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Zinc in PDB 7kdm: Ricin Bound to Vhh Antibody V5G6

Enzymatic activity of Ricin Bound to Vhh Antibody V5G6

All present enzymatic activity of Ricin Bound to Vhh Antibody V5G6:
3.2.2.22;

Protein crystallography data

The structure of Ricin Bound to Vhh Antibody V5G6, PDB code: 7kdm 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) 19.65 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.345, 77.438, 101.577, 89.97, 90.18, 89.98
R / Rfree (%) 18.7 / 23.8

Other elements in 7kdm:

The structure of Ricin Bound to Vhh Antibody V5G6 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Ricin Bound to Vhh Antibody V5G6 (pdb code 7kdm). 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 Bound to Vhh Antibody V5G6, PDB code: 7kdm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 7kdm

Go back to Zinc Binding Sites List in 7kdm
Zinc binding site 1 out of 9 in the Ricin Bound to Vhh Antibody V5G6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ricin Bound to Vhh Antibody V5G6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:55.8
occ:1.00
 OD1 B:ASP94 2.1 63.6 1.0
CD2 A:HIS40 2.3 36.5 1.0
O B:HOH514 2.5 35.7 1.0
OD2 B:ASP94 2.6 58.2 1.0
CG B:ASP94 2.6 53.6 1.0
CG A:HIS40 3.2 35.2 1.0
NE2 A:HIS40 3.2 34.7 1.0
O B:HOH464 3.4 37.0 1.0
O B:HOH534 3.5 37.3 1.0
CB A:HIS40 3.7 32.9 1.0
CA A:HIS40 4.0 32.4 1.0
CB B:ASP94 4.1 41.2 1.0
CE1 A:HIS40 4.2 34.5 1.0
ND1 A:HIS40 4.2 36.0 1.0
N B:ASP94 4.4 22.2 1.0
C A:GLN223 4.4 36.4 1.0
N A:HIS40 4.5 32.3 1.0
N A:GLY224 4.6 32.0 1.0
CA A:GLN223 4.6 40.1 1.0
CA B:ASP94 4.6 31.6 1.0
O A:GLN223 4.8 35.2 1.0
O B:HOH419 4.8 37.6 1.0
O B:ILE92 4.8 26.7 1.0

Zinc binding site 2 out of 9 in 7kdm

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Zinc binding site 2 out of 9 in the Ricin Bound to Vhh Antibody V5G6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ricin Bound to Vhh Antibody V5G6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:43.8
occ:1.00
 O A:HOH543 2.0 41.8 1.0
O A:HOH436 2.2 39.2 1.0
O A:HOH418 2.2 28.6 1.0
O A:HOH506 2.4 35.5 1.0
O A:HOH549 3.1 42.2 1.0
O A:HOH545 3.4 40.0 1.0
NH2 A:ARG134 3.7 28.9 1.0
O A:HOH528 3.9 48.8 1.0
OE2 A:GLU135 3.9 38.4 1.0
OE1 A:GLU135 4.1 32.8 1.0
OE2 A:GLU127 4.1 25.8 1.0
OE1 A:GLU127 4.2 30.0 1.0
O A:HOH536 4.4 50.9 1.0
CD A:GLU135 4.5 35.8 1.0
CD2 A:LEU133 4.6 28.0 1.0
CD A:GLU127 4.6 25.4 1.0
CZ A:ARG134 4.7 24.0 1.0
O A:HOH514 4.8 46.9 1.0
CG2 A:ILE205 4.8 30.8 1.0
ND2 A:ASN209 4.9 31.3 1.0
NE A:ARG134 5.0 20.6 1.0

Zinc binding site 3 out of 9 in 7kdm

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Zinc binding site 3 out of 9 in the Ricin Bound to Vhh Antibody V5G6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ricin Bound to Vhh Antibody V5G6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:99.2
occ:1.00
 CE1 A:HIS94 2.4 56.1 1.0
O A:HOH422 2.6 52.7 1.0
NE2 A:HIS94 2.6 56.6 1.0
ND1 A:HIS94 3.7 53.0 1.0
CD2 A:HIS94 4.0 54.2 1.0
CG A:HIS94 4.5 50.3 1.0

Zinc binding site 4 out of 9 in 7kdm

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Zinc binding site 4 out of 9 in the Ricin Bound to Vhh Antibody V5G6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ricin Bound to Vhh Antibody V5G6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:69.9
occ:1.00
 ND1 B:HIS29 2.5 63.8 1.0
CE1 B:HIS29 3.3 67.1 1.0
CG B:HIS29 3.5 58.0 1.0
CB B:HIS29 3.8 54.0 1.0
NE2 B:HIS29 4.5 66.6 1.0
CD2 B:HIS29 4.6 62.3 1.0
CB B:ARG27 5.0 50.9 1.0

