Magnesium in PDB 5ng6: Crystal Structure of FNCAS12A Bound to A Crrna
Protein crystallography data
The structure of Crystal Structure of FNCAS12A Bound to A Crrna, PDB code: 5ng6
was solved by
D.C.Swarts,
J.Van Der Oost,
M.Jinek,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.24 /
3.34
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
214.684,
277.061,
135.636,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.9 /
25.8
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of FNCAS12A Bound to A Crrna
(pdb code 5ng6). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Crystal Structure of FNCAS12A Bound to A Crrna, PDB code: 5ng6:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 5ng6
Go back to
Magnesium Binding Sites List in 5ng6
Magnesium binding site 1 out
of 8 in the Crystal Structure of FNCAS12A Bound to A Crrna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of FNCAS12A Bound to A Crrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1401
b:57.0
occ:1.00
|
O
|
A:HOH1502
|
1.7
|
26.9
|
1.0
|
O
|
A:HOH1504
|
1.8
|
0.8
|
1.0
|
O
|
B:HOH305
|
1.9
|
0.3
|
1.0
|
O
|
A:ARG800
|
2.1
|
54.4
|
1.0
|
OP2
|
B:A-3
|
2.1
|
56.2
|
1.0
|
O
|
B:HOH302
|
2.2
|
79.7
|
1.0
|
OP2
|
B:U-4
|
3.2
|
55.4
|
1.0
|
C
|
A:ARG800
|
3.3
|
54.6
|
1.0
|
P
|
B:A-3
|
3.6
|
57.3
|
1.0
|
N
|
A:ARG800
|
3.8
|
56.2
|
1.0
|
OD1
|
A:ASP792
|
4.0
|
52.9
|
1.0
|
CA
|
A:ARG800
|
4.1
|
55.7
|
1.0
|
N
|
A:PRO801
|
4.2
|
54.1
|
1.0
|
P
|
B:U-4
|
4.3
|
56.6
|
1.0
|
OP1
|
B:A-3
|
4.3
|
58.3
|
1.0
|
C
|
A:GLY799
|
4.3
|
56.9
|
1.0
|
O5'
|
B:A-3
|
4.3
|
56.8
|
1.0
|
CA
|
A:PRO801
|
4.4
|
53.3
|
1.0
|
C3'
|
B:U-4
|
4.5
|
57.3
|
1.0
|
OP1
|
B:U-4
|
4.5
|
57.7
|
1.0
|
O3'
|
B:U-4
|
4.5
|
57.9
|
1.0
|
CB
|
A:ARG800
|
4.6
|
56.0
|
1.0
|
C
|
A:PRO801
|
4.6
|
52.8
|
1.0
|
O5'
|
B:U-4
|
4.7
|
57.1
|
1.0
|
O
|
A:GLY799
|
4.8
|
56.5
|
1.0
|
CA
|
A:GLY799
|
4.9
|
57.7
|
1.0
|
OD1
|
A:ASN802
|
4.9
|
51.7
|
1.0
|
OP2
|
B:G-2
|
4.9
|
54.7
|
1.0
|
N
|
A:ASN802
|
4.9
|
52.1
|
1.0
|
CG
|
A:ASP792
|
5.0
|
52.4
|
1.0
|
O
|
A:PRO801
|
5.0
|
53.0
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 5ng6
Go back to
Magnesium Binding Sites List in 5ng6
Magnesium binding site 2 out
of 8 in the Crystal Structure of FNCAS12A Bound to A Crrna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of FNCAS12A Bound to A Crrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg200
b:62.0
occ:1.00
|
O
|
B:HOH306
|
1.7
|
62.0
|
1.0
|
O
|
B:HOH309
|
1.7
