Zinc in PDB 8f0v: Lipocalin-Like Milk Protein-2 - E38A Mutant
Protein crystallography data
The structure of Lipocalin-Like Milk Protein-2 - E38A Mutant, PDB code: 8f0v
was solved by
R.Subramanian,
D.Kanagavijayan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.18 /
2.95
|
Space group
|
P 2 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
39.771,
52.337,
136.348,
90,
90,
90
|
R / Rfree (%)
|
23.5 /
29.4
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Lipocalin-Like Milk Protein-2 - E38A Mutant
(pdb code 8f0v). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the
Lipocalin-Like Milk Protein-2 - E38A Mutant, PDB code: 8f0v:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 8f0v
Go back to
Zinc Binding Sites List in 8f0v
Zinc binding site 1 out
of 3 in the Lipocalin-Like Milk Protein-2 - E38A Mutant
![](/pictures/ZN/pdb/f0/8f0v-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/f0/8f0v-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Lipocalin-Like Milk Protein-2 - E38A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn204
b:122.6
occ:1.00
|
OD2
|
A:ASP53
|
2.0
|
101.6
|
1.0
|
OE2
|
A:GLU61
|
2.0
|
123.1
|
1.0
|
NE2
|
A:HIS63
|
2.3
|
138.4
|
1.0
|
O
|
A:HOH302
|
2.3
|
71.0
|
1.0
|
OD1
|
A:ASP53
|
2.5
|
88.0
|
1.0
|
CG
|
A:ASP53
|
2.5
|
98.1
|
1.0
|
CD
|
A:GLU61
|
2.9
|
109.4
|
1.0
|
CE1
|
A:HIS63
|
3.3
|
131.6
|
1.0
|
CD2
|
A:HIS63
|
3.3
|
125.2
|
1.0
|
HD2
|
A:HIS63
|
3.4
|
126.2
|
1.0
|
HE1
|
A:HIS63
|
3.4
|
129.7
|
1.0
|
OE1
|
A:GLU61
|
3.6
|
120.7
|
1.0
|
HG3
|
A:GLU61
|
3.6
|
105.8
|
1.0
|
CG
|
A:GLU61
|
3.9
|
104.0
|
1.0
|
CB
|
A:ASP53
|
4.0
|
104.4
|
1.0
|
O
|
A:ASP53
|
4.1
|
115.0
|
1.0
|
HG
|
A:SER55
|
4.1
|
142.8
|
0.0
|
HB2
|
A:ASP53
|
4.2
|
103.6
|
1.0
|
HB3
|
A:ASP53
|
4.4
|
103.6
|
1.0
|
ND1
|
A:HIS63
|
4.4
|
118.8
|
1.0
|
HG21
|
A:VAL33
|
4.4
|
103.8
|
1.0
|
CG
|
A:HIS63
|
4.4
|
118.0
|
1.0
|
HB2
|
A:GLU61
|
4.5
|
109.1
|
1.0
|
OG
|
A:SER55
|
4.5
|
140.6
|
1.0
|
HG2
|
A:GLU61
|
4.6
|
105.8
|
1.0
|
HE3
|
A:MET78
|
4.6
|
117.2
|
1.0
|
HG21
|
A:THR81
|
4.7
|
144.6
|
1.0
|
HG22
|
A:VAL33
|
4.7
|
103.8
|
1.0
|
CB
|
A:GLU61
|
4.8
|
106.1
|
1.0
|
C
|
A:ASP53
|
4.9
|
108.6
|
1.0
|
|
Zinc binding site 2 out
of 3 in 8f0v
Go back to
Zinc Binding Sites List in 8f0v
Zinc binding site 2 out
of 3 in the Lipocalin-Like Milk Protein-2 - E38A Mutant
![](/pictures/ZN/pdb/f0/8f0v-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/f0/8f0v-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Lipocalin-Like Milk Protein-2 - E38A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn205
b:112.3
occ:1.00
|
NE2
|
