Sodium in PDB 6cih: Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State
Protein crystallography data
The structure of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State, PDB code: 6cih
was solved by
R.T.Chan,
J.K.Peters,
A.R.Robart,
T.Wiryaman,
K.R.Rajashankar,
N.Toor,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
81.82 /
3.68
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
163.639,
255.361,
136.786,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.8 /
25.5
|
Other elements in 6cih:
The structure of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State
(pdb code 6cih). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the
Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State, PDB code: 6cih:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Sodium binding site 1 out
of 9 in 6cih
Go back to
Sodium Binding Sites List in 6cih
Sodium binding site 1 out
of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State
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 A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na822
b:93.5
occ:1.00
|
O6
|
A:G421
|
2.2
|
0.1
|
1.0
|
C2'
|
A:G550
|
3.0
|
1.0
|
1.0
|
O2'
|
A:G550
|
3.1
|
0.2
|
1.0
|
C6
|
A:G421
|
3.4
|
0.3
|
1.0
|
MG
|
A:MG741
|
3.8
|
0.1
|
1.0
|
C3'
|
A:G550
|
3.9
|
0.4
|
1.0
|
OP1
|
A:A574
|
3.9
|
0.3
|
1.0
|
O3'
|
A:A573
|
4.1
|
0.9
|
1.0
|
OP2
|
A:G550
|
4.1
|
0.5
|
1.0
|
C8
|
A:G550
|
4.2
|
0.7
|
1.0
|
C1'
|
A:G550
|
4.2
|
0.5
|
1.0
|
C5
|
A:G421
|
4.3
|
0.9
|
1.0
|
N9
|
A:G550
|
4.4
|
0.7
|
1.0
|
N7
|
A:G421
|
4.4
|
0.7
|
1.0
|
N1
|
A:G421
|
4.5
|
0.2
|
1.0
|
P
|
A:A574
|
4.5
|
0.9
|
1.0
|
C5'
|
A:G550
|
4.6
|
0.4
|
1.0
|
O5'
|
A:A574
|
4.6
|
0.2
|
1.0
|
O2'
|
A:A573
|
4.6
|
0.5
|
1.0
|
C4'
|
A:G550
|
4.7
|
0.7
|
1.0
|
OP2
|
A:A551
|
4.8
|
0.2
|
1.0
|
O4'
|
A:G550
|
4.9
|
0.2
|
1.0
|
N7
|
A:A551
|
4.9
|
0.0
|
1.0
|
C8
|
A:A551
|
5.0
|
0.6
|
1.0
|
|
Sodium binding site 2 out
of 9 in 6cih
Go back to
Sodium Binding Sites List in 6cih
Sodium binding site 2 out
of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State
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 A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na827
b:96.5
occ:1.00
|
N7
|
A:A152
|
2.5
|
0.5
|
1.0
|
N6
|
A:A152
|
2.7
|
0.6
|
1.0
|
O4'
|
A:A115
|
2.7
|
0.5
|
1.0
|
C5
|
A:A152
|
2.8
|
0.6
|
1.0
|
C6
|
A:A152
|
3.0
|
0.7
|
1.0
|
O6
|
A:G153
|
3.1
|
0.6
|
1.0
|
C4'
