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Zinc in PDB 1kn4: Catalytic Antibody D2.3 Complex

Protein crystallography data

The structure of Catalytic Antibody D2.3 Complex, PDB code: 1kn4 was solved by B.Gigant, M.Knossow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.251, 78.251, 158.805, 90.00, 90.00, 120.00
R / Rfree (%) 21.3 / 24.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Catalytic Antibody D2.3 Complex (pdb code 1kn4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Catalytic Antibody D2.3 Complex, PDB code: 1kn4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 1kn4

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Zinc binding site 1 out of 7 in the Catalytic Antibody D2.3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Antibody D2.3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn553

b:28.5
occ:1.00
O H:HOH251 1.5 34.1 1.0
OD1 H:ASP100C 2.0 26.6 1.0
NE2 L:HIS49 2.2 22.0 1.0
CG H:ASP100C 2.8 28.4 1.0
OD2 H:ASP100C 2.9 29.7 1.0
NZ L:LYS53 3.0 52.7 1.0
CE1 L:HIS49 3.2 19.0 1.0
CD2 L:HIS49 3.2 19.1 1.0
CD L:LYS53 3.3 40.2 1.0
CE L:LYS53 3.4 48.1 1.0
ND1 L:HIS49 4.3 20.1 1.0
CB H:ASP100C 4.3 24.6 1.0
CB L:LYS53 4.3 26.7 1.0
N H:TYR100D 4.3 22.9 1.0
CG L:HIS49 4.3 18.2 1.0
CG L:LYS53 4.5 32.0 1.0
O H:TYR100D 4.6 29.1 1.0
CA H:ASP100C 4.8 24.6 1.0
CD1 L:LEU50 4.8 21.5 1.0
CD1 H:TYR100D 5.0 17.7 1.0

Zinc binding site 2 out of 7 in 1kn4

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Zinc binding site 2 out of 7 in the Catalytic Antibody D2.3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Antibody D2.3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn554

b:26.5
occ:1.00
O L:HOH561 1.6 32.5 1.0
O L:HOH573 1.7 28.2 1.0
ND1 L:HIS93 2.3 20.7 1.0
CG L:HIS93 3.2 21.8 1.0
CE1 L:HIS93 3.2 22.2 1.0
ZN L:ZN559 3.4 35.1 1.0
CB L:HIS93 3.4 18.8 1.0
O L:HOH625 3.5 37.9 1.0
O L:HOH593 3.6 44.5 1.0
O L:HOH612 3.7 40.2 1.0
CA L:HIS93 3.9 19.0 1.0
NE2 L:HIS93 4.3 24.0 1.0
CD2 L:HIS93 4.3 22.3 1.0
O L:HOH580 4.6 33.6 1.0
O L:THR92 4.7 18.8 1.0
N L:PHE94 4.8 22.9 1.0
C L:HIS93 4.9 20.8 1.0
N L:HIS93 4.9 17.2 1.0

Zinc binding site 3 out of 7 in 1kn4

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Zinc binding site 3 out of 7 in the Catalytic Antibody D2.3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Catalytic Antibody D2.3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn555

b:34.5
occ:1.00
O L:HOH604 1.6 46.8 1.0
O L:HOH605 1.8 36.5 1.0
OD1 L:ASP151 2.1 27.3 1.0
ND1 L:HIS189 2.4 30.5 1.0
CG L:ASP151 3.1 22.9 1.0
CE1 L:HIS189 3.2 30.9 1.0
CG L:HIS189 3.2 31.8 1.0
ZN L:ZN557 3.3 36.4 1.0
CB L:ASP151 3.4 23.1 1.0
CB L:HIS189 3.5 28.8 1.0
O L:HOH607 3.5 50.7 1.0
ZN L:ZN558 3.6 39.6 1.0
CA L:HIS189 3.7 30.0 1.0
O L:HOH615 3.8 49.8 1.0
O L:HOH606 3.9 42.7 1.0
O L:HOH644 3.9 42.4 1.0
OD2 L:ASP151 4.2 25.5 1.0
NE2 L:HIS189 4.3 34.1 1.0
CD2 L:HIS189 4.3 33.7 1.0
O L:ARG188 4.3 32.1 1.0
CG2 L:ILE150 4.3 25.6 1.0
O L:HOH624 4.5 34.3 1.0
N L:HIS189 4.6 30.5 1.0
N L:ASN190 4.7 33.6 1.0
O L:ILE150 4.8 22.9 1.0
CA L:ASP151 4.8 24.2 1.0
C L:HIS189 4.8 32.7 1.0
C L:ARG188 4.8 32.0 1.0
ZN L:ZN556 5.0 37.3 1.0
C L:ILE150 5.0 24.7 1.0
N L:ASP151 5.0 23.4 1.0

