Sodium in PDB 5kxl: Hen Egg White Lysozyme at 100K, Data Set 2
Enzymatic activity of Hen Egg White Lysozyme at 100K, Data Set 2
All present enzymatic activity of Hen Egg White Lysozyme at 100K, Data Set 2:
3.2.1.17;
Protein crystallography data
The structure of Hen Egg White Lysozyme at 100K, Data Set 2, PDB code: 5kxl
was solved by
S.Russi,
A.Gonzalez,
L.R.Kenner,
D.A.Keedy,
J.S.Fraser,
H.Van Den Bedem,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.66 /
1.20
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.312,
77.312,
37.213,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15 /
16.4
|
Other elements in 5kxl:
The structure of Hen Egg White Lysozyme at 100K, Data Set 2 also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Hen Egg White Lysozyme at 100K, Data Set 2
(pdb code 5kxl). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the
Hen Egg White Lysozyme at 100K, Data Set 2, PDB code: 5kxl:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 5kxl
Go back to
Sodium Binding Sites List in 5kxl
Sodium binding site 1 out
of 2 in the Hen Egg White Lysozyme at 100K, Data Set 2
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Hen Egg White Lysozyme at 100K, Data Set 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na204
b:9.8
occ:1.00
|
O
|
A:SER60
|
2.3
|
8.3
|
0.4
|
O
|
A:SER60
|
2.3
|
9.6
|
0.3
|
O
|
A:SER60
|
2.4
|
8.9
|
0.3
|
O
|
A:HOH351
|
2.4
|
11.6
|
1.0
|
O
|
A:CYS64
|
2.4
|
8.6
|
1.0
|
O
|
A:ARG73
|
2.4
|
12.3
|
0.4
|
O
|
A:HOH354
|
2.4
|
8.9
|
1.0
|
O
|
A:ARG73
|
2.5
|
12.4
|
0.6
|
OG
|
A:SER72
|
2.5
|
12.1
|
0.4
|
OG
|
A:SER72
|
2.5
|
12.6
|
0.6
|
CB
|
A:SER72
|
3.2
|
12.1
|
0.4
|
CB
|
A:SER72
|
3.3
|
12.6
|
0.6
|
C
|
A:SER60
|
3.5
|
8.7
|
0.3
|
C
|
A:SER60
|
3.5
|
8.3
|
0.4
|
C
|
A:SER60
|
3.5
|
9.9
|
0.3
|
C
|
A:ARG73
|
3.5
|
12.3
|
0.4
|
C
|
A:CYS64
|
3.5
|
7.5
|
1.0
|
C
|
A:ARG73
|
3.5
|
12.2
|
0.6
|
N
|
A:ARG73
|
3.8
|
13.4
|
0.6
|
CA
|
A:ASN65
|
3.9
|
7.5
|
0.5
|
CA
|
A:ASN65
|
3.9
|
8.5
|
0.1
|
N
|
A:ARG73
|
3.9
|
13.1
|
0.4
|
CA
|
A:ASN65
|
3.9
|
8.1
|
0.4
|
C
|
A:SER72
|
4.0
|
13.0
|
0.6
|
CA
|
A:SER60
|
4.1
|
9.4
|
0.3
|
N
|
A:ASN65
|
4.1
|
7.6
|
0.5
|
CA
|
A:SER60
|
4.1
|
8.1
|
0.3
|
CA
|
A:SER60
|
4.1
|
7.0
|
0.4
|
N
|
A:ASN65
|
4.1
|
8.0
|
0.1
|
N
|
A:ASN65
|
4.1
|
8.0
|
0.4
|
C
|
A:SER72
|
4.2
|
12.3
|
0.4
|
CB
|
A:SER60
|
4.2
|
8.0
|
0.3
|
CB
|
A:SER60
|
4.2
|
9.1
|
0.3
|
CA
|
A:ARG73
|
4.3
|
13.3
|
0.6
|
CA
|
A:SER72
|
4.3
|
12.8
|
0.6
|
CA
|
A:ARG73
|
4.3
|
13.4
|
0.4
|
CB
|
A:SER60
|
4.3
|
7.5
|
0.4
|
O
|
A:ARG61
|
4.3
|
9.9
|
0.3
|
CA
|
A:SER72
|
4.3
|
12.4
|
0.4
|
N
|
A:CYS64
|
4.4
|
8.5
|
1.0
|
N
|
A:ASN74
|
4.4
|
11.9
|
1.0
|
C
|
A:ARG61
|
4.5
|
9.4
|
0.3
|
N
|
A:ARG61
|
4.5
|
8.7
|
0.3
|
C
|
A:ARG61
|
4.5
|
10.4
|
0.4
|
O
|
A:SER72
|
4.5
|
13.4
|
0.6
|
OD1
|
A:ASN65
|
4.5
|
7.8
|
0.5
|
N
|
A:ARG61
|
4.5
|
9.0
|
0.4
|
N
|
A:ASP66
|
4.5
|
6.9
|
0.5
|
O
|
A:ARG61
|
4.6
|
10.5
|
0.4
|
N
|
A:ARG61
|
4.6
|
10.4
|
0.3
|
C
|
A:ARG61
|
4.6
|
