Zinc in PDB 7z16: E. Coli C-P Lyase Bound to Phnk/Phnl Dual Abc Dimer with Amppnp and Phnk E171Q Mutation
Enzymatic activity of E. Coli C-P Lyase Bound to Phnk/Phnl Dual Abc Dimer with Amppnp and Phnk E171Q Mutation
All present enzymatic activity of E. Coli C-P Lyase Bound to Phnk/Phnl Dual Abc Dimer with Amppnp and Phnk E171Q Mutation:
2.7.8.37;
4.7.1.1;
Other elements in 7z16:
The structure of E. Coli C-P Lyase Bound to Phnk/Phnl Dual Abc Dimer with Amppnp and Phnk E171Q Mutation also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the E. Coli C-P Lyase Bound to Phnk/Phnl Dual Abc Dimer with Amppnp and Phnk E171Q Mutation
(pdb code 7z16). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
E. Coli C-P Lyase Bound to Phnk/Phnl Dual Abc Dimer with Amppnp and Phnk E171Q Mutation, PDB code: 7z16:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 7z16
Go back to
Zinc Binding Sites List in 7z16
Zinc binding site 1 out
of 4 in the E. Coli C-P Lyase Bound to Phnk/Phnl Dual Abc Dimer with Amppnp and Phnk E171Q Mutation
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of E. Coli C-P Lyase Bound to Phnk/Phnl Dual Abc Dimer with Amppnp and Phnk E171Q Mutation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn1000
b:61.2
occ:1.00
|
NE2
|
C:HIS328
|
2.3
|
14.4
|
1.0
|
NE2
|
C:HIS333
|
2.3
|
15.2
|
1.0
|
CD2
|
C:HIS333
|
3.0
|
15.2
|
1.0
|
HD2
|
C:HIS333
|
3.1
|
15.2
|
1.0
|
CE1
|
C:HIS328
|
3.1
|
14.4
|
1.0
|
HE1
|
C:HIS328
|
3.2
|
14.4
|
1.0
|
CD2
|
C:HIS328
|
3.3
|
14.4
|
1.0
|
CE1
|
C:HIS333
|
3.3
|
15.2
|
1.0
|
HD2
|
C:HIS328
|
3.5
|
14.4
|
1.0
|
HE1
|
C:HIS333
|
3.6
|
15.2
|
1.0
|
HD23
|
C:LEU329
|
3.7
|
15.3
|
1.0
|
HE1
|
D:HIS108
|
3.8
|
14.6
|
1.0
|
HH21
|
D:ARG107
|
4.0
|
14.9
|
1.0
|
CG
|
C:HIS333
|
4.2
|
15.2
|
1.0
|
ND1
|
C:HIS328
|
4.3
|
14.4
|
1.0
|
ND1
|
C:HIS333
|
4.3
|
15.2
|
1.0
|
HG3
|
D:PRO126
|
4.4
|
14.5
|
1.0
|
CG
|
C:HIS328
|
4.4
|
14.4
|
1.0
|
CD2
|
C:LEU329
|
4.5
|
15.3
|
1.0
|
HD21
|
C:LEU329
|
4.5
|
15.3
|
1.0
|
HA
|
C:LEU329
|
4.6
|
15.3
|
1.0
|
NH2
|
D:ARG107
|
4.6
|
14.9
|
1.0
|
CE1
|
D:HIS108
|
4.7
|
14.6
|
1.0
|
HH22
|
D:ARG107
|
4.7
|
14.9
|
1.0
|
HD22
|
C:LEU329
|
4.8
|
15.3
|
1.0
|
|
Zinc binding site 2 out
of 4 in 7z16
