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Potassium in PDB 8znt: Catalytic Antibody T99_C220A

Protein crystallography data

The structure of Catalytic Antibody T99_C220A, PDB code: 8znt was solved by J.Kobayashi, H.Yoshida, M.Tsuyuguchi, R.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.11 / 2.61
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 77.085, 85.326, 104.58, 106.77, 91.44, 116.91
R / Rfree (%) 19.5 / 25.4

Other elements in 8znt:

The structure of Catalytic Antibody T99_C220A also contains other interesting chemical elements:

Chlorine (Cl) 13 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Catalytic Antibody T99_C220A (pdb code 8znt). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the Catalytic Antibody T99_C220A, PDB code: 8znt:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Potassium binding site 1 out of 9 in 8znt

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Potassium binding site 1 out of 9 in the Catalytic Antibody T99_C220A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Catalytic Antibody T99_C220A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K310

b:53.3
occ:1.00
 O A:ASN144 2.9 37.5 1.0
O A:ALA118 2.9 42.8 1.0
OG A:SER120 3.0 44.6 1.0
O A:ASN143 3.2 38.6 1.0
N A:SER120 3.7 37.3 1.0
C A:ASN144 3.9 37.9 1.0
CB A:ASN144 3.9 35.5 1.0
C A:ALA118 4.1 34.5 1.0
CB A:SER120 4.1 40.4 1.0
C A:PRO119 4.2 40.2 1.0
C A:ASN143 4.3 38.6 1.0
CA A:PRO119 4.3 41.4 1.0
CA A:ASN144 4.4 25.8 1.0
CA A:SER120 4.4 36.8 1.0
N A:PRO119 4.7 30.7 1.0
N A:ASN144 4.8 26.5 1.0
ND2 A:ASN144 4.9 35.3 1.0
O A:PRO119 4.9 33.0 1.0
CG A:ASN144 5.0 37.3 1.0
N A:PHE145 5.0 31.6 1.0

Potassium binding site 2 out of 9 in 8znt

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Potassium binding site 2 out of 9 in the Catalytic Antibody T99_C220A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Catalytic Antibody T99_C220A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K306

b:65.7
occ:1.00
 O B:ASN144 2.7 43.5 1.0
O B:ALA118 2.9 41.9 1.0
O B:ASN143 3.3 42.0 1.0
O2 B:EDO304 3.4 54.1 1.0
OG B:SER120 3.4 58.3 1.0
CB B:ASN144 3.8 53.7 1.0
C B:ASN144 3.8 43.6 1.0
N B:SER120 3.8 36.6 1.0
C2 B:EDO304 4.1 56.5 1.0
C B:ALA118 4.1 35.5 1.0
CB B:SER120 4.2 53.5 1.0
C B:PRO119 4.3 44.9 1.0
CA B:ASN144 4.3 48.2 1.0
CA B:PRO119 4.3 46.7 1.0
C B:ASN143 4.3 36.0 1.0
CA B:SER120 4.6 45.0 1.0
N B:PRO119 4.7 38.5 1.0
N B:ASN144 4.8 39.2 1.0
N B:PHE145 4.9 35.9 1.0
CG B:ASN144 5.0 46.9 1.0

Potassium binding site 3 out of 9 in 8znt

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Potassium binding site 3 out of 9 in the Catalytic Antibody T99_C220A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Catalytic Antibody T99_C220A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K307

b:99.6
occ:1.00
 N B:VAL152 3.6 50.0 1.0
OE1 B:GLU167 3.8 47.1 1.0
CA B:LYS151 3.8 45.2 1.0
CG B:LYS151 3.9 70.6 1.0
O B:VAL152 4.0 42.9 1.0
O B:ALA150 4.1 55.6 1.0
NZ B:LYS151 4.1 79.0 1.0
C B:LYS151 4.2 43.6 1.0
CB B:LYS151 4.4 49.9 1.0
CD B:GLU167 4.4 58.7 1.0
OE2 B:GLU167 4.4 62.2 1.0
CA B:VAL152 4.7 43.1 1.0
C B:VAL152 4.7 40.9 1.0
N B:LYS151 4.8 38.9 1.0
C B:ALA150 4.8 43.4 1.0
CD B:LYS151 4.9 63.0 1.0

