Calcium in PDB 1q7b: The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+
Enzymatic activity of The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+
All present enzymatic activity of The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+:
1.1.1.100;
Protein crystallography data
The structure of The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+, PDB code: 1q7b
was solved by
A.C.Price,
Y.-M.Zhang,
C.O.Rock,
S.M.White,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.05
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.748,
76.182,
99.733,
90.00,
109.47,
90.00
|
R / Rfree (%)
|
20 /
22.1
|
Calcium Binding Sites:
The binding sites of Calcium atom in the The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+
(pdb code 1q7b). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+, PDB code: 1q7b:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 1q7b
Go back to
Calcium Binding Sites List in 1q7b
Calcium binding site 1 out
of 8 in the The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca9002
b:24.8
occ:1.00
|
O
|
A:THR234
|
2.4
|
23.2
|
1.0
|
O
|
D:HOH1037
|
2.4
|
24.1
|
1.0
|
O
|
A:HOH4037
|
2.4
|
33.4
|
1.0
|
O
|
D:THR234
|
2.4
|
22.1
|
1.0
|
OE2
|
D:GLU233
|
2.4
|
24.1
|
1.0
|
OE2
|
A:GLU233
|
2.5
|
22.6
|
1.0
|
CD
|
D:GLU233
|
3.2
|
24.2
|
1.0
|
CD
|
A:GLU233
|
3.2
|
22.8
|
1.0
|
OE1
|
D:GLU233
|
3.5
|
23.4
|
1.0
|
OE1
|
A:GLU233
|
3.5
|
24.4
|
1.0
|
C
|
A:THR234
|
3.6
|
23.5
|
1.0
|
C
|
D:THR234
|
3.6
|
21.8
|
1.0
|
ND1
|
A:HIS236
|
4.2
|
24.9
|
1.0
|
CA
|
A:LEU235
|
4.3
|
23.8
|
1.0
|
CA
|
D:LEU235
|
4.3
|
22.8
|
1.0
|
ND1
|
D:HIS236
|
4.3
|
26.7
|
1.0
|
CG
|
D:GLU233
|
4.3
|
21.3
|
1.0
|
N
|
A:LEU235
|
4.4
|
23.0
|
1.0
|
CG
|
A:GLU233
|
4.4
|
21.6
|
1.0
|
N
|
D:LEU235
|
4.4
|
21.1
|
1.0
|
N
|
A:THR234
|
4.5
|
22.0
|
1.0
|
N
|
D:THR234
|
4.6
|
20.8
|
1.0
|
CA
|
A:THR234
|
4.6
|
21.5
|
1.0
|
CA
|
D:THR234
|
4.6
|
22.0
|
1.0
|
N
|
A:HIS236
|
4.6
|
22.4
|
1.0
|
N
|
D:HIS236
|
4.7
|
22.1
|
1.0
|
CE1
|
A:HIS236
|
4.8
|
21.8
|
1.0
|
CE1
|
D:HIS236
|
4.9
|
23.5
|
1.0
|
O
|
D:HOH1051
|
4.9
|
36.1
|
1.0
|
CB
|
A:THR234
|
4.9
|
21.9
|
1.0
|
O
|
A:HOH4051
|
4.9
|
35.1
|
1.0
|
CB
|
D:THR234
|
5.0
|
22.2
|
1.0
|
|
Calcium binding site 2 out
of 8 in 1q7b
Go back to
Calcium Binding Sites List in 1q7b
Calcium binding site 2 out
of 8 in the The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca9006
b:56.1
occ:1.00
|
NZ
|
A:LYS54
|
3.7
|
50.6
|
1.0
|
OE2
|
A:GLU76
|
4.3
|
44.6
|
1.0
|
O
|
A:HOH1134
|
4.6
|
34.4
|
1.0
|
O
|
A:HOH1063
|
4.6
|
29.4
|
1.0
|
CG
|
A:LYS54
|
4.8
|
43.0
|
1.0
|
CD
|
A:LYS54
|
4.8
|
45.6
|
1.0
|
CE
|
A:LYS54
|
4.9
|
47.7
|
1.0
|
|
Calcium binding site 3 out
of 8 in 1q7b
Go back to
Calcium Binding Sites List in 1q7b
