Zinc in PDB 3ugi: Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta
Enzymatic activity of Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta
All present enzymatic activity of Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta:
2.7.11.13;
Protein crystallography data
The structure of Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta, PDB code: 3ugi
was solved by
S.Shanmugasundararaj,
T.Stehle,
K.W.Miller,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
9.98 /
1.36
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
43.530,
32.461,
49.591,
90.00,
94.55,
90.00
|
R / Rfree (%)
|
15.3 /
18.2
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta
(pdb code 3ugi). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta, PDB code: 3ugi:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 3ugi
Go back to
Zinc Binding Sites List in 3ugi
Zinc binding site 1 out
of 4 in the Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn3
b:12.6
occ:1.00
|
ND1
|
A:HIS231
|
2.1
|
13.2
|
1.0
|
SG
|
A:CYS264
|
2.3
|
11.8
|
1.0
|
SG
|
A:CYS261
|
2.3
|
11.8
|
1.0
|
SG
|
A:CYS280
|
2.3
|
13.9
|
1.0
|
CE1
|
A:HIS231
|
2.9
|
12.7
|
1.0
|
CB
|
A:CYS261
|
3.2
|
11.8
|
1.0
|
CG
|
A:HIS231
|
3.2
|
12.7
|
1.0
|
CB
|
A:CYS280
|
3.2
|
13.5
|
1.0
|
CB
|
A:CYS264
|
3.3
|
11.4
|
1.0
|
CA
|
A:HIS231
|
3.7
|
14.0
|
1.0
|
N
|
A:CYS264
|
3.7
|
12.2
|
1.0
|
CB
|
A:HIS231
|
3.7
|
12.9
|
1.0
|
O
|
A:HOH16
|
4.0
|
17.3
|
1.0
|
CA
|
A:CYS264
|
4.0
|
11.3
|
1.0
|
NE2
|
A:HIS231
|
4.1
|
12.1
|
1.0
|
CA
|
A:CYS280
|
4.2
|
13.3
|
1.0
|
CD2
|
A:HIS231
|
4.3
|
12.5
|
1.0
|
N
|
A:HIS231
|
4.5
|
14.5
|
1.0
|
CB
|
A:ASP263
|
4.6
|
15.9
|
1.0
|
N
|
A:ARG232
|
4.6
|
15.3
|
1.0
|
CA
|
A:CYS261
|
4.6
|
11.5
|
1.0
|
C
|
A:ASP263
|
4.7
|
13.2
|
1.0
|
C
|
A:HIS231
|
4.8
|
14.9
|
1.0
|
C
|
A:CYS264
|
4.8
|
10.3
|
1.0
|
CB
|
A:MET266
|
4.9
|
10.1
|
1.0
|
N
|
A:GLY265
|
4.9
|
10.4
|
1.0
|
C
|
A:CYS280
|
5.0
|
13.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 3ugi
Go back to
Zinc Binding Sites List in 3ugi
Zinc binding site 2 out
of 4 in the Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn4
b:11.4
occ:1.00
|
ND1
|
A:HIS269
|
2.1
|
10.0
|
1.0
|
SG
|
A:CYS272
|
2.3
|
12.0
|
1.0
|
SG
|
A:CYS247
|
2.3
|
10.5
|
1.0
|
SG
|
A:CYS244
|
2.4
|
10.1
|
1.0
|
CB
|
A:CYS244
|
3.0
|
9.8
|
1.0
|
CE1
|
A:HIS269
|
3.0
|
10.2
|
1.0
|
CG
|
A:HIS269
|
3.2
|
9.5
|
1.0
|
CB
|
A:CYS247
|
3.3
|
11.2
|
1.0
|
CB
|
A:CYS272
|
3.3
|
11.6
|
1.0
|
CB
|
A:HIS269
|
3.6
|
10.1
|
1.0
|
N
|
A:CYS247
|
3.8
|
10.9
|
1.0
|
N
|
A:HIS269
|
4.0
|
10.0
|
1.0
|
CA
|
A:CYS247
|
4.1
|
11.3
|
1.0
|
NE2
|
A:HIS269
|
4.2
|
9.8
|
1.0
|
CD2
|
A:HIS269
|
4.3
|
10.4
|
1.0
|
CA
|
A:HIS269
|
4.4
|
10.2
|
1.0
|
CA
|
A:CYS244
|
4.5
|
9.6
|
1.0
|
O
|
A:HOH17
|
4.5
|
19.2
|
1.0
|
CA
|
A:CYS272
|
4.7
|
11.3
|
1.0
|
CB
|
A:HIS246
|
4.7
|
11.5
|
1.0
|
C
|
A:CYS247
|
4.9
|
11.3
|
1.0
|
CD2
|
