Sodium in PDB 7r9x: Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis
Protein crystallography data
The structure of Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis, PDB code: 7r9x
was solved by
C.M.Fortinez,
T.M.Schmeing,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.70 /
2.14
|
Space group
|
I 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.94,
106.87,
108.909,
90,
96.25,
90
|
R / Rfree (%)
|
19 /
23.2
|
Other elements in 7r9x:
The structure of Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis also contains other interesting chemical elements:
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Sodium atom in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis
(pdb code 7r9x). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the
Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis, PDB code: 7r9x:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 12 in 7r9x
Go back to
Sodium Binding Sites List in 7r9x
Sodium binding site 1 out
of 12 in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis
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 Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1804
b:19.8
occ:1.00
|
O
|
A:HOH2086
|
2.1
|
34.5
|
1.0
|
O
|
A:HOH2145
|
2.2
|
39.4
|
1.0
|
O
|
A:HOH2120
|
2.6
|
20.8
|
1.0
|
H
|
A:GLY1502
|
2.9
|
18.4
|
1.0
|
HD21
|
A:ASN1700
|
3.0
|
40.8
|
1.0
|
HA3
|
A:GLY1502
|
3.1
|
26.1
|
1.0
|
HZ
|
A:PHE1704
|
3.4
|
35.9
|
1.0
|
N
|
A:GLY1502
|
3.6
|
15.4
|
1.0
|
HD11
|
A:LEU1648
|
3.7
|
23.6
|
1.0
|
CA
|
A:GLY1502
|
3.8
|
21.8
|
1.0
|
ND2
|
A:ASN1700
|
3.9
|
34.1
|
1.0
|
HB2
|
A:ASP1501
|
3.9
|
20.1
|
1.0
|
HD21
|
A:LEU1648
|
3.9
|
25.4
|
1.0
|
H
|
A:TRP1503
|
3.9
|
23.0
|
1.0
|
HG22
|
A:VAL1702
|
4.0
|
43.7
|
1.0
|
CZ
|
A:PHE1704
|
4.3
|
30.0
|
1.0
|
HD13
|
A:LEU1648
|
4.3
|
23.6
|
1.0
|
OD1
|
A:ASN1700
|
4.3
|
35.9
|
1.0
|
HD22
|
A:ASN1700
|
4.4
|
40.8
|
1.0
|
CD1
|
A:LEU1648
|
4.4
|
19.7
|
1.0
|
N
|
A:TRP1503
|
4.4
|
19.3
|
1.0
|
HD22
|
A:LEU1648
|
4.6
|
25.4
|
1.0
|
CG
|
A:ASN1700
|
4.6
|
38.3
|
1.0
|
C
|
A:GLY1502
|
4.6
|
20.5
|
1.0
|
HA2
|
A:GLY1502
|
