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
Go back to
Zinc Binding Sites List in 1kn4
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
Go back to
Zinc Binding Sites List in 1kn4
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
Go back to
Zinc Binding Sites List in 1kn4
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
Go back to
Zinc Binding Sites List in 1kn4
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
Go back to
Zinc Binding Sites List in 1kn4
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
Go back to
Zinc Binding Sites List in 1kn4
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: Sun Oct 13 04:32:29 2024
|