|
A:A115
|
3.3
|
0.7
|
1.0
|
C5'
|
A:A115
|
3.3
|
0.5
|
1.0
|
C8
|
A:A152
|
3.5
|
0.7
|
1.0
|
O4
|
A:U68
|
3.6
|
0.1
|
1.0
|
OP2
|
A:A115
|
3.6
|
0.8
|
1.0
|
C6
|
A:G153
|
3.9
|
0.0
|
1.0
|
N7
|
A:G153
|
4.0
|
0.0
|
1.0
|
C4
|
A:A152
|
4.0
|
0.6
|
1.0
|
C1'
|
A:A115
|
4.0
|
0.8
|
1.0
|
N1
|
A:A152
|
4.1
|
0.1
|
1.0
|
C8
|
A:A115
|
4.2
|
0.3
|
1.0
|
C5
|
A:G153
|
4.3
|
0.4
|
1.0
|
N9
|
A:A152
|
4.3
|
0.4
|
1.0
|
O5'
|
A:A115
|
4.3
|
0.4
|
1.0
|
O2'
|
A:G114
|
4.4
|
0.2
|
1.0
|
O
|
A:HOH1104
|
4.4
|
0.7
|
1.0
|
P
|
A:A115
|
4.4
|
0.5
|
1.0
|
N9
|
A:A115
|
4.5
|
0.7
|
1.0
|
O3'
|
A:G114
|
4.5
|
0.8
|
1.0
|
C4
|
A:U68
|
4.5
|
0.0
|
1.0
|
OP1
|
A:C116
|
4.6
|
0.3
|
1.0
|
C3'
|
A:A115
|
4.7
|
0.3
|
1.0
|
C2
|
A:A152
|
4.9
|
0.5
|
1.0
|
N4
|
A:C67
|
4.9
|
0.6
|
1.0
|
N3
|
A:A152
|
4.9
|
0.6
|
1.0
|
|
Sodium binding site 3 out
of 9 in 6cih
Go back to
Sodium Binding Sites List in 6cih
Sodium binding site 3 out
of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na828
b:0.1
occ:1.00
|
O2'
|
A:U447
|
2.6
|
1.0
|
1.0
|
C1'
|
A:U447
|
3.5
|
0.7
|
1.0
|
C2'
|
A:U447
|
3.6
|
0.7
|
1.0
|
O4'
|
A:G448
|
4.0
|
0.2
|
1.0
|
O4'
|
A:U447
|
4.1
|
0.3
|
1.0
|
O2
|
A:U447
|
4.1
|
0.1
|
1.0
|
C4'
|
A:U447
|
4.6
|
0.5
|
1.0
|
N2
|
A:G453
|
4.7
|
0.3
|
1.0
|
C1'
|
A:G448
|
4.7
|
0.5
|
1.0
|
N1
|
A:U447
|
4.8
|
0.1
|
1.0
|
C3'
|
A:U447
|
4.8
|
0.3
|
1.0
|
C2
|
A:U447
|
4.9
|
0.8
|
1.0
|
|
Sodium binding site 4 out
of 9 in 6cih
Go back to
Sodium Binding Sites List in 6cih
Sodium binding site 4 out
of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na829
b:0.7
occ:1.00
|
O6
|
A:G84
|
3.7
|
0.6
|
1.0
|
N7
|
A:G84
|
4.1
|
0.8
|
1.0
|
N4
|
A:C85
|
4.2
|
0.3
|
1.0
|
N6
|
A:A83
|
4.3
|
0.8
|
1.0
|
C6
|
A:G84
|
4.6
|
0.6
|
1.0
|
C5
|
A:G84
|
4.7
|
0.6
|
1.0
|
C6
|
A:A83
|
4.9
|
0.0
|
1.0
|
|
Sodium binding site 5 out
of 9 in 6cih
Go back to
Sodium Binding Sites List in 6cih
Sodium binding site 5 out
of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na831
b:0.6
occ:1.00
|
N6
|
A:A594
|
2.3
|
0.1
|
1.0
|
N1
|
A:A595
|
2.8
|
0.7
|
1.0
|
C6
|
A:A595
|
3.3
|
0.5
|
1.0
|
C2
|
A:A595
|
3.3
|
0.0
|
1.0
|
C6
|
A:A594
|
3.5
|
0.6
|
1.0
|
N6
|
A:A595
|
3.6
|
0.3
|
1.0
|
C1'
|
A:A611
|
3.8
|
0.0
|
1.0
|
N7
|
A:A594
|
3.8
|
0.8
|
1.0
|
N9
|
A:A611
|
3.8
|
0.2
|
1.0
|
O4'
|
A:A611
|
3.9
|
0.2
|
1.0
|
O2
|
A:U610
|
3.9
|
0.4
|
1.0
|
C5
|
A:A594
|
3.9
|
0.8
|
1.0
|
C5
|
A:A595