4.6
|
26.1
|
1.0
|
CD2
|
A:LEU1648
|
4.6
|
21.3
|
1.0
|
HE2
|
A:PHE1704
|
4.7
|
39.4
|
1.0
|
HG21
|
A:VAL1702
|
4.7
|
43.7
|
1.0
|
O
|
A:HOH2200
|
4.7
|
26.9
|
1.0
|
CG2
|
A:VAL1702
|
4.8
|
36.5
|
1.0
|
C
|
A:ASP1501
|
4.8
|
18.8
|
1.0
|
CB
|
A:ASP1501
|
4.8
|
16.8
|
1.0
|
CE2
|
A:PHE1704
|
5.0
|
32.9
|
1.0
|
|
Sodium binding site 2 out
of 12 in 7r9x
Go back to
Sodium Binding Sites List in 7r9x
Sodium binding site 2 out
of 12 in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis
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 Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1805
b:40.4
occ:1.00
|
H
|
A:VAL1724
|
2.5
|
31.4
|
1.0
|
HH22
|
A:ARG1458
|
2.5
|
62.3
|
1.0
|
HA
|
A:VAL1723
|
2.8
|
35.9
|
1.0
|
NH2
|
A:ARG1458
|
3.2
|
52.0
|
1.0
|
HG23
|
A:VAL1724
|
3.3
|
41.2
|
1.0
|
N
|
A:VAL1724
|
3.3
|
26.2
|
1.0
|
HH21
|
A:ARG1458
|
3.4
|
62.3
|
1.0
|
HB
|
A:VAL1723
|
3.5
|
37.6
|
1.0
|
CA
|
A:VAL1723
|
3.6
|
30.0
|
1.0
|
HG12
|
A:VAL1723
|
3.7
|
47.6
|
1.0
|
O
|
A:HOH2073
|
3.7
|
46.9
|
1.0
|
HB
|
A:VAL1724
|
3.9
|
36.0
|
1.0
|
CB
|
A:VAL1723
|
3.9
|
31.4
|
1.0
|
C
|
A:VAL1723
|
3.9
|
29.2
|
1.0
|
HH12
|
A:ARG1458
|
4.0
|
45.0
|
1.0
|
O
|
A:HOH1936
|
4.1
|
44.3
|
1.0
|
CZ
|
A:ARG1458
|
4.1
|
49.1
|
1.0
|
CG2
|
A:VAL1724
|
4.2
|
34.5
|
1.0
|
CB
|
A:VAL1724
|
4.3
|
30.1
|
1.0
|
CA
|
A:VAL1724
|
4.3
|
26.7
|
1.0
|
CG1
|
A:VAL1723
|
4.3
|
39.8
|
1.0
|
O
|
A:GLN1722
|
4.4
|
28.9
|
1.0
|
NH1
|
A:ARG1458
|
4.4
|
37.6
|
1.0
|
O
|
A:VAL1724
|
4.5
|
30.8
|
1.0
|
HG22
|
A:VAL1724
|
4.7
|
41.2
|
1.0
|
HG21
|
A:VAL1724
|
4.7
|
41.2
|
1.0
|
N
|
A:VAL1723
|
4.7
|
25.4
|
1.0
|
C
|
A:VAL1724
|
4.8
|
25.6
|
1.0
|
HG11
|
A:VAL1723
|
4.9
|
47.6
|
1.0
|
HE22
|
A:GLN1465
|
4.9
|
43.0
|
1.0
|
C
|
A:GLN1722
|
5.0
|
22.0
|
1.0
|
HG13
|
A:VAL1723
|
5.0
|
47.6
|
1.0
|
|
Sodium binding site 3 out
of 12 in 7r9x
Go back to
Sodium Binding Sites List in 7r9x
Sodium binding site 3 out
of 12 in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis
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 Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1806
