Atomistry » Zinc » PDB 6o3r-6ofd » 6obg
Atomistry »
  Zinc »
    PDB 6o3r-6ofd »
      6obg »

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

Go back to Zinc Binding Sites List in 6obg
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

Go back to Zinc Binding Sites List in 6obg
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

Go back to Zinc Binding Sites List in 6obg
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

Go back to Zinc Binding Sites List in 6obg
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

Go back to Zinc Binding Sites List in 6obg
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

Go back to Zinc Binding Sites List in 6obg
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

Go back to Zinc Binding Sites List in 6obg
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

Go back to Zinc Binding Sites List in 6obg
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

Go back to Zinc Binding Sites List in 6obg
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy