Magnesium in PDB 7ljn: Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp
Protein crystallography data
The structure of Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp, PDB code: 7ljn
was solved by
A.Govande,
B.Lowey,
J.B.Eaglesham,
A.T.Whiteley,
P.J.Kranzusch,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.94 /
1.60
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
111.996,
68.687,
112.432,
90,
108.41,
90
|
R / Rfree (%)
|
19.7 /
21.8
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp
(pdb code 7ljn). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp, PDB code: 7ljn:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7ljn
Go back to
Magnesium Binding Sites List in 7ljn
Magnesium binding site 1 out
of 4 in the Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:13.0
occ:1.00
|
O
|
A:HOH737
|
2.0
|
14.0
|
1.0
|
O
|
A:HOH685
|
2.1
|
12.3
|
1.0
|
O1A
|
A:GTP501
|
2.1
|
11.2
|
1.0
|
O3G
|
A:GTP501
|
2.1
|
13.8
|
1.0
|
O2B
|
A:GTP501
|
2.1
|
11.4
|
1.0
|
OD2
|
A:ASP91
|
2.1
|
13.6
|
1.0
|
CG
|
A:ASP91
|
3.1
|
13.9
|
1.0
|
PB
|
A:GTP501
|
3.1
|
12.4
|
1.0
|
PG
|
A:GTP501
|
3.3
|
12.1
|
1.0
|
PA
|
A:GTP501
|
3.3
|
13.7
|
1.0
|
OD1
|
A:ASP91
|
3.4
|
16.3
|
1.0
|
O3B
|
A:GTP501
|
3.4
|
11.9
|
1.0
|
O3A
|
A:GTP501
|
3.5
|
11.6
|
1.0
|
O
|
A:HOH761
|
3.8
|
19.5
|
1.0
|
O1G
|
A:GTP501
|
4.0
|
12.5
|
1.0
|
O
|
A:HOH673
|
4.0
|
13.6
|
1.0
|
O
|
A:HOH699
|
4.2
|
13.4
|
1.0
|
OG
|
A:SER72
|
4.2
|
12.9
|
1.0
|
O5'
|
A:GTP501
|
4.2
|
12.6
|
1.0
|
O
|
A:ASP89
|
4.2
|
19.9
|
1.0
|
C5'
|
A:GTP501
|
4.3
|
14.0
|
1.0
|
O2A
|
A:GTP501
|
4.4
|
14.5
|
1.0
|
O2G
|
A:GTP501
|
4.4
|
13.2
|
1.0
|
N
|
A:SER72
|
4.5
|
13.1
|
1.0
|
CB
|
A:ASP91
|
4.5
|
12.0
|
1.0
|
O1B
|
A:GTP501
|
4.5
|
13.6
|
1.0
|
O
|
A:HOH862
|
4.5
|
29.2
|
1.0
|
O
|
A:HOH668
|
4.6
|
14.9
|
1.0
|
CB
|
A:SER72
|
4.7
|
9.7
|
1.0
|
O
|
A:HOH983
|
4.8
|
27.9
|
1.0
|
N
|
A:ASP91
|
5.0
|
13.5
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7ljn
Go back to
Magnesium Binding Sites List in 7ljn
Magnesium binding site 2 out
of 4 in the Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:12.6
occ:1.00
|
O1A
|
B:GTP501
|
2.0
|
11.8
|
1.0
|
O3G
|
B:GTP501
|
2.1
|
11.2
|
1.0
|
O
|
B:HOH744
|
2.1
|
12.3
|
1.0
|
O1B
|
B:GTP501
|
2.1
|
11.3
|
1.0
|
O
|
B:HOH643
|
2.1
|
14.2
|
1.0
|
OD2
|
B:ASP91
|
2.2
|
14.7
|
1.0
|
PB
|
B:GTP501
|
3.1
|
11.7
|
1.0
|
CG
|
B:ASP91
|
3.1
|
16.2
|
1.0
|
PG
|
B:GTP501
|
3.2
|
11.0
|
1.0
|
PA
|
B:GTP501
|
3.3
|
12.3
|
1.0
|
O3B
|
B:GTP501
|
3.4
|
9.9
|
1.0
|
OD1
|
B:ASP91
|
3.5
|
19.4
|
1.0
|
O3A
|
B:GTP501
|
3.5
|
11.4
|
1.0
|
O1G
|
B:GTP501
|
4.0
|
12.8
|
1.0
|
O
|
B:ASP89
|
4.0
|
23.3
|
1.0
|
O
|
B:HOH910
|
4.0
|
22.2
|
1.0
|
O
|
B:HOH688
|
4.1
|
14.3
|
1.0
|
OG
|
B:SER72
|
4.2
|
12.7
|
1.0
|
O
|
B:HOH693
|
4.2
|
11.7
|
1.0
|
O5'
|
B:GTP501
|
4.2
|
13.2
|
1.0
|
C5'
|
B:GTP501
|
4.3
|
12.7
|
1.0
|
O
|
B:HOH894
|
4.3
|
36.9
|
1.0
|
O2G
|
B:GTP501
|
4.4
|
12.7
|
1.0
|
O2A
|
B:GTP501
|
4.4
|
14.6
|
1.0
|
N
|
B:SER72
|
4.4
|
10.5
|