b:30.8
occ:1.00
|
H
|
A:ASP1584
|
2.6
|
44.6
|
1.0
|
HB3
|
A:ASP1584
|
3.0
|
49.4
|
1.0
|
HB1
|
A:ALA1762
|
3.2
|
34.8
|
1.0
|
HG13
|
A:VAL1583
|
3.4
|
32.1
|
1.0
|
HB2
|
A:ARG1766
|
3.4
|
38.6
|
1.0
|
N
|
A:ASP1584
|
3.4
|
37.3
|
1.0
|
HA
|
A:VAL1583
|
3.5
|
35.1
|
1.0
|
HB2
|
A:ASP1584
|
3.5
|
49.4
|
1.0
|
O
|
A:ALA1762
|
3.5
|
25.1
|
1.0
|
HA2
|
A:GLY1763
|
3.6
|
29.6
|
1.0
|
CB
|
A:ASP1584
|
3.6
|
41.3
|
1.0
|
C
|
A:ALA1762
|
3.8
|
32.1
|
1.0
|
HB3
|
A:ALA1762
|
3.8
|
34.8
|
1.0
|
CB
|
A:ALA1762
|
3.9
|
29.1
|
1.0
|
HB3
|
A:ARG1766
|
4.0
|
38.6
|
1.0
|
HD2
|
A:ARG1766
|
4.0
|
45.2
|
1.0
|
N
|
A:GLY1763
|
4.1
|
37.2
|
1.0
|
CA
|
A:ASP1584
|
4.1
|
34.9
|
1.0
|
CB
|
A:ARG1766
|
4.1
|
32.2
|
1.0
|
CA
|
A:VAL1583
|
4.3
|
29.4
|
1.0
|
CG1
|
A:VAL1583
|
4.3
|
26.9
|
1.0
|
HD3
|
A:ARG1766
|
4.3
|
45.2
|
1.0
|
CA
|
A:GLY1763
|
4.3
|
24.8
|
1.0
|
C
|
A:VAL1583
|
4.4
|
31.8
|
1.0
|
CA
|
A:ALA1762
|
4.5
|
24.4
|
1.0
|
H
|
A:GLY1763
|
4.6
|
44.5
|
1.0
|
CD
|
A:ARG1766
|
4.6
|
37.8
|
1.0
|
HG12
|
A:VAL1583
|
4.6
|
32.1
|
1.0
|
H
|
A:ARG1766
|
4.6
|
28.1
|
1.0
|
HB2
|
A:ALA1762
|
4.7
|
34.8
|
1.0
|
HG22
|
A:VAL1583
|
4.7
|
29.7
|
1.0
|
O
|
A:ARG1582
|
4.8
|
31.5
|
1.0
|
O
|
A:ASP1584
|
4.8
|
32.6
|
1.0
|
HA
|
A:ALA1762
|
4.8
|
29.2
|
1.0
|
CB
|
A:VAL1583
|
4.8
|
27.9
|
1.0
|
C
|
A:ASP1584
|
4.9
|
27.3
|
1.0
|
HA3
|
A:GLY1763
|
4.9
|
29.6
|
1.0
|
HA
|
A:ASP1584
|
4.9
|
41.8
|
1.0
|
HG11
|
A:VAL1583
|
4.9
|
32.1
|
1.0
|
CG
|
A:ASP1584
|
4.9
|
43.0
|
1.0
|
CG
|
A:ARG1766
|
5.0
|
35.6
|
1.0
|
|
Sodium binding site 4 out
of 12 in 7r9x
Go back to
Sodium Binding Sites List in 7r9x
Sodium binding site 4 out
of 12 in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis
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 Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1807
b:31.1
occ:1.00
|
HE1
|
A:HIS1389
|
3.0
|
21.1
|
1.0
|
O
|
A:HOH2064
|
3.1
|
18.4
|
1.0
|
O
|
A:HOH1983
|
3.4
|
23.9
|
1.0
|
HG
|
A:LEU1505
|
3.4
|
29.4
|
1.0
|
HD23
|
A:LEU1505
|
3.6
|
37.2
|
1.0
|
O
|
A:HOH2030
|
3.7
|
48.3
|
1.0
|
CE1
|
A:HIS1389
|
3.8
|
17.7
|
1.0
|
HG11
|
A:VAL1387
|
3.8
|
25.0
|
1.0
|
O
|
A:HOH2062
|
3.9
|
31.7
|
1.0
|
HG21
|
A:VAL1387
|
4.0
|
30.9
|
1.0
|
HD21
|
A:LEU1505
|
4.0
|
37.2
|
1.0
|
HD11
|
A:ILE1719
|
4.0
|
50.5
|
1.0
|
CD2
|
A:LEU1505
|
4.1
|
31.1
|
1.0
|
CG
|
A:LEU1505
|
4.1
|
24.6
|
1.0
|
OE1
|
A:GLN1506
|
4.2
|
61.5
|
1.0
|
NE2
|
A:HIS1389
|
4.2
|
20.8
|
1.0
|
HB3
|
A:LEU1505
|
4.3
|
20.6
|
1.0
|
O
|
A:HOH2189
|
4.6
|
37.0
|
1.0
|
HG21
|
A:VAL1509
|
4.6
|
18.6
|
1.0
|
HA
|
A:GLN1506
|
4.6
|
19.7
|
1.0
|
HD13
|
A:ILE1719
|
4.6
|
50.5
|
1.0
|
CG1
|
A:VAL1387
|
4.8
|
20.9
|
1.0
|
CD1
|
A:ILE1719
|
4.8
|
42.2
|
1.0
|
CB
|
A:LEU1505
|
4.8
|
17.3
|
1.0
|
HE22
|
A:GLN1506
|
4.9
|
61.5
|
1.0
|
CG2
|
A:VAL1387
|
4.9
|
25.9
|
1.0
|
HB
|
A:VAL1387
|
4.9
|
22.7
|
1.0
|
CD
|
A:GLN1506
|
4.9
|
51.0
|
1.0
|
ND1
|
A:HIS1389
|
5.0
|
22.0
|
1.0
|
HB2
|
A:GLN1506
|
5.0
|
27.2
|
1.0
|
|
Sodium binding site 5 out
of 12 in 7r9x
Go back to
Sodium Binding Sites List in 7r9x
Sodium binding site 5 out
of 12 in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis
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 Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1808
b:25.5
occ:1.00
|
H
|
A:LEU1742
|
2.5
|
31.2
|
1.0
|
H
|
A:LEU1590
|
2.6
|
28.9
|
1.0
|
H
|
A:SER1589
|
3.0
|
35.0
|
1.0
|
HA
|
A:ARG1741
|
3.0
|
47.1
|
1.0
|
N
|
A:LEU1742
|
3.4
|
26.1
|
1.0
|
N
|
A:SER1589
|
3.5
|
29.3
|
1.0
|
HB2
|
A:SER1589
|
3.5
|
38.0
|
1.0
|
N
|
A:LEU1590
|
3.5
|
24.2
|
1.0
|
HB2
|
A:LEU1590
|
3.5
|
28.8
|
1.0
|
HA
|
A:ASP1588
|
3.6
|
32.0
|
1.0
|
HB3
|
A:LEU1742
|
3.6
|
28.1
|
1.0
|
HB3
|
A:LEU1590
|
3.7
|
28.8
|
1.0
|
O
|
A:ALA1587
|
3.7
|
54.6
|
1.0
|
CA
|
A:ARG1741
|
3.8
|
39.3
|
1.0
|
C
|
A:ASP1588
|
3.9
|
30.4
|
1.0
|
CB
|
A:LEU1590
|
4.0
|
24.1
|
1.0
|
HB3
|
A:ARG1741
|
4.0
|
51.8
|
1.0
|
C
|
A:ARG1741
|
4.1
|
38.5
|
1.0
|
HG12
|
A:VAL1585
|
4.1
|
34.8
|
1.0
|
CA
|
A:SER1589
|
4.2
|
33.0
|
1.0
|
CA
|
A:ASP1588
|
4.2
|
26.8
|
1.0
|
CB
|
A:SER1589
|
4.3
|
31.8
|
1.0
|
O
|
A:GLU1740
|
4.3
|
37.8
|
1.0
|
CB
|
A:LEU1742
|
4.3
|
23.5
|
1.0
|
HG2
|
A:ARG1741
|
4.3
|
69.4
|
1.0
|
C
|
A:SER1589
|
4.3
|
21.0
|