Potassium binding site 4 out of 9 in 8znt

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Potassium binding site 4 out of 9 in the Catalytic Antibody T99_C220A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Catalytic Antibody T99_C220A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K309

b:55.9
occ:1.00
 O C:ASN144 2.8 47.0 1.0
O C:ALA118 2.8 59.1 1.0
OG C:SER120 2.9 51.7 1.0
O C:ASN143 3.2 45.6 1.0
N C:SER120 3.8 39.0 1.0
CB C:ASN144 3.8 40.8 1.0
C C:ASN144 3.9 43.7 1.0
C C:ALA118 4.0 51.3 1.0
CB C:SER120 4.1 45.3 1.0
C C:PRO119 4.2 41.3 1.0
CA C:PRO119 4.3 42.9 1.0
C C:ASN143 4.3 42.0 1.0
CA C:ASN144 4.4 48.3 1.0
CA C:SER120 4.5 40.8 1.0
N C:PRO119 4.7 51.6 1.0
OD1 C:ASN144 4.8 46.7 1.0
N C:ASN144 4.8 42.3 1.0
CG C:ASN144 4.8 40.5 1.0
O C:PRO119 4.9 39.3 1.0
N C:PHE145 5.0 45.5 1.0

Potassium binding site 5 out of 9 in 8znt

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Potassium binding site 5 out of 9 in the Catalytic Antibody T99_C220A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Catalytic Antibody T99_C220A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K309

b:54.6
occ:1.00
 O D:ASN144 2.9 51.5 1.0
O D:ALA118 3.0 42.1 1.0
O D:ASN143 3.2 40.6 1.0
OG D:SER120 3.2 48.7 1.0
O D:HOH416 3.3 40.5 1.0
N D:SER120 3.6 43.7 1.0
CB D:SER120 3.8 43.0 1.0
O2 D:EDO308 3.8 59.2 1.0
CB D:ASN144 3.9 48.3 1.0
C D:ASN144 3.9 43.1 1.0
C2 D:EDO308 4.0 68.2 1.0
C D:PRO119 4.1 38.4 1.0
C D:ALA118 4.2 41.6 1.0
C D:ASN143 4.2 42.0 1.0
CA D:SER120 4.3 44.6 1.0
CA D:ASN144 4.4 41.2 1.0
CA D:PRO119 4.4 39.6 1.0
N D:ASN144 4.8 30.7 1.0
N D:PRO119 4.8 43.1 1.0
OD1 D:ASN144 4.8 44.2 1.0
O D:PRO119 4.9 41.1 1.0
CG D:ASN144 4.9 42.7 1.0
N D:PHE145 5.0 36.1 1.0

Potassium binding site 6 out of 9 in 8znt

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Potassium binding site 6 out of 9 in the Catalytic Antibody T99_C220A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Catalytic Antibody T99_C220A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K310

b:44.6
occ:1.00
 O E:ALA118 2.7 40.9 1.0
O E:ASN143 2.9 40.2 1.0
O E:ASN144 3.0 41.1 1.0
O E:HOH414 3.0 49.4 1.0
OG E:SER120 3.1 41.6 1.0
N E:SER120 3.6 42.6 1.0
C E:ASN144 3.8 37.0 1.0
C E:ALA118 3.9 43.4 1.0
C E:PRO119 3.9 34.6 1.0
CB E:ASN144 3.9 43.4 1.0
C E:ASN143 4.0 42.9 1.0
CB E:SER120 4.0 49.2 1.0
CA E:PRO119 4.0 36.9 1.0
CA E:ASN144 4.3 35.5 1.0
CA E:SER120 4.3 45.4 1.0
N E:PRO119 4.5 38.6 1.0
N E:ASN144 4.6 36.0 1.0
O E:PRO119 4.7 44.3 1.0
ND2 E:ASN144 4.7 46.3 1.0
N E:PHE145 4.9 32.6 1.0
CG E:ASN144 4.9 37.7 1.0