A:HIS103
|
1.9
|
78.2
|
1.0
|
OE2
|
A:GLU2
|
2.0
|
121.6
|
1.0
|
OE1
|
A:GLU2
|
2.0
|
116.6
|
1.0
|
CD
|
A:GLU2
|
2.3
|
119.9
|
1.0
|
CE1
|
A:HIS103
|
2.9
|
77.7
|
1.0
|
CD2
|
A:HIS103
|
2.9
|
73.2
|
1.0
|
HE1
|
A:HIS103
|
3.1
|
75.8
|
1.0
|
HD2
|
A:HIS103
|
3.1
|
72.8
|
1.0
|
HE1
|
A:TYR101
|
3.3
|
89.4
|
1.0
|
CG
|
A:GLU2
|
3.8
|
113.2
|
1.0
|
ND1
|
A:HIS103
|
3.9
|
69.5
|
1.0
|
CG
|
A:HIS103
|
4.0
|
67.1
|
1.0
|
HD1
|
A:TYR101
|
4.0
|
84.2
|
1.0
|
HA
|
A:GLU2
|
4.0
|
112.0
|
1.0
|
O
|
A:LYS1
|
4.0
|
136.7
|
1.0
|
CE1
|
A:TYR101
|
4.1
|
90.3
|
1.0
|
HG2
|
A:GLU2
|
4.1
|
114.5
|
1.0
|
HG3
|
A:GLU2
|
4.2
|
114.5
|
1.0
|
HD2
|
A:PRO3
|
4.3
|
121.2
|
1.0
|
CD1
|
A:TYR101
|
4.4
|
82.8
|
1.0
|
HB2
|
A:GLU2
|
4.6
|
111.9
|
1.0
|
CB
|
A:GLU2
|
4.6
|
112.5
|
1.0
|
HD1
|
A:HIS103
|
4.7
|
73.7
|
0.0
|
CA
|
A:GLU2
|
4.8
|
109.2
|
1.0
|
HD3
|
A:PRO3
|
4.9
|
121.1
|
1.0
|
HA2
|
A:GLY102
|
5.0
|
63.9
|
1.0
|
|
Zinc binding site 3 out
of 3 in 8f0v
Go back to
Zinc Binding Sites List in 8f0v
Zinc binding site 3 out
of 3 in the Lipocalin-Like Milk Protein-2 - E38A Mutant
![](/pictures/ZN/pdb/f0/8f0v-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/f0/8f0v-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Lipocalin-Like Milk Protein-2 - E38A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn206
b:88.1
occ:0.50
|
NE2
|
A:HIS150
|
2.0
|
72.0
|
1.0
|
OE2
|
A:GLU155
|
2.1
|
101.7
|
1.0
|
CD
|
A:GLU155
|
2.9
|
98.3
|
1.0
|
CE1
|
A:HIS150
|
2.9
|
73.0
|
1.0
|
CD2
|
A:HIS150
|
3.1
|
74.9
|
1.0
|
HE1
|
A:HIS150
|
3.1
|
73.2
|
1.0
|
OE1
|
A:GLU155
|
3.1
|
100.7
|
1.0
|
HA
|
A:ARG152
|
3.2
|
109.4
|
1.0
|
HD2
|
A:HIS150
|
3.3
|
75.6
|
1.0
|
HB3
|
A:ARG152
|
3.6
|
127.4
|
1.0
|
CA
|
A:ARG152
|
4.0
|
111.4
|
1.0
|
ND1
|
A:HIS150
|
4.1
|
72.5
|
1.0
|
CB
|
A:ARG152
|
4.1
|
127.1
|
1.0
|
HG3
|
A:ARG152
|
4.2
|
141.8
|
1.0
|
CG
|
A:HIS150
|
4.2
|
81.3
|
1.0
|
HG2
|
A:ARG152
|
4.2
|
142.4
|
1.0
|
CG
|
A:GLU155
|
4.3
|
96.1
|
1.0
|
HG3
|
A:GLU155
|
4.4
|
96.3
|
1.0
|
CG
|
A:ARG152
|
4.4
|
146.2
|
1.0
|
N
|
A:ARG152
|
4.6
|
95.7
|
1.0
|
HD1
|
A:HIS150
|
4.8
|
71.8
|
0.0
|
HG2
|
A:GLU155
|
4.9
|
96.2
|
1.0
|
C
|
A:CYS151
|
5.0
|
92.1
|
1.0
|
HB2
|
A:GLU155
|
5.0
|
95.5
|
1.0
|
|
Reference:
P.R.Santhakumari,
K.Dhanabalan,
S.Virani,
A.S.Hopf-Jannasch,
J.B.Benoit,
G.Chopra,
R.Subramanian.
Variability in Phenylalanine Side Chain Conformations Facilitates Broad Substrate Tolerance of Fatty Acid Binding in Cockroach Milk Proteins. Plos One V. 18 80009 2023.
ISSN: ESSN 1932-6203
PubMed: 37384723
DOI: 10.1371/JOURNAL.PONE.0280009
Page generated: Thu Dec 28 13:00:03 2023
|