Sodium in PDB 5u4h: 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid.
Enzymatic activity of 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid.
All present enzymatic activity of 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid.:
2.5.1.7;
Protein crystallography data
The structure of 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid., PDB code: 5u4h
was solved by
G.Minasov,
L.Shuvalova,
O.Kiryukhina,
I.Dubrovska,
S.Grimshaw,
K.Kwon,
W.F.Anderson,
Center For Structural Genomics Of Infectious Diseases(Csgid),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.96 /
1.05
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.289,
70.085,
78.109,
90.00,
110.05,
90.00
|
R / Rfree (%)
|
16.2 /
17.6
|
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Sodium atom in the 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid.
(pdb code 5u4h). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the
1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid., PDB code: 5u4h:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 12 in 5u4h
Go back to
Sodium Binding Sites List in 5u4h
Sodium binding site 1 out
of 12 in the 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na501
b:10.3
occ:1.00
|
O
|
B:HOH841
|
2.3
|
10.6
|
0.4
|
O
|
A:HOH801
|
2.3
|
14.2
|
0.6
|
O
|
B:HOH837
|
2.4
|
10.9
|
1.0
|
O
|
A:HOH852
|
2.4
|
10.4
|
1.0
|
O
|
A:GLU330
|
2.4
|
9.2
|
1.0
|
O
|
B:GLU330
|
2.4
|
9.2
|
1.0
|
O
|
B:HOH841
|
2.5
|
12.6
|
0.6
|
O
|
A:HOH801
|
2.5
|
10.2
|
0.4
|
O
|
A:HOH1073
|
3.0
|
12.3
|
0.4
|
O
|
B:HOH1080
|
3.1
|
8.3
|
0.3
|
C
|
B:GLU330
|
3.5
|
9.3
|
1.0
|
C
|
A:GLU330
|
3.5
|
9.1
|
1.0
|
CE1
|
B:HIS351
|
4.1
|
14.8
|
0.7
|
CB
|
B:GLU330
|
4.2
|
13.4
|
1.0
|
CB
|
A:GLU330
|
4.2
|
13.0
|
1.0
|
O
|
A:HOH1073
|
4.2
|
18.2
|
0.6
|
O
|
B:HOH1080
|
4.2
|
20.1
|
0.7
|
CE1
|
A:HIS351
|
4.2
|
20.3
|
1.0
|
N
|
B:ASN331
|
4.3
|
8.5
|
1.0
|
N
|
A:ASN331
|
4.3
|
8.3
|
1.0
|
CA
|
B:GLU330
|
4.3
|
10.9
|
1.0
|
CA
|
A:GLU330
|
4.3
|
10.7
|
1.0
|
CA
|
B:ASN331
|
4.3
|
7.9
|
1.0
|
CA
|
A:ASN331
|
4.3
|
7.8
|
1.0
|
CB
|
B:ASN331
|
4.5
|
8.5
|
1.0
|
CB
|
A:ASN331
|
4.5
|
8.2
|
1.0
|
OE1
|
A:GLU330
|
4.5
|
22.5
|
1.0
|
OE1
|
B:GLU330
|
4.5
|
22.7
|
1.0
|
OD1
|
B:ASN331
|
4.6
|
9.4
|
1.0
|
OD1
|
A:ASN331
|
4.6
|
9.2
|
1.0
|
O
|
B:HOH611
|
4.9
|
22.6
|
0.7
|
ND1
|
B:HIS351
|
5.0
|
13.8
|
0.7
|
CG
|
B:ASN331
|
5.0
|
8.5
|
1.0
|
NE2
|
B:HIS351
|
5.0
|
15.5
|
0.7
|
CG
|
A:ASN331
|
5.0
|
8.3
|
1.0
|
O
|
A:HOH618
|
5.0
|
19.5
|
0.5
|
O
|
A:HOH1107
|
5.0
|
22.1
|
1.0
|
|
Sodium binding site 2 out
of 12 in 5u4h
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Sodium Binding Sites List in 5u4h
Sodium binding site 2 out
of 12 in the 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na502
b:10.9
occ:1.00
|
O
|
A:HOH1033
|
2.3
|
14.3
|
1.0
|
O
|
A:HOH1042
|
2.3
|
14.8
|
1.0
|
OD1
|
A:ASN23
|
2.4
|
9.1
|
1.0
|
O
|
A:HOH833
|
2.4
|
15.2
|
1.0
|
O
|
A:HOH781
|
2.4
|
10.1
|
1.0
|
CG
|
A:ASN23
|
3.2
|
7.8
|
1.0
|
NZ
|
A:LYS22
|
3.7
|
9.5
|
1.0
|
O1
|
A:FMT508
|
3.7
|
10.5
|
0.8
|
ND2
|
A:ASN23
|
3.8
|
8.7
|
1.0
|
O
|
A:HOH1084
|
3.9
|
13.0
|
1.0
|
O
|
A:HOH1191
|
3.9
|
16.4
|
1.0
|
O
|
A:HOH1110
|
4.1
|
12.9
|
1.0
|
O2
|
A:FMT507
|
4.1
|
8.5
|
1.0
|
O
|
A:HOH674
|
4.2
|
13.8
|
0.7
|
CB
|
A:ASN23
|
4.3
|
7.0
|
1.0
|
C
|
A:FMT507
|
4.4
|
8.9
|
1.0
|
O
|
A:HOH695
|
4.4
|
14.4
|
1.0
|
O
|
A:HOH788
|
4.4
|
13.7
|
1.0
|
O
|
A:HOH674
|
4.5
|
8.7
|
0.3
|
O
|
A:HOH758
|
4.5
|
9.1
|
1.0
|
O
|
A:HOH846
|
4.5
|
13.9
|
1.0
|
O
|
A:HOH625
|
4.7
|
14.2
|
1.0
|
O
|
A:HOH707
|
4.7
|
10.6
|
1.0
|
CE
|
A:LYS22
|
4.8
|
9.5
|
1.0
|
C
|
A:FMT508
|
4.8
|
10.6
|
0.8
|
OD2
|
A:ASP306
|
4.8
|
7.8
|
1.0
|
CA
|
A:ASN23
|
5.0
|
6.8
|
1.0
|
|
Sodium binding site 3 out
of 12 in 5u4h
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Sodium Binding Sites List in 5u4h
Sodium binding site 3 out
of 12 in the 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na503
b:16.8
occ:0.50
|
NA
|
A:NA503
|
0.0
|
16.8
|
0.5
|
NA
|
A:NA503
|
1.8
|
17.6
|
0.5
|
O
|
B:HOH895
|
2.0
|
15.6
|
0.5
|
O
|
B:HOH711
|
2.2
|
18.6
|
1.0
|
O
|
B:HOH1144
|
2.3
|
12.2
|
1.0
|
O
|
B:HOH895
|
2.4
|
13.6
|
0.5
|
O
|
B:ILE346
|
2.4
|
10.3
|
1.0
|
O
|
B:HOH824
|
2.5
|
10.7
|
1.0
|
O
|
A:HOH954
|
2.7
|
27.2
|
1.0
|
C
|
B:ILE346
|
3.6
|
8.7
|
1.0
|
O
|
A:HOH1059
|
3.9
|
25.1
|
1.0
|
N
|
B:ILE346
|
4.0
|
8.8
|
1.0
|
O
|
B:HOH1161
|
4.1
|
24.2
|
1.0
|
O
|
B:HOH1007
|
4.1
|
24.3
|
1.0
|
OG
|
B:SER340
|
4.1
|
9.4
|
1.0
|
O
|
B:HOH960
|
4.3
|
17.0
|
1.0
|
O
|
B:HOH1073
|
4.4
|
22.5
|
1.0
|
OD2
|
A:ASP124
|
4.4
|
17.4
|
1.0
|
CA
|
B:ILE346
|
4.4
|
8.8
|
1.0
|
N
|
B:GLN347
|
4.5
|
8.6
|
1.0
|
OD1
|
A:ASP124
|
4.5
|
15.7
|
1.0
|
CA
|
B:GLN347
|
4.6
|
8.8
|
1.0
|
O
|
B:HOH744
|
4.6
|
34.5
|
1.0
|
O
|
B:HOH1111
|
4.7
|
26.0
|
1.0
|
CG
|
A:ASP124
|
4.9
|
14.5
|
1.0
|
CG
|
A:PRO122
|
4.9
|
15.1
|
1.0
|
OD1
|
B:ASN345
|
4.9
|
13.5
|
1.0
|
CB
|
A:PRO122
|
5.0
|
14.2
|
1.0
|
CB
|
B:SER340
|
5.0
|
8.4
|
1.0
|
C
|
B:ASN345
|
5.0
|
9.4
|
1.0
|
|
Sodium binding site 4 out
of 12 in 5u4h
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Sodium Binding Sites List in 5u4h
Sodium binding site 4 out
of 12 in the 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na503
b:17.6
occ:0.50
|
NA
|
A:NA503
|
0.0
|
17.6
|
0.5
|
NA
|
A:NA503
|
1.8
|
16.8
|
0.5
|
O
|
B:HOH1144
|
2.3
|
12.2
|
1.0
|
OD1
|
A:ASP124
|
2.8
|
15.7
|
1.0
|
O
|
B:HOH711
|
2.8
|
18.6
|
1.0
|
O
|
A:HOH954
|
2.9
|
27.2
|
1.0
|
O
|
B:HOH895
|
3.1
|
15.6
|
0.5
|
O
|
A:HOH1059
|
3.2
|
25.1
|
1.0
|
OD2
|
A:ASP124
|
3.3
|
17.4
|
1.0
|
O
|
B:HOH895
|
3.4
|
13.6
|
0.5
|
O
|
B:HOH1161
|
3.4
|
24.2
|
1.0
|
CG
|
A:ASP124
|
3.5
|
14.5
|
1.0
|
O
|
B:HOH824
|
3.6
|
10.7
|
1.0
|
O
|
B:HOH1111
|
3.8
|
26.0
|
1.0
|
CB
|
A:PRO122
|
3.8
|
14.2
|
1.0
|
CG
|
A:PRO122
|
4.0
|
15.1
|
1.0
|
O
|
A:HOH676
|
4.1
|
27.1
|
1.0
|
O
|
B:ILE346
|
4.2
|
10.3
|
1.0
|
O
|
B:HOH1007
|
4.2
|
24.3
|
1.0
|
O
|
A:HOH1043
|
4.6
|
17.9
|
0.5
|
O
|
B:HOH1073
|
4.7
|
22.5
|
1.0
|
O
|
B:HOH960
|
4.8
|
17.0
|
1.0
|
OG
|
B:SER340
|
4.8
|
9.4
|
1.0
|
O
|
B:HOH744
|
4.9
|
34.5
|
1.0
|
CB
|
A:ASP124
|
5.0
|
12.5
|
1.0
|
|
Sodium binding site 5 out
of 12 in 5u4h
Go back to
Sodium Binding Sites List in 5u4h
Sodium binding site 5 out
of 12 in the 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na504
b:19.1
occ:1.00
|
O
|
A:LYS89
|
2.1
|
7.9
|
0.3
|
O
|
A:HOH623
|
2.3
|
26.3
|
1.0
|
O
|
A:HOH837
|
2.3
|
21.6
|
1.0
|
O
|
A:LYS89
|
2.4
|
12.9
|
0.7
|
O
|
A:HOH932
|
2.6
|
21.3
|
1.0
|
O
|
A:HOH644
|
2.7
|
20.0
|
1.0
|
C
|
A:LYS89
|
3.3
|
7.5
|
0.3
|
C
|
A:LYS89
|
3.5
|
11.1
|
0.7
|
O
|
A:GLY115
|
3.8
|
12.5
|
1.0
|
CA
|
A:THR90
|
3.9
|
8.0
|
0.3
|
N
|
A:THR90
|
4.0
|
7.7
|
0.3
|
C
|
A:THR90
|
4.1
|
8.2
|
0.3
|
O
|
A:HOH613
|
4.3
|
17.7
|
1.0
|