Zinc binding site 5 out of 9 in 7kdm

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Zinc binding site 5 out of 9 in the Ricin Bound to Vhh Antibody V5G6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Ricin Bound to Vhh Antibody V5G6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:32.6
occ:1.00
 NE2 D:HIS65 2.2 38.8 1.0
O D:HOH523 2.5 19.0 1.0
CD2 D:HIS65 3.1 37.2 1.0
CE1 D:HIS65 3.2 35.9 1.0
O D:HOH441 3.3 22.7 1.0
N D:GLY15 3.8 22.9 1.0
ND1 D:HIS65 4.2 35.4 1.0
CG D:HIS65 4.3 36.0 1.0
CA D:GLY15 4.3 23.6 1.0
C D:ALA14 4.6 25.7 1.0
CA D:ALA14 4.7 29.6 1.0

Zinc binding site 6 out of 9 in 7kdm

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Zinc binding site 6 out of 9 in the Ricin Bound to Vhh Antibody V5G6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Ricin Bound to Vhh Antibody V5G6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:29.9
occ:1.00
 OE1 D:GLU102 2.0 33.9 1.0
CE1 D:HIS106 2.1 39.4 1.0
NE2 D:HIS106 2.8 38.6 1.0
CD D:GLU102 2.9 37.1 1.0
OE2 D:GLU102 3.1 33.8 1.0
ND1 D:HIS106 3.3 35.6 1.0
CD2 D:HIS106 4.0 36.3 1.0
O D:HOH454 4.1 36.1 1.0
CG D:GLU102 4.2 36.0 1.0
CG D:HIS106 4.3 33.9 1.0
OG1 D:THR105 4.4 28.0 1.0
O D:GLU102 4.5 28.1 1.0

Zinc binding site 7 out of 9 in 7kdm

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Zinc binding site 7 out of 9 in the Ricin Bound to Vhh Antibody V5G6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Ricin Bound to Vhh Antibody V5G6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn303

b:45.8
occ:1.00
 O D:HOH531 2.1 41.0 1.0
O D:HOH411 2.1 42.9 1.0
O D:HOH425 2.2 33.2 1.0
O D:HOH420 2.3 29.3 1.0
O D:HOH514 2.4 41.7 1.0
O D:HOH530 3.5 45.3 1.0
NH2 D:ARG134 3.7 22.9 1.0
OE1 D:GLU127 4.0 25.3 1.0
O D:HOH516 4.1 45.6 1.0
OE2 D:GLU135 4.2 30.8 1.0
OE2 D:GLU127 4.3 19.3 1.0
OE1 D:GLU135 4.3 29.0 1.0
CD D:GLU127 4.6 23.7 1.0
CD2 D:LEU133 4.6 26.0 1.0
CD D:GLU135 4.7 28.1 1.0
CZ D:ARG134 4.7 20.8 1.0
O D:HOH446 4.9 39.9 1.0
CG2 D:ILE205 5.0 34.5 1.0

Zinc binding site 8 out of 9 in 7kdm

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Zinc binding site 8 out of 9 in the Ricin Bound to Vhh Antibody V5G6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Ricin Bound to Vhh Antibody V5G6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn304

b:97.0
occ:1.00
 CE1 D:HIS94 2.5 61.5 1.0
O D:HOH447 2.5 52.9 1.0
NE2 D:HIS94 2.7 61.1 1.0
O D:HOH517 2.8 47.3 1.0
ND1 D:HIS94 3.7 57.0 1.0
CD2 D:HIS94 4.1 57.1 1.0
CG D:HIS94 4.6 52.9 1.0
O D:HOH515 4.6 52.4 1.0

Zinc binding site 9 out of 9 in 7kdm

Go back to Zinc Binding Sites List in 7kdm
Zinc binding site 9 out of 9 in the Ricin Bound to Vhh Antibody V5G6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Ricin Bound to Vhh Antibody V5G6 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:76.2
occ:1.00
 ND1 E:HIS29 2.5 63.9 1.0
CE1 E:HIS29 3.5 65.8 1.0
CG E:HIS29 3.5 58.8 1.0
CB E:HIS29 3.8 49.6 1.0
NE2 E:HIS29 4.6 65.3 1.0
CD2 E:HIS29 4.7 62.2 1.0

Reference:

M.J.Rudolph, A.Y.Poon, S.Kavaliauskiene, A.G.Myrann, C.Reynolds-Peterson, S.A.Davis, K.Sandvig, D.J.Vance, N.J.Mantis. Structural Analysis of Toxin-Neutralizing, Single-Domain Antibodies That Bridge Ricin'S A-B Subunit Interface. J.Mol.Biol. V. 433 67086 2021.
ISSN: ESSN 1089-8638
PubMed: 34089718
DOI: 10.1016/J.JMB.2021.167086
Page generated: Fri Aug 22 01:32:37 2025

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