1.0
|
CA
|
A:LEU1742
|
4.4
|
30.6
|
1.0
|
O
|
A:LEU1742
|
4.4
|
32.0
|
1.0
|
CA
|
A:LEU1590
|
4.4
|
23.8
|
1.0
|
CB
|
A:ARG1741
|
4.4
|
43.2
|
1.0
|
O
|
A:PRO1586
|
4.5
|
37.3
|
1.0
|
HG11
|
A:VAL1585
|
4.5
|
34.8
|
1.0
|
C
|
A:ALA1587
|
4.5
|
47.6
|
1.0
|
HB2
|
A:LEU1742
|
4.6
|
28.1
|
1.0
|
O
|
A:ASP1588
|
4.6
|
32.7
|
1.0
|
H
|
A:SER1591
|
4.7
|
29.4
|
1.0
|
N
|
A:ASP1588
|
4.8
|
33.5
|
1.0
|
CG1
|
A:VAL1585
|
4.8
|
29.1
|
1.0
|
C
|
A:LEU1742
|
4.8
|
28.8
|
1.0
|
HB3
|
A:SER1589
|
4.9
|
38.0
|
1.0
|
N
|
A:ARG1741
|
4.9
|
37.0
|
1.0
|
CG
|
A:ARG1741
|
4.9
|
57.9
|
1.0
|
HA
|
A:LEU1590
|
4.9
|
28.5
|
1.0
|
HG
|
A:SER1589
|
5.0
|
31.6
|
1.0
|
|
Sodium binding site 6 out
of 12 in 7r9x
Go back to
Sodium Binding Sites List in 7r9x
Sodium binding site 6 out
of 12 in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis
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 Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1809
b:31.7
occ:1.00
|
HA
|
A:PHE1619
|
2.9
|
30.7
|
1.0
|
HB2
|
A:ALA1764
|
3.1
|
28.0
|
1.0
|
O
|
A:HOH1962
|
3.5
|
24.6
|
1.0
|
HB3
|
A:ARG1618
|
3.6
|
29.5
|
1.0
|
CA
|
A:PHE1619
|
3.7
|
25.6
|
1.0
|
N
|
A:PHE1619
|
3.8
|
30.3
|
1.0
|
HB2
|
A:PHE1619
|
3.9
|
28.5
|
1.0
|
CB
|
A:ALA1764
|
4.0
|
23.4
|
1.0
|
C
|
A:ARG1618
|
4.0
|
30.5
|
1.0
|
HB1
|
A:ALA1764
|
4.1
|
28.0
|
1.0
|
O
|
A:ARG1618
|
4.1
|
32.3
|
1.0
|
H
|
A:PHE1619
|
4.1
|
36.2
|
1.0
|
HD2
|
A:PHE1619
|
4.2
|
32.5
|
1.0
|
HB2
|
A:ARG1618
|
4.3
|
29.5
|
1.0
|
CB
|
A:PHE1619
|
4.3
|
23.9
|
1.0
|
CB
|
A:ARG1618
|
4.3
|
24.6
|
1.0
|
HA
|
A:ALA1764
|
4.4
|
27.6
|
1.0
|
HB3
|
A:ALA1764
|
4.7
|
28.0
|
1.0
|
CA
|
A:ALA1764
|
4.7
|
23.1
|
1.0
|
CA
|
A:ARG1618
|
4.9
|
27.9
|
1.0
|
OE1
|
A:GLU1767
|
4.9
|
61.1
|
1.0
|
C
|
A:PHE1619
|
4.9
|
27.2
|
1.0
|
CD2
|
A:PHE1619
|
4.9
|
27.2
|
1.0
|
O
|
A:ALA1760
|
4.9
|
31.3
|
1.0
|
H
|
A:ALA1764
|
4.9
|
30.3
|
1.0
|
|
Sodium binding site 7 out
of 12 in 7r9x
Go back to
Sodium Binding Sites List in 7r9x
Sodium binding site 7 out
of 12 in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis
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 Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1803
b:48.0
occ:1.00
|
O
|
B:HOH2061
|
2.2
|
48.3
|
1.0
|
HA
|
B:PRO1380
|
3.2
|
50.6
|
1.0
|
O
|
B:HOH2000
|
3.5
|
35.6
|
1.0
|
O
|
B:GLY1378
|
3.6
|
56.0
|
1.0
|
C
|
B:GLY1378
|
3.9
|
45.3
|
1.0
|
HB3
|
B:PRO1380
|
3.9
|
55.6
|
1.0
|
N
|
B:PRO1380
|
3.9
|
41.9
|
1.0
|
HA2
|
B:GLY1378
|
3.9
|
57.5
|
1.0
|
CA
|
B:PRO1380
|
3.9
|
42.2
|
1.0
|
HD3
|
B:PRO1380
|
4.0
|
54.1
|
1.0
|
O
|
B:SER1374
|
4.0
|
55.8
|
1.0
|
HB3
|
B:PRO1468
|
4.0
|
48.0
|
1.0
|
C
|
B:ASP1379
|
4.1
|
38.5
|
1.0
|
O
|
B:HOH1991
|
4.1
|
38.7
|
1.0
|
O
|
B:ASP1379
|
4.2
|
46.4
|
1.0
|
HB3
|
B:SER1374
|
4.3
|
59.0
|
1.0
|
N
|
B:ASP1379
|
4.3
|
45.7
|
1.0
|
CB
|
B:PRO1380
|
4.4
|
46.4
|
1.0
|
HE1
|
B:TRP1471
|
4.4
|
56.4
|
1.0
|
CA
|
B:GLY1378
|
4.5
|
48.0
|
1.0
|
CD
|
B:PRO1380
|
4.5
|
45.2
|
1.0
|
HZ2
|
B:TRP1471
|
4.6
|
51.9
|
1.0
|
O
|
B:HOH2010
|
4.6
|
29.5
|
1.0
|
HB2
|
B:PRO1468
|
4.6
|
48.0
|
1.0
|
H
|
B:ASP1379
|
4.6
|
54.8
|
1.0
|
HA
|
B:GLU1375
|
4.7
|
59.0
|
1.0
|
CB
|
B:PRO1468
|
4.8
|
40.0
|
1.0
|
CA
|
B:ASP1379
|
4.8
|
46.7
|
1.0
|
C
|
B:SER1374
|
4.9
|
51.6
|
1.0
|
|
Sodium binding site 8 out
of 12 in 7r9x
Go back to
Sodium Binding Sites List in 7r9x
Sodium binding site 8 out
of 12 in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis
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 Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1804
b:22.5
occ:1.00
|
HH21
|
B:ARG1402
|
2.4
|
70.9
|
1.0
|
HH22
|
B:ARG1402
|
2.5
|
70.9
|
1.0
|
H
|
B:ALA1525
|
2.7
|
41.9
|
1.0
|
NH2
|
B:ARG1402
|
2.7
|
59.2
|
1.0
|
HB2
|
B:ALA1525
|
3.3
|
41.5
|
1.0
|
HD21
|
B:LEU1519
|
3.5
|
57.4
|
1.0
|
HB3
|
B:ALA1525
|
3.5
|
41.5
|
1.0
|
HG13
|
B:VAL1524
|
3.5
|
44.9
|
1.0
|
HA
|
B:VAL1524
|
3.5
|
47.8
|
1.0
|
N
|
B:ALA1525
|
3.5
|
35.0
|
1.0
|
CB
|
B:ALA1525
|
3.8
|
34.7
|
1.0
|
CZ
|
B:ARG1402
|
4.0
|
66.9
|
1.0
|
HD23
|
B:LEU1519
|
4.1
|
57.4
|
1.0
|
HD13
|
B:ILE1406
|
4.1
|
47.4
|
1.0
|
CD2
|
B:LEU1519
|
4.1
|
47.9
|
1.0
|
HD11
|
B:ILE1406
|
4.1
|
47.4
|
1.0
|
HD22
|
B:LEU1519
|
4.3
|
57.4
|
1.0
|
CA
|