Calcium binding site 3 out
of 8 in the The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca9007
b:50.8
occ:1.00
|
OD1
|
A:ASN145
|
2.5
|
30.7
|
1.0
|
O
|
A:HOH1046
|
2.6
|
34.1
|
1.0
|
O
|
A:HOH1159
|
2.7
|
49.6
|
1.0
|
O
|
A:HOH2041
|
2.9
|
26.4
|
1.0
|
O
|
A:HOH1056
|
3.0
|
47.1
|
1.0
|
CG
|
A:ASN145
|
3.6
|
30.4
|
1.0
|
O
|
A:HOH2082
|
3.9
|
53.5
|
1.0
|
ND2
|
A:ASN145
|
4.1
|
30.4
|
1.0
|
O
|
A:HOH2077
|
4.5
|
36.1
|
1.0
|
N
|
A:GLY146
|
4.7
|
26.7
|
1.0
|
O
|
A:HOH1084
|
4.9
|
42.2
|
1.0
|
O
|
B:HOH2050
|
4.9
|
28.1
|
1.0
|
CB
|
A:ASN145
|
4.9
|
28.7
|
1.0
|
O
|
A:GLY146
|
4.9
|
27.4
|
1.0
|
OE1
|
A:GLN203
|
5.0
|
34.7
|
1.0
|
|
Calcium binding site 4 out
of 8 in 1q7b
Go back to
Calcium Binding Sites List in 1q7b
Calcium binding site 4 out
of 8 in the The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca9001
b:25.0
occ:1.00
|
O
|
C:HOH2037
|
2.3
|
27.4
|
1.0
|
O
|
B:HOH3037
|
2.4
|
24.6
|
1.0
|
O
|
B:THR234
|
2.4
|
21.4
|
1.0
|
O
|
C:THR234
|
2.4
|
19.2
|
1.0
|
OE2
|
B:GLU233
|
2.5
|
20.4
|
1.0
|
OE2
|
C:GLU233
|
2.5
|
23.5
|
1.0
|
CD
|
B:GLU233
|
3.2
|
23.2
|
1.0
|
CD
|
C:GLU233
|
3.3
|
23.1
|
1.0
|
OE1
|
B:GLU233
|
3.5
|
23.2
|
1.0
|
OE1
|
C:GLU233
|
3.6
|
24.5
|
1.0
|
C
|
B:THR234
|
3.6
|
21.5
|
1.0
|
C
|
C:THR234
|
3.6
|
21.7
|
1.0
|
ND1
|
C:HIS236
|
4.3
|
21.4
|
1.0
|
ND1
|
B:HIS236
|
4.3
|
26.2
|
1.0
|
CG
|
B:GLU233
|
4.4
|
21.6
|
1.0
|
CA
|
C:LEU235
|
4.4
|
21.2
|
1.0
|
CA
|
B:LEU235
|
4.4
|
23.1
|
1.0
|
N
|
B:LEU235
|
4.4
|
22.5
|
1.0
|
CG
|
C:GLU233
|
4.4
|
22.5
|
1.0
|
N
|
C:LEU235
|
4.4
|
18.8
|
1.0
|
N
|
B:THR234
|
4.5
|
20.9
|
1.0
|
CA
|
B:THR234
|
4.6
|
21.3
|
1.0
|
N
|
C:THR234
|
4.6
|
21.1
|
1.0
|
CA
|
C:THR234
|
4.7
|
21.3
|
1.0
|
N
|
C:HIS236
|
4.7
|
19.9
|
1.0
|
N
|
B:HIS236
|
4.7
|
23.1
|
1.0
|
CE1
|
B:HIS236
|
4.8
|
24.4
|
1.0
|
CE1
|
C:HIS236
|
4.8
|
21.4
|
1.0
|
O
|
C:HOH2051
|
4.9
|
35.7
|
1.0
|
CB
|
B:THR234
|
4.9
|
24.1
|
1.0
|
O
|
B:HOH3051
|
4.9
|
37.2
|
1.0
|
CB
|
C:THR234
|
5.0
|
22.1
|
1.0
|
|
Calcium binding site 5 out
of 8 in 1q7b
Go back to
Calcium Binding Sites List in 1q7b
Calcium binding site 5 out
of 8 in the The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca9003
b:42.3
occ:1.00
|
O
|
B:GLY50
|
2.2
|
34.9
|
1.0
|
O
|
B:GLY53
|
2.3
|
35.6
|
1.0
|
O
|
B:HOH2063
|
2.4
|
30.1
|
1.0
|
C
|
B:GLY50
|
3.3
|
36.0
|
1.0
|
C
|
B:GLY53
|
3.5
|
37.3
|
1.0
|
N
|
B:ALA51
|
4.1
|
35.9
|
1.0
|
N
|
B:GLY53
|
4.2
|
38.3
|
1.0
|
CA
|
B:ALA51
|
4.2
|
37.2
|
1.0
|
CA
|
B:GLY50
|
4.2
|
35.9
|
1.0
|
CA
|
B:GLY53
|
4.4
|
37.8
|
1.0
|
N
|
B:LYS54
|
4.4
|
36.5
|
1.0
|
CA
|
B:LYS54
|
4.5
|
37.0
|
1.0
|
C
|
B:ALA51
|
4.6
|
38.0
|
1.0
|
O
|
B:SER46
|
4.6
|
27.4
|
1.0
|
N
|
B:GLY50
|
4.6
|
36.0
|
1.0
|
CB
|
