Zinc in PDB 3ncj: Crystal Structure of FAB15 MUT8
Protein crystallography data
The structure of Crystal Structure of FAB15 MUT8, PDB code: 3ncj
was solved by
J.Luo,
Y.Feng,
G.L.Gilliland,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.18 /
1.60
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.550,
74.700,
65.390,
90.00,
104.23,
90.00
|
R / Rfree (%)
|
20 /
22.5
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of FAB15 MUT8
(pdb code 3ncj). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of FAB15 MUT8, PDB code: 3ncj:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 3ncj
Go back to
Zinc Binding Sites List in 3ncj
Zinc binding site 1 out
of 4 in the Crystal Structure of FAB15 MUT8
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of FAB15 MUT8 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn215
b:14.9
occ:0.82
|
OD2
|
L:ASP151
|
1.9
|
14.3
|
1.0
|
OXT
|
L:ACT217
|
1.9
|
17.6
|
1.0
|
ND1
|
L:HIS189
|
2.1
|
15.4
|
1.0
|
C
|
L:ACT217
|
2.8
|
15.6
|
1.0
|
O
|
L:ACT217
|
2.8
|
24.1
|
1.0
|
CG
|
L:ASP151
|
2.9
|
16.7
|
1.0
|
CE1
|
L:HIS189
|
3.0
|
19.6
|
1.0
|
CG
|
L:HIS189
|
3.2
|
13.9
|
1.0
|
CB
|
L:ASP151
|
3.5
|
13.2
|
1.0
|
CB
|
L:HIS189
|
3.6
|
13.8
|
1.0
|
CA
|
L:HIS189
|
3.8
|
12.0
|
1.0
|
OD1
|
L:ASP151
|
4.0
|
14.8
|
1.0
|
NE2
|
L:HIS189
|
4.1
|
20.5
|
1.0
|
O
|
L:LYS188
|
4.2
|
17.9
|
1.0
|
CH3
|
L:ACT217
|
4.2
|
27.2
|
1.0
|
CD2
|
L:HIS189
|
4.3
|
14.1
|
1.0
|
N
|
L:HIS189
|
4.4
|
13.9
|
1.0
|
C
|
L:LYS188
|
4.6
|
19.4
|
1.0
|
CA
|
L:ASP151
|
4.9
|
13.6
|
1.0
|
C
|
L:HIS189
|
4.9
|
14.8
|
1.0
|
N
|
L:LYS190
|
5.0
|
13.5
|
1.0
|
|
Zinc binding site 2 out
of 4 in 3ncj
Go back to
Zinc Binding Sites List in 3ncj
Zinc binding site 2 out
of 4 in the Crystal Structure of FAB15 MUT8
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of FAB15 MUT8 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn216
b:20.3
occ:0.40
|
O
|
L:HOH330
|
2.2
|
20.0
|
1.0
|
OD1
|
L:ASN137
|
2.2
|
33.5
|
1.0
|
OD1
|
L:ASN138
|
2.2
|
24.6
|
1.0
|
O
|
H:HOH245
|
2.3
|
26.2
|
1.0
|
NE2
|
H:HIS164
|
2.3
|
25.5
|
1.0
|
O
|
L:HOH380
|
2.6
|
48.8
|
1.0
|
CD2
|
H:HIS164
|
2.8
|
20.9
|
1.0
|
CG
|
L:ASN137
|
2.9
|
24.2
|
1.0
|
ND2
|
L:ASN137
|
3.1
|
28.6
|
1.0
|
CG
|
L:ASN138
|
3.2
|
29.7
|
1.0
|
CE1
|
H:HIS164
|
3.5
|
24.8
|
1.0
|
ND2
|
L:ASN138
|
3.7
|
38.8
|
1.0
|
CG
|
H:HIS164
|
4.1
|
18.1
|
1.0
|
OG
|
L:SER174
|
4.1
|
13.0
|
1.0
|
O
|
L:HOH400
|
4.3
|
39.4
|
1.0
|
CB
|
L:ASN137
|
4.3
|
16.5
|
1.0
|
CB
|
L:ASN138
|
4.3
|
22.2
|
1.0
|
OG1
|
H:THR183
|
4.4
|
31.7
|
1.0
|
O
|
H:GLY162
|
4.4
|
20.9
|
1.0
|
ND1
|
H:HIS164
|
4.4
|