|
62.0
|
1.0
|
O
|
B:HOH308
|
1.8
|
62.0
|
1.0
|
O
|
A:HOH1505
|
1.9
|
62.0
|
1.0
|
O
|
B:HOH307
|
1.9
|
62.0
|
1.0
|
O
|
B:HOH310
|
1.9
|
72.4
|
1.0
|
O
|
B:HOH301
|
3.7
|
17.6
|
1.0
|
OP2
|
B:A-17
|
4.1
|
50.8
|
1.0
|
O4
|
B:U-16
|
4.2
|
49.3
|
1.0
|
OP2
|
B:A-11
|
4.3
|
47.7
|
1.0
|
O
|
A:HOH1503
|
4.6
|
17.6
|
1.0
|
OP1
|
B:A-17
|
4.6
|
53.1
|
1.0
|
OP2
|
B:U-12
|
4.7
|
45.3
|
1.0
|
C5
|
B:C-10
|
4.8
|
52.3
|
1.0
|
P
|
B:A-17
|
4.9
|
50.7
|
1.0
|
N7
|
B:A-11
|
5.0
|
50.2
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 5ng6
Go back to
Magnesium Binding Sites List in 5ng6
Magnesium binding site 3 out
of 8 in the Crystal Structure of FNCAS12A Bound to A Crrna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of FNCAS12A Bound to A Crrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1401
b:57.0
occ:1.00
|
O
|
C:ARG800
|
2.0
|
70.7
|
1.0
|
OP2
|
D:A-3
|
2.3
|
75.3
|
1.0
|
C
|
C:ARG800
|
3.2
|
71.2
|
1.0
|
OP2
|
D:U-4
|
3.6
|
81.2
|
1.0
|
P
|
D:A-3
|
3.7
|
75.6
|
1.0
|
N
|
C:ARG800
|
3.8
|
72.8
|
1.0
|
OD1
|
C:ASP792
|
3.8
|
70.6
|
1.0
|
CA
|
C:ARG800
|
4.0
|
72.2
|
1.0
|
C
|
C:GLY799
|
4.1
|
84.1
|
1.0
|
N
|
C:PRO801
|
4.2
|
71.1
|
1.0
|
CA
|
C:PRO801
|
4.3
|
70.4
|
1.0
|
OP1
|
D:A-3
|
4.4
|
76.6
|
1.0
|
O5'
|
D:A-3
|
4.4
|
73.9
|
1.0
|
O
|
C:GLY799
|
4.5
|
84.7
|
1.0
|
C
|
C:PRO801
|
4.5
|
69.4
|
1.0
|
CB
|
C:ARG800
|
4.6
|
71.8
|
1.0
|
CA
|
C:GLY799
|
4.6
|
91.2
|
1.0
|
C3'
|
D:U-4
|
4.7
|
76.4
|
1.0
|
CG
|
C:ASP792
|
4.7
|
70.2
|
1.0
|
OD1
|
C:ASN802
|
4.7
|
67.4
|
1.0
|
O3'
|
D:U-4
|
4.7
|
76.5
|
1.0
|
OP2
|
D:G-2
|
4.7
|
70.8
|
1.0
|
P
|
D:U-4
|
4.8
|
79.7
|
1.0
|
O5'
|
D:U-4
|
4.8
|
78.8
|
1.0
|
OD2
|
C:ASP792
|
4.8
|
69.4
|
1.0
|
N
|
C:ASN802
|
4.8
|
68.8
|
1.0
|
O
|
C:PRO801
|
4.9
|
69.2
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 5ng6
Go back to
Magnesium Binding Sites List in 5ng6
Magnesium binding site 4 out
of 8 in the Crystal Structure of FNCAS12A Bound to A Crrna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of FNCAS12A Bound to A Crrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg200
b:62.0
occ:1.00
|
O
|
D:HOH306
|
1.8
|
62.0
|
1.0
|
O
|
D:HOH304
|
1.9
|
62.0
|
1.0
|
O
|
D:HOH303
|
1.9
|
62.0
|
1.0
|
O
|
D:HOH302
|
1.9
|
64.4
|
1.0
|
O
|
D:HOH301
|
2.0
|
64.4
|
1.0
|
O
|
D:HOH305
|
2.0
|
65.7
|
1.0
|
OP2
|
D:A-11
|
3.9
|
62.1
|
1.0
|
O4
|
D:U-16
|
4.1
|
70.0
|
1.0
|
OP2
|
D:A-17
|
4.2
|
73.0
|
1.0
|
N7
|
D:A-11
|
4.7
|
66.1
|
1.0
|
OP2
|
D:U-12
|
4.7