|
4.1
|
0.5
|
1.0
|
N3
|
A:A595
|
4.2
|
0.4
|
1.0
|
C8
|
A:A611
|
4.2
|
0.7
|
1.0
|
C4
|
A:A611
|
4.2
|
0.1
|
1.0
|
C4
|
A:A595
|
4.4
|
0.8
|
1.0
|
N3
|
A:A611
|
4.6
|
0.2
|
1.0
|
N1
|
A:A594
|
4.6
|
0.7
|
1.0
|
C5
|
A:A611
|
4.7
|
0.3
|
1.0
|
N7
|
A:A611
|
4.7
|
0.2
|
1.0
|
O2'
|
A:U610
|
4.8
|
0.1
|
1.0
|
C2'
|
A:U610
|
4.8
|
0.7
|
1.0
|
C2
|
A:U610
|
4.9
|
0.3
|
1.0
|
|
Sodium binding site 6 out
of 9 in 6cih
Go back to
Sodium Binding Sites List in 6cih
Sodium binding site 6 out
of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na832
b:0.9
occ:1.00
|
O5'
|
A:A64
|
2.1
|
0.8
|
1.0
|
O3'
|
A:G63
|
2.2
|
1.0
|
1.0
|
P
|
A:A64
|
2.5
|
0.7
|
1.0
|
OP2
|
A:A64
|
2.7
|
0.6
|
1.0
|
C5'
|
A:A64
|
3.3
|
0.4
|
1.0
|
C8
|
A:A64
|
3.5
|
0.0
|
1.0
|
C3'
|
A:G63
|
3.5
|
0.8
|
1.0
|
OP2
|
A:G65
|
3.7
|
0.4
|
1.0
|
OP1
|
A:A64
|
3.9
|
0.9
|
1.0
|
C4'
|
A:A64
|
4.0
|
0.0
|
1.0
|
N7
|
A:A64
|
4.0
|
0.8
|
1.0
|
C3'
|
A:A64
|
4.1
|
0.7
|
1.0
|
C4'
|
A:G63
|
4.1
|
0.8
|
1.0
|
O4'
|
A:A64
|
4.2
|
0.4
|
1.0
|
C5'
|
A:G63
|
4.2
|
0.5
|
1.0
|
N9
|
A:A64
|
4.4
|
0.5
|
1.0
|
C2'
|
A:G63
|
4.7
|
0.3
|
1.0
|
O2'
|
A:G63
|
4.7
|
0.7
|
1.0
|
C1'
|
A:A64
|
4.8
|
0.4
|
1.0
|
O3'
|
A:A64
|
4.9
|
0.6
|
1.0
|
P
|
A:G65
|
5.0
|
0.9
|
1.0
|
|
Sodium binding site 7 out
of 9 in 6cih
Go back to
Sodium Binding Sites List in 6cih
Sodium binding site 7 out
of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na834
b:0.1
occ:1.00
|
OP1
|
A:U294
|
4.6
|
0.4
|
1.0
|
OP2
|
A:A295
|
4.8
|
0.3
|
1.0
|
|
Sodium binding site 8 out
of 9 in 6cih
Go back to
Sodium Binding Sites List in 6cih
Sodium binding site 8 out
of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na835
b:0.3
occ:1.00
|
N6
|
A:A543
|
3.9
|
0.0
|
1.0
|
O4
|
A:U511
|
4.3
|
0.8
|
1.0
|
O4
|
A:U510
|
4.6
|
0.9
|
1.0
|
|
Sodium binding site 9 out
of 9 in 6cih
Go back to
Sodium Binding Sites List in 6cih
Sodium binding site 9 out
of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na837
b:0.9
occ:1.00
|
OP1
|
A:C374
|
3.3
|
0.1
|
1.0
|
P
|
A:C374
|
4.4
|
0.6
|
1.0
|
O3'
|
A:A373
|
4.7
|
0.1
|
1.0
|
OP2
|
A:C374
|
4.8
|
0.9
|
1.0
|
|
Reference:
R.T.Chan,
J.K.Peters,
A.R.Robart,
T.Wiryaman,
K.R.Rajashankar,
N.Toor.
Structural Basis For the Second Step of Group II Intron Splicing. Nat Commun V. 9 4676 2018.
ISSN: ESSN 2041-1723
PubMed: 30410046
DOI: 10.1038/S41467-018-06678-0
Page generated: Tue Oct 8 06:35:41 2024
|