Zinc binding site 4 out of 7 in 1kn4

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Zinc binding site 4 out of 7 in the Catalytic Antibody D2.3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Catalytic Antibody D2.3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn556

b:37.3
occ:1.00
O L:HOH606 1.8 42.7 1.0
O L:HOH624 1.8 34.3 1.0
O L:HOH560 2.1 32.5 1.0
ZN L:ZN558 3.3 39.6 1.0
ZN L:ZN557 3.5 36.4 1.0
O L:HOH615 3.8 49.8 1.0
O L:HOH644 3.9 42.4 1.0
O L:HOH604 4.3 46.8 1.0
O L:HOH605 4.3 36.5 1.0
O L:HOH639 4.9 48.8 1.0
ZN L:ZN555 5.0 34.5 1.0

Zinc binding site 5 out of 7 in 1kn4

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Zinc binding site 5 out of 7 in the Catalytic Antibody D2.3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Catalytic Antibody D2.3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn557

b:36.4
occ:1.00
O L:HOH605 1.7 36.5 1.0
O L:HOH606 1.7 42.7 1.0
O L:HOH644 2.3 42.4 1.0
ZN L:ZN555 3.3 34.5 1.0
O L:HOH607 3.5 50.7 1.0
ZN L:ZN556 3.5 37.3 1.0
O L:HOH604 3.9 46.8 1.0
O L:HOH560 4.0 32.5 1.0
O L:HOH624 4.4 34.3 1.0
CB L:ASP151 4.5 23.1 1.0
ZN L:ZN558 4.7 39.6 1.0
OD1 L:ASP151 4.8 27.3 1.0
OG L:SER153 4.9 36.8 1.0
ND1 L:HIS189 5.0 30.5 1.0
O L:HOH615 5.0 49.8 1.0

Zinc binding site 6 out of 7 in 1kn4

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Zinc binding site 6 out of 7 in the Catalytic Antibody D2.3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Catalytic Antibody D2.3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn558

b:39.6
occ:1.00
O L:HOH624 1.7 34.3 1.0
O L:HOH615 1.9 49.8 1.0
O L:HOH604 2.0 46.8 1.0
ZN L:ZN556 3.3 37.3 1.0
ZN L:ZN555 3.6 34.5 1.0
O L:HOH606 3.7 42.7 1.0
O L:ARG188 3.9 32.1 1.0
OD1 L:ASP151 4.1 27.3 1.0
O L:HOH605 4.3 36.5 1.0
O L:HOH644 4.6 42.4 1.0
ZN L:ZN557 4.7 36.4 1.0
ND2 L:ASN190 4.8 48.2 1.0
CG L:ASP151 4.8 22.9 1.0
O L:HOH560 4.9 32.5 1.0

Zinc binding site 7 out of 7 in 1kn4

Go back to Zinc Binding Sites List in 1kn4
Zinc binding site 7 out of 7 in the Catalytic Antibody D2.3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Catalytic Antibody D2.3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn559

b:35.1
occ:1.00
O L:HOH625 1.7 37.9 1.0
O L:HOH573 2.1 28.2 1.0
ZN L:ZN554 3.4 26.5 1.0
O L:HOH612 3.7 40.2 1.0
O L:HOH629 4.1 44.4 1.0
O L:HOH561 4.1 32.5 1.0
O L:HOH611 4.5 47.7 1.0
O L:HOH593 4.5 44.5 1.0
ND1 L:HIS93 4.8 20.7 1.0

Reference:

L.J.D'souza, B.Gigant, M.Knossow, B.S.Green. Remarkable Remote Chiral Recognition in A Reaction Mediated By A Catalytic Antibody. J.Am.Chem.Soc. V. 124 2114 2002.
ISSN: ISSN 0002-7863
PubMed: 11878955
DOI: 10.1021/JA0170504
Page generated: Wed Dec 16 02:55:22 2020

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