Potassium binding site 7 out of 9 in 8znt

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Potassium binding site 7 out of 9 in the Catalytic Antibody T99_C220A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Catalytic Antibody T99_C220A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K309

b:63.1
occ:1.00
 O F:ASN144 2.8 47.7 1.0
O F:ASN143 3.0 49.2 1.0
O F:ALA118 3.1 47.2 1.0
O F:HOH402 3.5 41.2 1.0
OG F:SER120 3.5 47.4 1.0
N F:SER120 3.7 36.0 1.0
CB F:ASN144 3.7 52.3 1.0
C F:ASN144 3.8 46.7 1.0
CB F:SER120 3.8 39.1 1.0
C F:ASN143 4.1 45.0 1.0
CA F:ASN144 4.2 42.7 1.0
C F:ALA118 4.3 51.3 1.0
C F:PRO119 4.3 38.5 1.0
CA F:SER120 4.4 41.5 1.0
CA F:PRO119 4.5 44.2 1.0
ND2 F:ASN144 4.5 44.8 1.0
N F:ASN144 4.6 54.1 1.0
CG F:ASN144 4.7 53.4 1.0
N F:PHE145 4.9 38.2 1.0
N F:PRO119 4.9 56.0 1.0

Potassium binding site 8 out of 9 in 8znt

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Potassium binding site 8 out of 9 in the Catalytic Antibody T99_C220A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Catalytic Antibody T99_C220A within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K312

b:54.1
occ:1.00
 O G:ALA118 2.7 45.8 1.0
O G:ASN143 2.9 42.8 1.0
O G:ASN144 2.9 49.2 1.0
OG G:SER120 3.2 42.6 1.0
N G:SER120 3.5 47.3 1.0
O G:HOH428 3.5 49.0 1.0
C G:ASN144 3.9 40.5 1.0
C G:ALA118 3.9 38.2 1.0
C G:PRO119 3.9 42.8 1.0
CB G:SER120 3.9 41.9 1.0
CB G:ASN144 4.0 38.9 1.0
CA G:PRO119 4.0 42.8 1.0
C G:ASN143 4.0 44.5 1.0
CA G:SER120 4.3 40.0 1.0
CA G:ASN144 4.4 38.3 1.0
N G:PRO119 4.5 47.8 1.0
ND2 G:ASN144 4.6 46.4 1.0
N G:ASN144 4.7 41.9 1.0
O G:PRO119 4.7 39.2 1.0
CG G:ASN144 4.9 34.5 1.0
N G:PHE145 4.9 30.1 1.0
O G:HOH409 5.0 45.2 1.0

Potassium binding site 9 out of 9 in 8znt

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Potassium binding site 9 out of 9 in the Catalytic Antibody T99_C220A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Catalytic Antibody T99_C220A within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K308

b:66.0
occ:1.00
 O H:ALA118 2.8 49.9 1.0
O H:ASN144 2.8 45.8 1.0
O H:HOH413 3.0 41.2 1.0
OG H:SER120 3.1 50.1 1.0
O H:ASN143 3.2 53.2 1.0
N H:SER120 3.6 43.9 1.0
C H:ASN144 3.9 43.8 1.0
C H:ALA118 4.0 51.4 1.0
CB H:SER120 4.0 41.8 1.0
CB H:ASN144 4.1 44.2 1.0
C H:PRO119 4.2 40.8 1.0
CA H:PRO119 4.3 44.4 1.0
C H:ASN143 4.4 45.7 1.0
CA H:SER120 4.4 43.1 1.0
CA H:ASN144 4.5 40.8 1.0
N H:PRO119 4.7 48.1 1.0
N H:ASN144 4.9 53.4 1.0
N H:PHE145 4.9 42.5 1.0

Reference:

T.Uda, R.Kato, Y.Shigeta, S.Hirota, J.Kobayashi, H.Yoshida, M.Tsuyuguchi, K.Hengphasatporn, M.Tsujita, H.Taguchi, E.Hifumi. Structural and Biochemical Differences Between Non-Catalytic and Catalytic Antibodies. Mabs V. 17 03978 2025.
ISSN: ESSN 1942-0870
PubMed: 40356286
DOI: 10.1080/19420862.2025.2503978
Page generated: Sat Aug 9 18:27:06 2025

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