Sodium in PDB 3f3e: Crystal Structure of Leut Bound to L-Leucine (30 Mm) and Sodium
Protein crystallography data
The structure of Crystal Structure of Leut Bound to L-Leucine (30 Mm) and Sodium, PDB code: 3f3e
was solved by
S.K.Singh,
C.L.Piscitelli,
A.Yamashita,
E.Gouaux,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.44 /
1.80
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.361,
86.664,
81.382,
90.00,
95.94,
90.00
|
R / Rfree (%)
|
18 /
20.5
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Leut Bound to L-Leucine (30 Mm) and Sodium
(pdb code 3f3e). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the
Crystal Structure of Leut Bound to L-Leucine (30 Mm) and Sodium, PDB code: 3f3e:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 3f3e
Go back to
Sodium Binding Sites List in 3f3e
Sodium binding site 1 out
of 2 in the Crystal Structure of Leut Bound to L-Leucine (30 Mm) and Sodium
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of Leut Bound to L-Leucine (30 Mm) and Sodium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na751
b:22.5
occ:1.00
|
O
|
A:VAL23
|
2.2
|
21.4
|
1.0
|
O
|
A:GLY20
|
2.3
|
22.8
|
1.0
|
O
|
A:ALA351
|
2.4
|
19.8
|
1.0
|
OG1
|
A:THR354
|
2.4
|
24.8
|
1.0
|
OG
|
A:SER355
|
2.5
|
19.7
|
1.0
|
N
|
A:SER355
|
2.9
|
21.5
|
1.0
|
C
|
A:VAL23
|
3.2
|
21.2
|
1.0
|
CB
|
A:SER355
|
3.3
|
20.4
|
1.0
|
C
|
A:THR354
|
3.3
|
21.5
|
1.0
|
C
|
A:GLY20
|
3.4
|
21.5
|
1.0
|
CB
|
A:THR354
|
3.4
|
24.8
|
1.0
|
C
|
A:ALA351
|
3.4
|
22.8
|
1.0
|
CA
|
A:SER355
|
3.5
|
20.1
|
1.0
|
CA
|
A:GLY24
|
3.6
|
20.9
|
1.0
|
CA
|
A:THR354
|
3.7
|
19.5
|
1.0
|
N
|
A:GLY24
|
3.9
|
21.8
|
1.0
|
CA
|
A:ALA351
|
4.0
|
20.4
|
1.0
|
O
|
A:THR354
|
4.0
|
21.9
|
1.0
|
CA
|
A:GLY20
|
4.0
|
28.5
|
1.0
|
N
|
A:THR354
|
4.1
|
19.7
|
1.0
|
O
|
A:ASN21
|
4.3
|
20.9
|
1.0
|
CA
|
A:VAL23
|
4.3
|
18.7
|
1.0
|
N
|
A:VAL23
|
4.3
|
19.6
|
1.0
|
O
|
A:PHE350
|
4.4
|
21.9
|
1.0
|
N
|
A:ASN21
|
4.5
|
19.8
|
1.0
|
C
|
A:ASN21
|
4.6
|
27.2
|
1.0
|
N
|
A:GLY352
|
4.6
|
19.1
|
1.0
|
O
|
A:GLY352
|
4.6
|
20.5
|
1.0
|
C
|
A:GLY352
|
4.7
|
18.4
|
1.0
|
CG2
|
A:THR354
|
4.8
|
20.2
|
1.0
|
C
|
A:ALA22
|
4.8
|
22.8
|
1.0
|
CB
|
A:VAL23
|
4.8
|
20.4
|
1.0
|
CA
|
A:ASN21
|
4.8
|
21.2
|
1.0
|
CB
|
A:ALA351
|
4.8
|
19.9
|
1.0
|
CA
|
A:GLY352
|
4.8
|
18.4
|
1.0
|
C
|
A:SER355
|
5.0
|
22.8
|
1.0
|
O
|
A:ALA22
|
5.0
|
20.6
|
1.0
|
|
Sodium binding site 2 out
of 2 in 3f3e
Go back to
Sodium Binding Sites List in 3f3e
Sodium binding site 2 out
of 2 in the Crystal Structure of Leut Bound to L-Leucine (30 Mm) and Sodium
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of Leut Bound to L-Leucine (30 Mm) and Sodium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na752
b:22.8
occ:1.00
|
O
|
A:ALA22
|
2.3
|
20.6
|
1.0
|
OD1
|
A:ASN27
|
2.3
|
21.6
|
1.0
|
O
|
A:THR254
|
2.4
|
20.5
|
1.0
|
OG1
|
A:THR254
|
2.5
|
22.6
|
1.0
|
OD1
|
A:ASN286
|
2.6
|
21.8
|
1.0
|
OXT
|
A:LEU601
|
2.6
|
20.9
|
1.0
|
C
|
A:THR254
|
3.2
|
25.5
|
1.0
|
C
|
A:ALA22
|
3.2
|
22.8
|
1.0
|
CG
|
A:ASN27
|
3.2
|
24.2
|
1.0
|
CA
|
A:THR254
|
3.2
|
24.0
|
1.0
|
CG
|
A:ASN286
|
3.4
|
23.6
|
1.0
|
CB
|
A:THR254
|
3.4
|
24.5
|
1.0
|
ND2
|
A:ASN27
|
3.6
|
23.7
|
1.0
|
C
|
A:LEU601
|
3.6
|
21.1
|
1.0
|
ND2
|
A:ASN286
|
3.6
|
26.9
|
1.0
|
N
|
A:LEU601
|
3.6
|
21.0
|
1.0
|
CA
|
A:VAL23
|
3.8
|
18.7
|
1.0
|
N
|
A:GLY24
|
3.9
|
21.8
|
1.0
|
N
|
A:VAL23
|
3.9
|
19.6
|
1.0
|
CA
|
A:ALA22
|
4.1
|
19.8
|
1.0
|
CA
|
A:LEU601
|
4.2
|
24.0
|
1.0
|
OE2
|
A:GLU290
|
4.2
|
26.1
|
1.0
|
N
|
A:ASN27
|
4.3
|
22.1
|
1.0
|
C
|
A:VAL23
|
4.3
|
21.2
|
1.0
|
N
|
A:LEU255
|
4.4
|
21.6
|
1.0
|
CB
|
A:ALA22
|
4.4
|
23.7
|
1.0
|
CB
|
A:ASN27
|
4.5
|
23.5
|
1.0
|
CG2
|
A:THR254
|
4.5
|
22.7
|
1.0
|
O
|
A:LEU601
|
4.5
|
21.9
|
1.0
|
N
|
A:THR254
|
4.6
|
20.7
|
1.0
|
O
|
A:PHE253
|
4.7
|
21.4
|
1.0
|
C
|
A:GLY26
|
4.8
|
23.9
|
1.0
|
CA
|
A:ASN27
|
4.8
|
24.8
|
1.0
|
CB
|
A:ASN286
|
4.8
|
20.8
|
1.0
|
CA
|
A:GLY26
|
4.9
|
22.8
|
1.0
|
CA
|
A:GLY24
|
4.9
|
20.9
|
1.0
|
|
Reference:
S.K.Singh,
C.L.Piscitelli,
A.Yamashita,
E.Gouaux.
A Competitive Inhibitor Traps Leut in An Open-to-Out Conformation. Science V. 322 1655 2008.
ISSN: ISSN 0036-8075
PubMed: 19074341
DOI: 10.1126/SCIENCE.1166777
Page generated: Tue Dec 15 06:10:17 2020
|