1.0
|
O2B
|
B:GTP501
|
4.5
|
11.8
|
1.0
|
CB
|
B:ASP91
|
4.5
|
11.0
|
1.0
|
O
|
B:HOH685
|
4.6
|
12.4
|
1.0
|
CB
|
B:SER72
|
4.7
|
13.1
|
1.0
|
O
|
B:HOH1040
|
4.9
|
22.7
|
1.0
|
C
|
B:ASP89
|
5.0
|
18.7
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7ljn
Go back to
Magnesium Binding Sites List in 7ljn
Magnesium binding site 3 out
of 4 in the Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg502
b:11.4
occ:1.00
|
O2G
|
C:GTP501
|
2.0
|
10.8
|
1.0
|
O1A
|
C:GTP501
|
2.1
|
13.9
|
1.0
|
O
|
C:HOH727
|
2.1
|
14.4
|
1.0
|
O
|
C:HOH679
|
2.1
|
13.0
|
1.0
|
O2B
|
C:GTP501
|
2.1
|
12.7
|
1.0
|
OD2
|
C:ASP91
|
2.1
|
13.9
|
1.0
|
CG
|
C:ASP91
|
3.1
|
12.7
|
1.0
|
PB
|
C:GTP501
|
3.1
|
12.4
|
1.0
|
PG
|
C:GTP501
|
3.2
|
12.2
|
1.0
|
PA
|
C:GTP501
|
3.3
|
11.0
|
1.0
|
OD1
|
C:ASP91
|
3.4
|
17.2
|
1.0
|
O3B
|
C:GTP501
|
3.5
|
11.5
|
1.0
|
O3A
|
C:GTP501
|
3.6
|
12.8
|
1.0
|
O
|
C:HOH830
|
3.9
|
23.7
|
1.0
|
O3G
|
C:GTP501
|
4.0
|
15.4
|
1.0
|
O
|
C:HOH785
|
4.1
|
15.9
|
1.0
|
O
|
C:ASP89
|
4.1
|
23.6
|
1.0
|
O
|
C:HOH713
|
4.2
|
12.2
|
1.0
|
OG
|
C:SER72
|
4.2
|
10.2
|
1.0
|
O5'
|
C:GTP501
|
4.2
|
13.1
|
1.0
|
C5'
|
C:GTP501
|
4.3
|
14.4
|
1.0
|
O1G
|
C:GTP501
|
4.4
|
13.9
|
1.0
|
N
|
C:SER72
|
4.5
|
13.5
|
1.0
|
CB
|
C:ASP91
|
4.5
|
10.8
|
1.0
|
O2A
|
C:GTP501
|
4.5
|
14.6
|
1.0
|
O1B
|
C:GTP501
|
4.5
|
11.3
|
1.0
|
O
|
C:HOH654
|
4.5
|
13.8
|
1.0
|
CB
|
C:SER72
|
4.7
|
13.3
|
1.0
|
O
|
C:HOH931
|
4.7
|
25.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7ljn
Go back to
Magnesium Binding Sites List in 7ljn
Magnesium binding site 4 out
of 4 in the Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg502
b:12.8
occ:1.00
|
O1A
|
D:GTP501
|
2.0
|
13.3
|
1.0
|
O2B
|
D:GTP501
|
2.1
|
11.6
|
1.0
|
O
|
D:HOH743
|
2.1
|
13.4
|
1.0
|
O
|
D:HOH665
|
2.1
|
13.5
|
1.0
|
O1G
|
D:GTP501
|
2.1
|
11.2
|
1.0
|
OD2
|
D:ASP91
|
2.1
|
16.2
|
1.0
|
PB
|
D:GTP501
|
3.1
|
12.5
|
1.0
|
CG
|
D:ASP91
|
3.1
|
17.4
|
1.0
|
PG
|
D:GTP501
|
3.2
|
12.7
|
1.0
|
PA
|
D:GTP501
|
3.3
|
13.1
|
1.0
|
O3B
|
D:GTP501
|
3.4
|
9.6
|
1.0
|
OD1
|
D:ASP91
|
3.5
|
16.4
|
1.0
|
O3A
|
D:GTP501
|
3.5
|
11.1
|
1.0
|
O
|
D:HOH809
|
3.8
|
20.4
|
1.0
|
O
|
D:HOH772
|
3.8
|
46.9
|
1.0
|
O2G
|
D:GTP501
|
4.0
|
12.4
|
1.0
|
O
|
D:HOH711
|
4.1
|
16.6
|
1.0
|
O
|
D:ASP89
|
4.2
|
24.0
|
1.0
|
O
|
D:HOH732
|
4.2
|
13.2
|
1.0
|
O5'
|
D:GTP501
|
4.2
|
13.9
|
1.0
|
C5'
|
D:GTP501
|
4.2
|
14.2
|
1.0
|
OG
|
D:SER72
|
4.3
|
14.3
|
1.0
|
O2A
|
D:GTP501
|
4.3
|
16.8
|
1.0
|
O3G
|
D:GTP501
|
4.4
|
21.4
|
1.0
|
O1B
|
D:GTP501
|
4.5
|
13.2
|
1.0
|
CB
|
D:ASP91
|
4.5
|
14.1
|
1.0
|
N
|
D:SER72
|
4.5
|
13.4
|
1.0
|
O
|
D:HOH708
|
4.7
|
13.6
|
1.0
|
CB
|
D:SER72
|
4.7
|
14.3
|
1.0
|
O
|
D:HOH972
|
4.9
|
30.3
|
1.0
|
CA
|
D:GLY71
|
5.0
|
12.0
|
1.0
|
|
Reference:
A.A.Govande,
B.Duncan-Lowey,
J.B.Eaglesham,
A.T.Whiteley,
P.J.Kranzusch.
Molecular Basis of Cd-Ntase Nucleotide Selection in Cbass Anti-Phage Defense Cell Rep 2021.
ISSN: ESSN 2211-1247
Page generated: Wed Oct 2 23:25:36 2024
|