CA
|
A:LYS89
|
4.3
|
10.4
|
0.7
|
O
|
A:THR90
|
4.4
|
11.5
|
0.7
|
O
|
A:THR90
|
4.4
|
8.5
|
0.3
|
O1P
|
A:0V5509
|
4.4
|
9.7
|
1.0
|
CA
|
A:LYS89
|
4.4
|
7.5
|
0.3
|
O3P
|
A:0V5509
|
4.5
|
10.9
|
1.0
|
CG
|
A:LYS89
|
4.5
|
8.4
|
0.3
|
C
|
A:THR90
|
4.5
|
10.4
|
0.7
|
O
|
A:HOH654
|
4.5
|
14.5
|
1.0
|
O
|
B:HOH765
|
4.5
|
14.6
|
0.4
|
N
|
A:THR90
|
4.5
|
11.0
|
0.7
|
N
|
A:MET91
|
4.6
|
8.5
|
0.3
|
O
|
A:HOH646
|
4.6
|
14.4
|
1.0
|
CA
|
A:THR90
|
4.7
|
11.6
|
0.7
|
O
|
A:VAL88
|
4.8
|
6.7
|
0.3
|
CB
|
A:LYS89
|
4.9
|
11.3
|
0.7
|
N
|
A:MET91
|
5.0
|
10.3
|
0.7
|
|
Sodium binding site 6 out
of 12 in 5u4h
Go back to
Sodium Binding Sites List in 5u4h
Sodium binding site 6 out
of 12 in the 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na505
b:24.7
occ:1.00
|
O
|
A:HOH609
|
2.3
|
22.1
|
0.5
|
O
|
A:HOH665
|
2.3
|
22.9
|
1.0
|
O
|
A:HOH1180
|
2.4
|
54.0
|
1.0
|
O
|
A:HOH868
|
2.5
|
28.8
|
1.0
|
O
|
A:HOH820
|
2.5
|
22.1
|
0.5
|
O
|
A:VAL139
|
2.6
|
14.4
|
0.7
|
O
|
A:VAL139
|
2.6
|
10.0
|
0.3
|
C
|
A:VAL139
|
3.6
|
13.1
|
0.7
|
C
|
A:VAL139
|
3.6
|
9.8
|
0.3
|
OE1
|
A:GLU140
|
3.7
|
13.7
|
0.3
|
N
|
A:VAL139
|
3.9
|
10.5
|
0.3
|
CB
|
A:GLU140
|
3.9
|
19.5
|
0.7
|
CA
|
A:VAL139
|
4.2
|
9.8
|
0.3
|
O
|
B:HOH609
|
4.2
|
14.1
|
0.5
|
OE1
|
A:GLU138
|
4.2
|
15.6
|
0.3
|
N
|
A:VAL139
|
4.3
|
15.3
|
0.7
|
CB
|
A:VAL139
|
4.3
|
9.7
|
0.3
|
CA
|
A:GLU140
|
4.3
|
15.9
|
0.7
|
N
|
A:GLU140
|
4.4
|
14.6
|
0.7
|
O
|
B:HOH759
|
4.4
|
18.6
|
1.0
|
O
|
A:HOH965
|
4.4
|
22.6
|
0.7
|
O
|
A:HOH1100
|
4.4
|
21.3
|
1.0
|
CD
|
A:GLU140
|
4.5
|
12.9
|
0.3
|
CA
|
A:VAL139
|
4.6
|
13.9
|
0.7
|
CG
|
A:GLU140
|
4.7
|
22.1
|
0.7
|
N
|
A:GLU140
|
4.8
|
9.6
|
0.3
|
O
|
B:HOH609
|
4.8
|
15.0
|
0.5
|
OE1
|
B:GLN362
|
4.9
|
18.3
|
1.0
|
CD
|
A:GLU140
|
5.0
|
24.6
|
0.7
|
|
Sodium binding site 7 out
of 12 in 5u4h
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Sodium Binding Sites List in 5u4h
Sodium binding site 7 out
of 12 in the 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na506
b:32.0
occ:1.00
|
O
|
A:HOH1015
|
2.3
|
26.1
|
0.7
|
O
|
A:HOH1192
|
2.5
|
33.0
|
1.0
|
O
|
A:HOH1199
|
2.5
|
39.1
|
1.0
|
O
|
A:HOH647
|
2.5
|
24.6
|
1.0
|
O
|
A:HOH1015
|
3.5
|
20.7
|
0.3
|
ND1
|
A:HIS223
|
3.9
|
14.3
|
0.7
|
CE1