B:ALA1525
|
4.3
|
40.0
|
1.0
|
CA
|
B:VAL1524
|
4.3
|
39.9
|
1.0
|
C
|
B:VAL1524
|
4.4
|
30.6
|
1.0
|
CG1
|
B:VAL1524
|
4.5
|
37.5
|
1.0
|
HG22
|
B:VAL1524
|
4.5
|
49.7
|
1.0
|
HE
|
B:ARG1402
|
4.6
|
85.8
|
1.0
|
CD1
|
B:ILE1406
|
4.6
|
39.5
|
1.0
|
O
|
B:HOH1904
|
4.7
|
45.8
|
1.0
|
HB1
|
B:ALA1525
|
4.7
|
41.5
|
1.0
|
HH12
|
B:ARG1402
|
4.7
|
74.8
|
1.0
|
NE
|
B:ARG1402
|
4.8
|
71.6
|
1.0
|
HG12
|
B:VAL1524
|
4.8
|
44.9
|
1.0
|
NH1
|
B:ARG1402
|
4.8
|
62.4
|
1.0
|
HA
|
B:ALA1525
|
4.9
|
47.9
|
1.0
|
CB
|
B:VAL1524
|
4.9
|
36.8
|
1.0
|
|
Sodium binding site 9 out
of 12 in 7r9x
Go back to
Sodium Binding Sites List in 7r9x
Sodium binding site 9 out
of 12 in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis
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 Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1805
b:19.1
occ:1.00
|
O
|
B:HOH2026
|
2.6
|
28.9
|
1.0
|
HD3
|
B:ARG1543
|
2.9
|
37.6
|
1.0
|
HA
|
B:ALA1540
|
3.1
|
34.6
|
1.0
|
HG2
|
B:PRO1362
|
3.2
|
39.4
|
1.0
|
O
|
B:HOH2022
|
3.3
|
32.5
|
1.0
|
HG12
|
B:VAL1539
|
3.3
|
33.8
|
1.0
|
HB2
|
B:ALA1540
|
3.4
|
29.5
|
1.0
|
HD2
|
B:PRO1362
|
3.7
|
46.5
|
1.0
|
CD
|
B:ARG1543
|
3.8
|
31.4
|
1.0
|
HG3
|
B:PRO1362
|
3.8
|
39.4
|
1.0
|
HE
|
B:ARG1543
|
3.8
|
41.8
|
1.0
|
CA
|
B:ALA1540
|
3.8
|
29.0
|
1.0
|
CG
|
B:PRO1362
|
3.8
|
32.9
|
1.0
|
O
|
B:HOH2018
|
3.9
|
33.6
|
1.0
|
CB
|
B:ALA1540
|
4.0
|
24.7
|
1.0
|
HD2
|
B:ARG1543
|
4.1
|
37.6
|
1.0
|
N
|
B:ALA1540
|
4.1
|
23.1
|
1.0
|
NE
|
B:ARG1543
|
4.2
|
34.9
|
1.0
|
CG1
|
B:VAL1539
|
4.3
|
28.3
|
1.0
|
CD
|
B:PRO1362
|
4.3
|
38.8
|
1.0
|
HB1
|
B:ALA1540
|
4.3
|
29.5
|
1.0
|
HB2
|
B:ARG1543
|
4.3
|
31.4
|
1.0
|
H
|
B:ALA1540
|
4.4
|
27.6
|
1.0
|
HG11
|
B:VAL1539
|
4.4
|
33.8
|
1.0
|
C
|
B:VAL1539
|
4.5
|
26.8
|
1.0
|
O
|
B:VAL1539
|
4.5
|
23.4
|
1.0
|
HB
|
B:VAL1539
|
4.6
|
29.8
|
1.0
|
HD3
|
B:PRO1362
|
4.7
|
46.5
|
1.0
|
HB2
|
B:TYR1361
|
4.8
|
42.4
|
1.0
|
O
|
B:HOH1984
|
4.8
|
33.0
|
1.0
|
HG13
|
B:VAL1539
|
4.9
|
33.8
|
1.0
|
CG
|
B:ARG1543
|
4.9
|
38.7
|
1.0
|
HB3
|
B:ALA1540
|
4.9
|
29.5
|
1.0
|
CB
|
B:VAL1539
|
5.0
|