|
62.2
|
1.0
|
C5
|
D:C-10
|
4.8
|
70.5
|
1.0
|
OP1
|
D:A-17
|
4.9
|
73.5
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 5ng6
Go back to
Magnesium Binding Sites List in 5ng6
Magnesium binding site 5 out
of 8 in the Crystal Structure of FNCAS12A Bound to A Crrna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of FNCAS12A Bound to A Crrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg1401
b:78.2
occ:1.00
|
O
|
E:HOH1505
|
1.9
|
0.3
|
1.0
|
O
|
F:HOH303
|
1.9
|
0.1
|
1.0
|
O
|
E:HOH1502
|
2.0
|
0.2
|
1.0
|
O
|
E:ARG800
|
2.0
|
60.2
|
1.0
|
O
|
F:HOH308
|
2.1
|
17.6
|
1.0
|
OP2
|
F:A-3
|
2.1
|
56.0
|
1.0
|
C
|
E:ARG800
|
3.2
|
60.1
|
1.0
|
P
|
F:A-3
|
3.5
|
56.5
|
1.0
|
N
|
E:ARG800
|
3.9
|
60.8
|
1.0
|
OP2
|
F:U-4
|
4.0
|
56.1
|
1.0
|
CA
|
E:ARG800
|
4.1
|
60.2
|
1.0
|
O
|
E:HOH1504
|
4.1
|
20.9
|
1.0
|
OD1
|
E:ASP792
|
4.2
|
59.7
|
1.0
|
OP1
|
F:A-3
|
4.2
|
57.3
|
1.0
|
N
|
E:PRO801
|
4.2
|
59.9
|
1.0
|
O5'
|
F:A-3
|
4.2
|
55.9
|
1.0
|
CA
|
E:PRO801
|
4.3
|
59.9
|
1.0
|
O
|
E:HOH1503
|
4.3
|
17.6
|
1.0
|
C
|
E:PRO801
|
4.4
|
60.1
|
1.0
|
C
|
E:GLY799
|
4.4
|
95.2
|
1.0
|
OD1
|
E:ASN802
|
4.5
|
60.6
|
1.0
|
CB
|
E:ARG800
|
4.5
|
60.5
|
1.0
|
OP1
|
F:U-4
|
4.5
|
57.7
|
1.0
|
OP2
|
F:G-2
|
4.5
|
54.3
|
1.0
|
O3'
|
F:U-4
|
4.6
|
57.1
|
1.0
|
P
|
F:U-4
|
4.6
|
57.1
|
1.0
|
C3'
|
F:U-4
|
4.7
|
56.7
|
1.0
|
O
|
E:PRO801
|
4.7
|
60.4
|
1.0
|
N
|
E:ASN802
|
4.7
|
60.2
|
1.0
|
O
|
E:GLY799
|
4.9
|
0.5
|
1.0
|
O5'
|
F:U-4
|
5.0
|
57.2
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 5ng6
Go back to
Magnesium Binding Sites List in 5ng6
Magnesium binding site 6 out
of 8 in the Crystal Structure of FNCAS12A Bound to A Crrna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of FNCAS12A Bound to A Crrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg200
b:62.4
occ:1.00
|
O
|
F:HOH307
|
1.7
|
62.0
|
1.0
|
O
|
F:HOH306
|
1.7
|
62.0
|
1.0
|
O
|
F:HOH310
|
1.7
|
62.0
|
1.0
|
O
|
F:HOH304
|
1.8
|
62.0
|
1.0
|
O
|
F:HOH309
|
1.8
|
62.0
|
1.0
|
O
|
F:HOH302
|
1.8
|
62.0
|
1.0
|
OP2
|
F:A-11
|
3.9
|
48.9
|
1.0
|
O4
|
F:U-16
|
4.1
|
50.9
|
1.0
|
O
|
E:HOH1501
|
4.2
|
58.7
|
1.0
|
OP2
|
F:A-17
|
4.4
|
52.2
|
1.0
|
N7
|
F:A-11
|
4.6
|
51.0
|
1.0
|
OP2
|
F:U-12
|
4.7
|
47.6
|
1.0
|
C5
|
F:C-10
|
4.8
|
52.8
|
1.0
|
OP1
|
F:A-17
|
5.0
|
51.4
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 5ng6
Go back to
Magnesium Binding Sites List in 5ng6
Magnesium binding site 7 out