|
A:HIS223
|
4.2
|
14.1
|
0.7
|
O
|
A:GLY224
|
4.2
|
13.2
|
1.0
|
O
|
A:HOH1079
|
4.3
|
25.3
|
1.0
|
CG
|
A:HIS223
|
4.4
|
13.0
|
0.7
|
O
|
A:HOH732
|
4.5
|
23.6
|
1.0
|
NE2
|
A:HIS223
|
4.8
|
15.0
|
0.7
|
CB
|
A:HIS223
|
4.9
|
12.6
|
0.7
|
CB
|
A:HIS223
|
4.9
|
11.8
|
0.3
|
CD2
|
A:HIS223
|
5.0
|
13.9
|
0.7
|
|
Sodium binding site 8 out
of 12 in 5u4h
Go back to
Sodium Binding Sites List in 5u4h
Sodium binding site 8 out
of 12 in the 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na501
b:11.2
occ:1.00
|
O
|
B:HOH1026
|
2.3
|
14.3
|
1.0
|
O
|
B:HOH1034
|
2.4
|
15.3
|
1.0
|
OD1
|
B:ASN23
|
2.4
|
9.4
|
1.0
|
O
|
B:HOH828
|
2.4
|
15.9
|
1.0
|
O
|
B:HOH772
|
2.4
|
10.3
|
1.0
|
CG
|
B:ASN23
|
3.2
|
7.9
|
1.0
|
NZ
|
B:LYS22
|
3.7
|
9.7
|
1.0
|
O1
|
B:FMT505
|
3.7
|
10.7
|
0.8
|
ND2
|
B:ASN23
|
3.8
|
8.7
|
1.0
|
O
|
B:HOH1184
|
3.9
|
16.7
|
1.0
|
O
|
B:HOH1086
|
3.9
|
13.4
|
1.0
|
O
|
B:HOH1104
|
4.1
|
13.2
|
1.0
|
O2
|
B:FMT504
|
4.1
|
8.6
|
1.0
|
O
|
B:HOH655
|
4.2
|
14.5
|
0.7
|
CB
|
B:ASN23
|
4.3
|
7.0
|
1.0
|
O
|
B:HOH689
|
4.4
|
14.2
|
1.0
|
O
|
B:HOH815
|
4.4
|
14.3
|
1.0
|
C
|
B:FMT504
|
4.4
|
9.0
|
1.0
|
O
|
B:HOH655
|
4.5
|
8.5
|
0.3
|
O
|
B:HOH757
|
4.5
|
9.3
|
1.0
|
O
|
B:HOH851
|
4.5
|
13.3
|
1.0
|
O
|
B:HOH625
|
4.5
|
13.4
|
0.7
|
O
|
B:HOH721
|
4.7
|
10.4
|
1.0
|
CE
|
B:LYS22
|
4.8
|
9.5
|
1.0
|
C
|
B:FMT505
|
4.8
|
10.6
|
0.8
|
OD2
|
B:ASP306
|
4.8
|
7.8
|
1.0
|
O
|
B:HOH625
|
4.8
|
7.9
|
0.3
|
CA
|
B:ASN23
|
5.0
|
6.7
|
1.0
|
|
Sodium binding site 9 out
of 12 in 5u4h
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Sodium Binding Sites List in 5u4h
Sodium binding site 9 out
of 12 in the 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na502
b:16.2
occ:0.50
|
NA
|
B:NA502
|
0.0
|
16.2
|
0.5
|
NA
|
B:NA502
|
1.8
|
17.4
|
0.5
|
O
|
A:HOH842
|
2.0
|
15.9
|
0.5
|
O
|
A:HOH723
|
2.2
|
18.3
|
1.0
|
O
|
A:HOH1147
|
2.3
|
11.9
|
1.0
|
O
|
A:HOH842
|
2.4
|
12.7
|
0.5
|
O
|
A:ILE346
|
2.4
|
10.3
|
1.0
|
O
|
A:HOH810
|
2.5
|
11.1
|
1.0
|
O
|
B:HOH934
|
2.7
|
22.9
|
0.7
|
O
|
B:HOH934
|
2.9
|
12.2
|
0.3
|
C
|
A:ILE346
|
3.5
|
8.6
|
1.0
|
O
|
B:HOH1053
|
3.9
|
25.7
|
1.0
|
N
|
A:ILE346
|
3.9
|
8.6
|
1.0
|
O
|
A:HOH921
|
4.0
|
17.0
|
0.7
|
O
|
A:HOH1164
|
4.0
|
19.5
|
0.7
|
OG
|