11.3
|
0.3
|
CA
|
A:ASN74
|
4.6
|
10.9
|
1.0
|
CA
|
A:CYS64
|
4.6
|
8.0
|
1.0
|
CL
|
A:CL201
|
4.6
|
11.5
|
1.0
|
N
|
A:ASP66
|
4.6
|
7.4
|
0.4
|
N
|
A:ASP66
|
4.6
|
8.6
|
0.1
|
OD1
|
A:ASN65
|
4.7
|
8.5
|
0.1
|
O
|
A:ARG61
|
4.7
|
11.8
|
0.3
|
CB
|
A:THR69
|
4.7
|
9.1
|
0.4
|
CB
|
A:ASN65
|
4.7
|
8.8
|
0.1
|
CB
|
A:THR69
|
4.7
|
10.3
|
0.4
|
CA
|
A:ARG61
|
4.7
|
11.0
|
0.4
|
CA
|
A:ARG61
|
4.7
|
9.8
|
0.3
|
C
|
A:ASN65
|
4.7
|
6.8
|
0.5
|
CB
|
A:ASN65
|
4.7
|
8.8
|
0.5
|
CB
|
A:ASN74
|
4.8
|
10.6
|
1.0
|
O
|
A:SER72
|
4.8
|
12.7
|
0.4
|
C
|
A:ASN65
|
4.8
|
8.5
|
0.1
|
CA
|
A:ARG61
|
4.8
|
11.7
|
0.3
|
CB
|
A:THR69
|
4.8
|
11.8
|
0.2
|
C
|
A:ASN65
|
4.8
|
7.4
|
0.4
|
N
|
A:TRP62
|
4.8
|
10.5
|
0.4
|
N
|
A:TRP62
|
4.9
|
10.9
|
0.3
|
CB
|
A:ASN65
|
4.9
|
8.8
|
0.4
|
O
|
A:HOH434
|
4.9
|
23.1
|
1.0
|
OD1
|
A:ASN65
|
4.9
|
9.7
|
0.4
|
N
|
A:TRP62
|
5.0
|
8.7
|
0.3
|
N
|
A:TRP63
|
5.0
|
8.3
|
0.4
|
N
|
A:TRP63
|
5.0
|
9.8
|
0.3
|
|
Sodium binding site 2 out
of 2 in 5kxl
Go back to
Sodium Binding Sites List in 5kxl
Sodium binding site 2 out
of 2 in the Hen Egg White Lysozyme at 100K, Data Set 2
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Hen Egg White Lysozyme at 100K, Data Set 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na205
b:49.7
occ:1.00
|
O
|
A:HOH410
|
2.4
|
26.9
|
1.0
|
O
|
A:HOH360
|
2.4
|
15.3
|
1.0
|
OE1
|
A:GLU35
|
2.5
|
9.4
|
0.5
|
OE1
|
A:GLU35
|
2.5
|
9.1
|
0.2
|
O
|
A:HOH327
|
2.6
|
22.2
|
1.0
|
OE1
|
A:GLU35
|
2.6
|
8.6
|
0.4
|
O
|
A:HOH302
|
2.9
|
13.5
|
1.0
|
OD2
|
A:ASP52
|
3.3
|
10.6
|
0.4
|
CD
|
A:GLU35
|
3.4
|
8.5
|
0.2
|
CD
|
A:GLU35
|
3.4
|
9.2
|
0.5
|
OD2
|
A:ASP52
|
3.4
|
17.6
|
0.6
|
OE2
|
A:GLU35
|
3.5
|
7.9
|
0.2
|
CD
|
A:GLU35
|
3.6
|
8.1
|
0.4
|
OE2
|
A:GLU35
|
3.6
|
9.6
|
0.5
|
CB
|
A:GLN57
|
3.8
|
8.2
|
0.3
|
CB
|
A:GLN57
|
3.9
|
6.6
|
0.3
|
OE2
|
A:GLU35
|
3.9
|
7.7
|
0.4
|
CB
|
A:GLN57
|
4.1
|
7.9
|
0.4
|
O
|
A:HOH398
|
4.1
|
17.0
|
1.0
|
CG
|
A:ASP52
|
4.2
|
7.4
|
0.4
|
CG
|
A:ASP52
|
4.2
|
15.1
|
0.6
|
CG
|
A:GLN57
|
4.2
|
8.7
|
0.3
|
CG
|
A:GLN57
|
4.4
|
7.0
|
0.3
|
O
|
A:HOH317
|
4.4
|
12.4
|
1.0
|
O
|
A:GLN57
|
4.5
|
6.6
|
0.3
|
CG
|
A:GLN57
|
4.5
|
8.3
|
0.4
|
O
|
A:HOH326
|
4.6
|
27.0
|
1.0
|
O
|
A:GLN57
|
4.6
|
8.5
|
0.3
|
OE1
|
A:GLN57
|
4.7
|
9.0
|
0.4
|
OE1
|
A:GLN57
|
4.7
|
7.1
|
0.3
|
OE1
|
A:GLN57
|
4.7
|
8.9
|
0.3
|
CB
|
A:ASP52
|
4.8
|
6.1
|
0.4
|
CG
|
A:GLU35
|
4.8
|
8.7
|
0.5
|
CB
|
A:ASP52
|
4.8
|
11.5
|
0.6
|
CG
|
A:GLU35
|
4.8
|
8.8
|
0.2
|
O
|
A:GLN57
|
4.9
|
8.0
|
0.4
|
OD1
|
A:ASP52
|
4.9
|
16.3
|
0.6
|
OD1
|
A:ASP52
|
4.9
|
7.6
|
0.4
|
CG
|
A:GLU35
|
5.0
|
8.2
|
0.4
|
CD
|
A:GLN57
|
5.0
|
8.5
|
0.3
|
|
Reference:
S.Russi,
A.Gonzalez,
L.R.Kenner,
D.A.Keedy,
J.S.Fraser,
H.Van Den Bedem.
Conformational Variation of Proteins at Room Temperature Is Not Dominated By Radiation Damage. J Synchrotron Radiat V. 24 73 2017.
ISSN: ESSN 1600-5775
PubMed: 28009548
DOI: 10.1107/S1600577516017343
Page generated: Mon Oct 7 22:11:59 2024
|