of 8 in the Crystal Structure of FNCAS12A Bound to A Crrna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Crystal Structure of FNCAS12A Bound to A Crrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg1401
b:57.0
occ:1.00
|
O
|
H:HOH302
|
1.8
|
0.1
|
1.0
|
O
|
G:HOH1501
|
1.8
|
0.8
|
1.0
|
O
|
G:ARG800
|
2.0
|
58.6
|
1.0
|
OP2
|
H:A-3
|
2.1
|
57.7
|
1.0
|
O
|
G:HOH1502
|
2.1
|
93.1
|
1.0
|
C
|
G:ARG800
|
3.2
|
58.6
|
1.0
|
P
|
H:A-3
|
3.5
|
58.0
|
1.0
|
OP2
|
H:U-4
|
3.7
|
59.0
|
1.0
|
N
|
G:ARG800
|
3.8
|
60.1
|
1.0
|
CA
|
G:ARG800
|
4.0
|
59.6
|
1.0
|
N
|
G:PRO801
|
4.2
|
58.0
|
1.0
|
OP1
|
H:A-3
|
4.2
|
57.5
|
1.0
|
OP1
|
H:U-4
|
4.2
|
58.7
|
1.0
|
O5'
|
H:A-3
|
4.2
|
57.8
|
1.0
|
OD1
|
G:ASP792
|
4.3
|
56.8
|
1.0
|
C
|
G:GLY799
|
4.3
|
93.8
|
1.0
|
P
|
H:U-4
|
4.4
|
59.4
|
1.0
|
CA
|
G:PRO801
|
4.4
|
57.2
|
1.0
|
CB
|
G:ARG800
|
4.4
|
60.2
|
1.0
|
C3'
|
H:U-4
|
4.5
|
60.0
|
1.0
|
C
|
G:PRO801
|
4.5
|
57.0
|
1.0
|
O3'
|
H:U-4
|
4.5
|
59.3
|
1.0
|
OP2
|
H:G-2
|
4.7
|
55.2
|
1.0
|
O5'
|
H:U-4
|
4.7
|
60.3
|
1.0
|
O
|
G:PRO801
|
4.8
|
57.4
|
1.0
|
O
|
G:GLY799
|
4.8
|
0.9
|
1.0
|
OD1
|
G:ASN802
|
4.8
|
56.6
|
1.0
|
N
|
G:ASN802
|
4.9
|
56.4
|
1.0
|
CA
|
G:GLY799
|
4.9
|
93.4
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 5ng6
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Magnesium Binding Sites List in 5ng6
Magnesium binding site 8 out
of 8 in the Crystal Structure of FNCAS12A Bound to A Crrna
Mono view
Stereo pair view
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A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Crystal Structure of FNCAS12A Bound to A Crrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg200
b:62.0
occ:1.00
|
O
|
H:HOH305
|
1.7
|
62.0
|
1.0
|
O
|
G:HOH1503
|
1.8
|
62.0
|
1.0
|
O
|
H:HOH304
|
1.9
|
62.0
|
1.0
|
O
|
H:HOH303
|
1.9
|
62.0
|
1.0
|
O
|
H:HOH306
|
1.9
|
65.0
|
1.0
|
O
|
H:HOH301
|
2.0
|
62.0
|
1.0
|
O4
|
H:U-16
|
4.1
|
59.9
|
1.0
|
OP2
|
H:A-17
|
4.2
|
60.2
|
1.0
|
OP2
|
H:A-11
|
4.4
|
60.5
|
1.0
|
OP2
|
H:U-12
|
4.6
|
59.9
|
1.0
|
OP1
|
H:A-17
|
4.6
|
60.1
|
1.0
|
C5
|
H:C-10
|
4.9
|
63.8
|
1.0
|
P
|
H:A-17
|
5.0
|
59.8
|
1.0
|
|
Reference:
D.C.Swarts,
J.Van Der Oost,
M.Jinek.
Structural Basis For Guide Rna Processing and Seed-Dependent Dna Targeting By Crispr-CAS12A. Mol. Cell V. 66 221 2017.
ISSN: ISSN 1097-4164
PubMed: 28431230
DOI: 10.1016/J.MOLCEL.2017.03.016
Page generated: Sun Sep 29 23:16:23 2024
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