A:HIS246
|
4.9
|
13.4
|
1.0
|
N
|
A:CYS272
|
4.9
|
11.7
|
1.0
|
C
|
A:HIS246
|
4.9
|
11.8
|
1.0
|
N
|
A:GLY248
|
5.0
|
10.1
|
1.0
|
|
Zinc binding site 3 out
of 4 in 3ugi
Go back to
Zinc Binding Sites List in 3ugi
Zinc binding site 3 out
of 4 in the Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1
b:12.8
occ:1.00
|
ND1
|
B:HIS231
|
2.1
|
13.0
|
1.0
|
SG
|
B:CYS280
|
2.3
|
13.8
|
1.0
|
SG
|
B:CYS261
|
2.3
|
11.2
|
1.0
|
SG
|
B:CYS264
|
2.3
|
11.8
|
1.0
|
CE1
|
B:HIS231
|
2.9
|
12.6
|
1.0
|
CB
|
B:CYS261
|
3.2
|
11.2
|
1.0
|
CB
|
B:CYS280
|
3.2
|
13.2
|
1.0
|
CB
|
B:CYS264
|
3.3
|
11.3
|
1.0
|
CG
|
B:HIS231
|
3.3
|
12.3
|
1.0
|
N
|
B:CYS264
|
3.7
|
12.0
|
1.0
|
CA
|
B:HIS231
|
3.7
|
13.3
|
1.0
|
CB
|
B:HIS231
|
3.7
|
12.5
|
1.0
|
CA
|
B:CYS264
|
4.0
|
11.4
|
1.0
|
O
|
B:HOH290
|
4.1
|
13.8
|
1.0
|
NE2
|
B:HIS231
|
4.1
|
12.1
|
1.0
|
CA
|
B:CYS280
|
4.2
|
12.7
|
1.0
|
CD2
|
B:HIS231
|
4.3
|
12.2
|
1.0
|
N
|
B:HIS231
|
4.5
|
13.8
|
1.0
|
CB
|
B:ASP263
|
4.6
|
15.6
|
1.0
|
CA
|
B:CYS261
|
4.6
|
11.3
|
1.0
|
N
|
B:ARG232
|
4.6
|
14.0
|
1.0
|
C
|
B:ASP263
|
4.7
|
13.6
|
1.0
|
C
|
B:HIS231
|
4.8
|
13.4
|
1.0
|
C
|
B:CYS264
|
4.8
|
10.5
|
1.0
|
CB
|
B:MET266
|
4.9
|
10.1
|
1.0
|
N
|
B:GLY265
|
4.9
|
10.9
|
1.0
|
CA
|
B:ASP263
|
5.0
|
14.2
|
1.0
|
C
|
B:CYS280
|
5.0
|
12.7
|
1.0
|
|
Zinc binding site 4 out
of 4 in 3ugi
Go back to
Zinc Binding Sites List in 3ugi
Zinc binding site 4 out
of 4 in the Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase C Delta within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn2
b:11.5
occ:1.00
|
ND1
|
B:HIS269
|
2.1
|
10.5
|
1.0
|
SG
|
B:CYS272
|
2.3
|
12.1
|
1.0
|
SG
|
B:CYS247
|
2.3
|
10.9
|
1.0
|
SG
|
B:CYS244
|
2.4
|
10.3
|
1.0
|
CB
|
B:CYS244
|
3.0
|
10.0
|
1.0
|
CE1
|
B:HIS269
|
3.0
|
10.2
|
1.0
|
CG
|
B:HIS269
|
3.2
|
9.9
|
1.0
|
CB
|
B:CYS247
|
3.3
|
11.2
|
1.0
|
CB
|
B:CYS272
|
3.3
|
11.7
|
1.0
|
CB
|
B:HIS269
|
3.5
|
10.2
|
1.0
|
N
|
B:CYS247
|
3.8
|
10.8
|
1.0
|
N
|
B:HIS269
|
4.0
|
10.3
|
1.0
|
CA
|
B:CYS247
|
4.1
|
11.2
|
1.0
|
NE2
|
B:HIS269
|
4.2
|
9.9
|
1.0
|
CD2
|
B:HIS269
|
4.3
|
10.4
|
1.0
|
O
|
B:HOH10
|
4.4
|
20.8
|
1.0
|
CA
|
B:HIS269
|
4.4
|
10.4
|
1.0
|
CA
|
B:CYS244
|
4.5
|
9.6
|
1.0
|
O
|
B:HOH72
|
4.6
|
34.8
|
1.0
|
CB
|
B:HIS246
|
4.7
|
12.5
|
1.0
|
CA
|
B:CYS272
|
4.7
|
12.1
|
1.0
|
C
|
B:CYS247
|
4.9
|
11.2
|
1.0
|
CD2
|
B:HIS246
|
4.9
|
14.1
|
1.0
|
C
|
B:HIS246
|
4.9
|
12.4
|
1.0
|
N
|
B:GLY248
|
4.9
|
10.5
|
1.0
|
N
|
B:CYS272
|
5.0
|
11.8
|
1.0
|
|
Reference:
S.Shanmugasundararaj,
J.Das,
W.S.Sandberg,
X.Zhou,
D.Wang,
R.O.Messing,
K.S.Bruzik,
T.Stehle,
K.W.Miller.
Structural and Functional Characterization of An Anesthetic Binding Site in the Second Cysteine-Rich Domain of Protein Kinase Cdelta Biophys.J. V. 103 2331 2012.
ISSN: ISSN 0006-3495
PubMed: 23283232
DOI: 10.1016/J.BPJ.2012.10.034
Page generated: Sat Oct 26 17:17:48 2024
|