 3.4 49.6 1.0
N B:SER246 4.1 44.7 1.0
CB B:ASP244 4.2 69.5 1.0
CA B:SER246 4.4 43.5 1.0
O B:GLY224 4.6 58.3 1.0
N B:VAL245 4.8 50.6 1.0
CA B:GLY224 5.0 54.9 1.0
CA B:ASP244 5.0 66.3 1.0

Zinc binding site 8 out of 9 in 6obg

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Zinc binding site 8 out of 9 in the Ricin A Chain Bound to Vhh Antibody V8E6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Ricin A Chain Bound to Vhh Antibody V8E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:50.0
occ:0.70
 ND1 C:HIS102 1.9 58.2 1.0
OE2 C:GLU106 1.9 58.1 1.0
O C:HOH326 2.1 43.6 1.0
CE1 C:HIS102 2.6 65.6 1.0
CG C:HIS102 2.8 61.3 1.0
CD C:GLU106 2.8 46.9 1.0
O C:HOH304 2.9 59.0 1.0
OE1 C:GLU106 3.1 49.8 1.0
CB C:HIS102 3.5 46.6 1.0
NE2 C:HIS102 3.6 63.4 1.0
CD2 C:HIS102 3.7 58.8 1.0
O C:HOH325 4.2 45.8 1.0
CG C:GLU106 4.2 43.6 1.0
ND2 A:ASN78 4.3 44.6 1.0
OH C:TYR107 4.6 64.1 1.0
CA C:HIS102 4.9 40.5 1.0
CE1 C:TYR103 4.9 37.4 1.0

Zinc binding site 9 out of 9 in 6obg

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Zinc binding site 9 out of 9 in the Ricin A Chain Bound to Vhh Antibody V8E6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Ricin A Chain Bound to Vhh Antibody V8E6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:55.3
occ:0.98
 OE2 D:GLU106 2.0 70.3 1.0
CD2 D:HIS102 2.1 77.2 1.0
O D:HOH321 2.3 55.4 1.0
O D:HOH329 2.3 60.1 1.0
CD D:GLU106 2.7 66.4 1.0
OE1 D:GLU106 2.8 67.4 1.0
CG D:HIS102 3.0 65.3 1.0
NE2 D:HIS102 3.0 74.0 1.0
CB D:HIS102 3.5 54.1 1.0
ND1 D:HIS102 4.0 74.1 1.0
CE1 D:HIS102 4.0 75.5 1.0
CG D:GLU106 4.2 49.3 1.0
ND2 B:ASN78 4.2 38.8 1.0
OD2 B:ASP96 4.5 89.7 1.0
OH D:TYR107 4.6 63.5 1.0
O D:HOH308 4.6 48.5 1.0
CE1 D:TYR103 4.7 52.7 1.0
CA D:HIS102 4.9 39.1 1.0

Reference:

M.J.Rudolph, M.J.Rudolph. N/A N/A.
Page generated: Tue Oct 29 04:13:16 2024

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