B:LYS54
|
4.6
|
38.8
|
1.0
|
N
|
B:ASN52
|
4.9
|
38.2
|
1.0
|
|
Calcium binding site 6 out
of 8 in 1q7b
Go back to
Calcium Binding Sites List in 1q7b
Calcium binding site 6 out
of 8 in the The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca9008
b:60.1
occ:1.00
|
O
|
B:HOH2046
|
2.5
|
36.8
|
1.0
|
OD1
|
B:ASN145
|
2.5
|
25.1
|
1.0
|
O
|
B:HOH1041
|
3.0
|
31.2
|
1.0
|
O
|
B:HOH2056
|
3.2
|
46.1
|
1.0
|
CG
|
B:ASN145
|
3.6
|
26.4
|
1.0
|
ND2
|
B:ASN145
|
4.0
|
25.5
|
1.0
|
N
|
B:GLY146
|
4.7
|
26.2
|
1.0
|
O
|
B:HOH2160
|
4.7
|
44.3
|
1.0
|
O
|
B:GLY146
|
4.9
|
25.2
|
1.0
|
CB
|
B:ASN145
|
4.9
|
24.5
|
1.0
|
O
|
A:HOH1050
|
5.0
|
31.2
|
1.0
|
|
Calcium binding site 7 out
of 8 in 1q7b
Go back to
Calcium Binding Sites List in 1q7b
Calcium binding site 7 out
of 8 in the The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca9004
b:53.7
occ:1.00
|
O
|
C:HOH3046
|
2.5
|
32.9
|
1.0
|
OD1
|
C:ASN145
|
2.5
|
26.1
|
1.0
|
O
|
C:HOH4041
|
2.8
|
31.6
|
1.0
|
O
|
C:HOH3204
|
3.0
|
58.4
|
1.0
|
O
|
C:HOH3056
|
3.2
|
44.8
|
1.0
|
O
|
C:HOH3209
|
3.4
|
60.3
|
1.0
|
CG
|
C:ASN145
|
3.6
|
26.8
|
1.0
|
O
|
C:HOH4082
|
3.9
|
41.5
|
1.0
|
ND2
|
C:ASN145
|
4.1
|
26.2
|
1.0
|
N
|
C:GLY146
|
4.6
|
22.5
|
1.0
|
O
|
C:HOH4077
|
4.7
|
42.3
|
1.0
|
O
|
D:HOH4050
|
4.8
|
26.4
|
1.0
|
O
|
C:HOH3084
|
4.8
|
37.5
|
1.0
|
O
|
C:GLY146
|
4.8
|
24.7
|
1.0
|
CB
|
C:ASN145
|
4.9
|
23.1
|
1.0
|
|
Calcium binding site 8 out
of 8 in 1q7b
Go back to
Calcium Binding Sites List in 1q7b
Calcium binding site 8 out
of 8 in the The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of The Structure of Betaketoacyl-[Acp] Reductase From E. Coli in Complex with Nadp+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca9005
b:55.0
occ:1.00
|
O
|
D:HOH4213
|
2.3
|
52.8
|
1.0
|
OD1
|
D:ASN145
|
2.4
|
24.0
|
1.0
|
O
|
D:HOH4046
|
2.7
|
37.3
|
1.0
|
O
|
D:HOH3041
|
2.7
|
30.2
|
1.0
|
O
|
D:HOH4214
|
2.9
|
51.0
|
1.0
|
O
|
D:HOH4056
|
3.1
|
49.2
|
1.0
|
CG
|
D:ASN145
|
3.5
|
24.7
|
1.0
|
O
|
D:HOH3082
|
3.6
|
52.5
|
1.0
|
ND2
|
D:ASN145
|
3.9
|
22.0
|
1.0
|
O
|
D:HOH4241
|
4.3
|
53.8
|
1.0
|
O
|
D:HOH3077
|
4.5
|
43.9
|
1.0
|
O
|
C:HOH3050
|
4.6
|
30.7
|
1.0
|
N
|
D:GLY146
|
4.7
|
26.1
|
1.0
|
O
|
D:HOH4225
|
4.7
|
53.5
|
1.0
|
CB
|
D:ASN145
|
4.8
|
24.1
|
1.0
|
OE1
|
D:GLN203
|
4.9
|
31.7
|
1.0
|
O
|
D:GLY146
|
4.9
|
27.6
|
1.0
|
|
Reference:
A.C.Price,
Y.-M.Zhang,
C.O.Rock,
S.M.White.
Cofactor-Induced Conformational Rearrangements Establish A Catalytically Competent Active Site and A Proton Relay Conduit in Fabg Structure V. 12 417 2004.
ISSN: ISSN 0969-2126
PubMed: 15016358
DOI: 10.1016/J.STR.2004.02.008
Page generated: Thu Jul 11 14:00:58 2024
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