24.9
|
1.0
|
CB
|
B:ARG1543
|
5.0
|
26.3
|
1.0
|
|
Sodium binding site 10 out
of 12 in 7r9x
Go back to
Sodium Binding Sites List in 7r9x
Sodium binding site 10 out
of 12 in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1806
b:41.2
occ:1.00
|
H
|
B:ASP1584
|
2.5
|
49.2
|
1.0
|
HB3
|
B:ASP1584
|
2.9
|
57.8
|
1.0
|
O
|
B:HOH1906
|
3.0
|
48.8
|
1.0
|
HB2
|
B:ASP1584
|
3.1
|
57.8
|
1.0
|
N
|
B:ASP1584
|
3.3
|
41.1
|
1.0
|
HB1
|
B:ALA1762
|
3.4
|
53.3
|
1.0
|
CB
|
B:ASP1584
|
3.4
|
48.2
|
1.0
|
HA2
|
B:GLY1763
|
3.5
|
45.4
|
1.0
|
HG13
|
B:VAL1583
|
3.6
|
41.1
|
1.0
|
HA
|
B:VAL1583
|
3.6
|
53.7
|
1.0
|
O
|
B:ALA1762
|
3.7
|
37.1
|
1.0
|
HB2
|
B:ARG1766
|
3.7
|
49.6
|
1.0
|
C
|
B:ALA1762
|
3.9
|
39.0
|
1.0
|
HB3
|
B:ALA1762
|
3.9
|
53.3
|
1.0
|
CA
|
B:ASP1584
|
3.9
|
44.2
|
1.0
|
CB
|
B:ALA1762
|
4.0
|
44.5
|
1.0
|
N
|
B:GLY1763
|
4.1
|
41.9
|
1.0
|
HD2
|
B:ARG1766
|
4.2
|
47.6
|
1.0
|
CA
|
B:GLY1763
|
4.2
|
37.9
|
1.0
|
HB3
|
B:ARG1766
|
4.3
|
49.6
|
1.0
|
C
|
B:VAL1583
|
4.3
|
36.8
|
1.0
|
CA
|
B:VAL1583
|
4.4
|
44.8
|
1.0
|
CB
|
B:ARG1766
|
4.4
|
41.4
|
1.0
|
H
|
B:GLY1763
|
4.5
|
50.2
|
1.0
|
CG1
|
B:VAL1583
|
4.6
|
34.4
|
1.0
|
CA
|
B:ALA1762
|
4.6
|
48.4
|
1.0
|
HA
|
B:ASP1584
|
4.7
|
52.9
|
1.0
|
O
|
B:ASP1584
|
4.7
|
31.7
|
1.0
|
HA3
|
B:GLY1763
|
4.7
|
45.4
|
1.0
|
C
|
B:ASP1584
|
4.8
|
29.7
|
1.0
|
CG
|
B:ASP1584
|
4.8
|
46.6
|
1.0
|
H
|
B:ARG1766
|
4.8
|
40.3
|
1.0
|
HB2
|
B:ALA1762
|
4.8
|
53.3
|
1.0
|
O
|
B:ARG1582
|
4.9
|
38.2
|
1.0
|
HG22
|
B:VAL1583
|
4.9
|
40.1
|
1.0
|
CD
|
B:ARG1766
|
4.9
|
39.8
|
1.0
|
HG12
|
B:VAL1583
|
4.9
|
41.1
|
1.0
|
HD3
|
B:ARG1766
|
4.9
|
47.6
|
1.0
|
HA
|
B:ALA1762
|
5.0
|
57.9
|
1.0
|
|
Reference:
J.B.Patteson,
C.M.Fortinez,
A.T.Putz,
J.Rodriguez-Rivas,
L.H.Bryant 3Rd,
K.Adhikari,
M.Weigt,
T.M.Schmeing,
B.Li.
Structure and Function of A Dehydrating Condensation Domain in Nonribosomal Peptide Biosynthesis. J.Am.Chem.Soc. V. 144 14057 2022.
ISSN: ESSN 1520-5126
PubMed: 35895935
DOI: 10.1021/JACS.1C13404
Page generated: Wed Oct 9 08:28:15 2024
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