21.2
|
1.0
|
O
|
H:HOH258
|
4.4
|
48.7
|
1.0
|
N
|
L:ASN138
|
4.5
|
14.1
|
1.0
|
CA
|
L:ASN137
|
4.8
|
13.0
|
1.0
|
CG2
|
H:THR183
|
4.8
|
33.2
|
1.0
|
O
|
L:HOH246
|
4.9
|
16.0
|
1.0
|
C
|
L:ASN137
|
4.9
|
15.8
|
1.0
|
CA
|
L:ASN138
|
4.9
|
17.0
|
1.0
|
|
Zinc binding site 3 out
of 4 in 3ncj
Go back to
Zinc Binding Sites List in 3ncj
Zinc binding site 3 out
of 4 in the Crystal Structure of FAB15 MUT8
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of FAB15 MUT8 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn218
b:18.5
occ:0.77
|
O
|
L:CYS214
|
1.9
|
19.8
|
1.0
|
O
|
H:ACT220
|
2.0
|
25.8
|
1.0
|
NE2
|
H:HIS213
|
2.0
|
18.5
|
1.0
|
NE2
|
H:HIS217
|
2.1
|
25.5
|
1.0
|
OXT
|
H:ACT220
|
2.6
|
25.7
|
1.0
|
C
|
H:ACT220
|
2.7
|
27.2
|
1.0
|
C
|
L:CYS214
|
2.7
|
20.7
|
1.0
|
OXT
|
L:CYS214
|
2.9
|
18.8
|
1.0
|
CD2
|
H:HIS213
|
3.0
|
19.2
|
1.0
|
CE1
|
H:HIS213
|
3.0
|
18.7
|
1.0
|
CE1
|
H:HIS217
|
3.1
|
25.0
|
1.0
|
CD2
|
H:HIS217
|
3.2
|
23.9
|
1.0
|
O
|
H:HIS214
|
3.4
|
24.5
|
1.0
|
ND1
|
H:HIS213
|
4.1
|
20.3
|
1.0
|
CG
|
H:HIS213
|
4.1
|
19.4
|
1.0
|
CH3
|
H:ACT220
|
4.2
|
30.2
|
1.0
|
CA
|
L:CYS214
|
4.2
|
21.4
|
1.0
|
ND1
|
H:HIS217
|
4.2
|
27.7
|
1.0
|
OG
|
H:SER128
|
4.2
|
28.3
|
1.0
|
O
|
L:HOH447
|
4.2
|
29.0
|
1.0
|
CG
|
H:HIS217
|
4.3
|
27.7
|
1.0
|
C
|
H:HIS214
|
4.6
|
24.1
|
1.0
|
CB
|
L:CYS214
|
4.7
|
22.5
|
1.0
|
SG
|
L:CYS214
|
4.7
|
23.6
|
1.0
|
N
|
L:CYS214
|
4.8
|
20.0
|
1.0
|
C
|
H:HIS215
|
4.8
|
31.6
|
1.0
|
CA
|
H:HIS215
|
4.8
|
30.7
|
1.0
|
N
|
H:SER128
|
4.9
|
20.5
|
1.0
|
CB
|
H:SER128
|
4.9
|
26.0
|
1.0
|
O
|
H:HIS215
|
5.0
|
31.6
|
1.0
|
|
Zinc binding site 4 out
of 4 in 3ncj
Go back to
Zinc Binding Sites List in 3ncj
Zinc binding site 4 out
of 4 in the Crystal Structure of FAB15 MUT8
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of FAB15 MUT8 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn219
b:27.4
occ:0.78
|
OD2
|
H:ASP54
|
2.1
|
32.4
|
1.0
|
OD2
|
H:ASP52
|
2.2
|
35.3
|
1.0
|
CG
|
H:ASP54
|
2.8
|
33.9
|
1.0
|
OD1
|
H:ASP54
|
2.8
|
34.4
|
1.0
|
CG
|
H:ASP52
|
3.1
|
29.2
|
1.0
|
CB
|
H:ASP52
|
3.6
|
24.0
|
1.0
|
O
|
H:HOH311
|
4.1
|
41.0
|
1.0
|
OD1
|
H:ASP52
|
4.2
|
27.2
|
1.0
|
CB
|
H:TYR56
|
4.2
|
28.6
|
1.0
|
CB
|
H:ASP54
|
4.2
|
36.0
|
1.0
|
OG
|
H:SER53
|
4.3
|
33.6
|
1.0
|
CZ2
|
H:TRP33
|
4.6
|
33.9
|
1.0
|
NE1
|
H:TRP33
|
4.8
|
25.9
|
1.0
|
CG
|
H:TYR56
|
4.9
|
27.5
|
1.0
|
CE2
|
H:TRP33
|
4.9
|
28.6
|
1.0
|
|
Reference:
J.Luo,
Y.Feng,
G.L.Gilliland.
Co-Evolution of Antibody Stability and Vk Cdr-L3 Canonical Structure To Be Published.
Page generated: Sat Oct 26 10:10:18 2024
|