A:SER340
|
4.1
|
9.2
|
1.0
|
O
|
A:HOH946
|
4.3
|
17.5
|
1.0
|
CA
|
A:ILE346
|
4.4
|
8.7
|
1.0
|
O
|
A:HOH1072
|
4.4
|
21.6
|
1.0
|
O
|
A:HOH860
|
4.4
|
26.1
|
0.5
|
OD2
|
B:ASP124
|
4.4
|
17.1
|
1.0
|
N
|
A:GLN347
|
4.4
|
8.4
|
1.0
|
OD1
|
B:ASP124
|
4.5
|
15.4
|
1.0
|
CA
|
A:GLN347
|
4.6
|
8.7
|
1.0
|
O
|
A:HOH1112
|
4.7
|
25.4
|
1.0
|
O
|
A:HOH1164
|
4.7
|
18.5
|
0.3
|
O
|
A:HOH921
|
4.8
|
14.6
|
0.3
|
OD1
|
A:ASN345
|
4.9
|
12.6
|
1.0
|
CG
|
B:ASP124
|
4.9
|
14.2
|
1.0
|
CG
|
B:PRO122
|
4.9
|
14.6
|
1.0
|
C
|
A:ASN345
|
5.0
|
8.9
|
1.0
|
CB
|
B:PRO122
|
5.0
|
13.9
|
1.0
|
|
Sodium binding site 10 out
of 12 in 5u4h
Go back to
Sodium Binding Sites List in 5u4h
Sodium binding site 10 out
of 12 in the 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of 1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na502
b:17.4
occ:0.50
|
NA
|
B:NA502
|
0.0
|
17.4
|
0.5
|
NA
|
B:NA502
|
1.8
|
16.2
|
0.5
|
O
|
A:HOH1147
|
2.3
|
11.9
|
1.0
|
O
|
B:HOH934
|
2.8
|
12.2
|
0.3
|
OD1
|
B:ASP124
|
2.8
|
15.4
|
1.0
|
O
|
A:HOH723
|
2.9
|
18.3
|
1.0
|
O
|
B:HOH934
|
2.9
|
22.9
|
0.7
|
O
|
B:HOH1053
|
3.1
|
25.7
|
1.0
|
O
|
A:HOH842
|
3.1
|
15.9
|
0.5
|
O
|
A:HOH1164
|
3.2
|
19.5
|
0.7
|
OD2
|
B:ASP124
|
3.3
|
17.1
|
1.0
|
O
|
A:HOH842
|
3.4
|
12.7
|
0.5
|
CG
|
B:ASP124
|
3.5
|
14.2
|
1.0
|
O
|
A:HOH810
|
3.5
|
11.1
|
1.0
|
O
|
A:HOH1112
|
3.8
|
25.4
|
1.0
|
CB
|
B:PRO122
|
3.8
|
13.9
|
1.0
|
CG
|
B:PRO122
|
4.0
|
14.6
|
1.0
|
O
|
A:HOH1164
|
4.1
|
18.5
|
0.3
|
O
|
A:HOH921
|
4.1
|
17.0
|
0.7
|
O
|
B:HOH795
|
4.1
|
25.6
|
1.0
|
O
|
A:ILE346
|
4.2
|
10.3
|
1.0
|
O
|
B:HOH1040
|
4.6
|
17.8
|
0.5
|
O
|
A:HOH1072
|
4.7
|
21.6
|
1.0
|
O
|
A:HOH860
|
4.8
|
26.1
|
0.5
|
OG
|
A:SER340
|
4.8
|
9.2
|
1.0
|
O
|
A:HOH946
|
4.8
|
17.5
|
1.0
|
CB
|
B:ASP124
|
5.0
|
12.3
|
1.0
|
O
|
A:HOH921
|
5.0
|
14.6
|
0.3
|
|
Reference:
G.Minasov,
L.Shuvalova,
O.Kiryukhina,
I.Dubrovska,
S.Grimshaw,
K.Kwon,
W.F.Anderson,
Center For Structural Genomics Of Infectious Diseases(Csgid).
1.05 Angstrom Resolution Crystal Structure of Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase From Acinetobacter Baumannii in Covalently Bound Complex with (2R)-2-(Phosphonooxy)Propanoic Acid. To Be Published.
Page generated: Tue Oct 8 00:22:50 2024
|