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Zinc Binding Sites List in 7z16
Zinc binding site 2 out
of 4 in the E. Coli C-P Lyase Bound to Phnk/Phnl Dual Abc Dimer with Amppnp and Phnk E171Q Mutation
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of E. Coli C-P Lyase Bound to Phnk/Phnl Dual Abc Dimer with Amppnp and Phnk E171Q Mutation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn1000
b:34.2
occ:1.00
|
SG
|
D:CYS241
|
2.3
|
23.4
|
1.0
|
SG
|
D:CYS244
|
2.3
|
24.4
|
1.0
|
SG
|
D:CYS266
|
2.3
|
20.8
|
1.0
|
SG
|
D:CYS272
|
2.3
|
23.1
|
1.0
|
HB3
|
D:CYS241
|
2.9
|
23.4
|
1.0
|
H
|
D:CYS244
|
3.0
|
24.4
|
1.0
|
HB2
|
D:CYS241
|
3.0
|
23.4
|
1.0
|
CB
|
D:CYS241
|
3.0
|
23.4
|
1.0
|
HB3
|
D:CYS244
|
3.0
|
24.4
|
1.0
|
H
|
D:CYS266
|
3.1
|
20.8
|
1.0
|
HB2
|
D:CYS266
|
3.1
|
20.8
|
1.0
|
CB
|
D:CYS244
|
3.3
|
24.4
|
1.0
|
HA
|
D:CYS272
|
3.3
|
23.1
|
1.0
|
CB
|
D:CYS266
|
3.3
|
20.8
|
1.0
|
HB2
|
D:CYS272
|
3.4
|
23.1
|
1.0
|
CB
|
D:CYS272
|
3.4
|
23.1
|
1.0
|
N
|
D:CYS244
|
3.7
|
24.4
|
1.0
|
HB
|
D:ILE243
|
3.8
|
25.3
|
1.0
|
N
|
D:CYS266
|
3.8
|
20.8
|
1.0
|
CA
|
D:CYS272
|
3.9
|
23.1
|
1.0
|
H
|
D:SER246
|
4.0
|
22.9
|
1.0
|
HB3
|
D:SER246
|
4.0
|
22.9
|
1.0
|
CA
|
D:CYS244
|
4.0
|
24.4
|
1.0
|
HB2
|
D:CYS244
|
4.0
|
24.4
|
1.0
|
HB3
|
D:CYS266
|
4.1
|
20.8
|
1.0
|
H
|
D:GLY245
|
4.2
|
23.1
|
1.0
|
HG
|
D:SER249
|
4.2
|
20.3
|
1.0
|
CA
|
D:CYS266
|
4.2
|
20.8
|
1.0
|
HB3
|
D:CYS272
|
4.2
|
23.1
|
1.0
|
H
|
D:ILE243
|
4.3
|
25.3
|
1.0
|
CA
|
D:CYS241
|
4.5
|
23.4
|
1.0
|
HG22
|
D:ILE243
|
4.6
|
25.3
|
1.0
|
HA
|
D:VAL265
|
4.6
|
22.5
|
1.0
|
HB2
|
D:SER246
|
4.6
|
22.9
|
1.0
|
N
|
D:GLY245
|
4.6
|
23.1
|
1.0
|
HA
|
D:CYS266
|
4.7
|
20.8
|
1.0
|
C
|
D:CYS244
|
4.7
|
24.4
|
1.0
|
HB2
|
D:GLN275
|
4.7
|
25.6
|
1.0
|
CB
|
D:ILE243
|
4.7
|
25.3
|
1.0
|
CB
|
D:SER246
|
4.7
|
22.9
|
1.0
|
N
|
D:SER246
|
4.8
|
22.9
|
1.0
|
HA
|
D:CYS241
|
4.8
|
23.4
|
1.0
|
C
|
D:ILE243
|
4.8
|
25.3
|
1.0
|
O
|
D:CYS272
|
4.8
|
23.1
|
1.0
|
C
|
D:CYS272
|
4.8
|
23.1
|
1.0
|
HA
|
D:CYS244
|
4.9
|
24.4
|
1.0
|
HD2
|
D:TYR271
|
4.9
|
22.1
|
1.0
|
N
|
D:CYS272
|
4.9
|
23.1
|
1.0
|
HB
|
D:VAL265
|
4.9
|
22.5
|
1.0
|
HG
|
D:SER276
|
4.9
|
27.9
|
1.0
|
C
|
D:VAL265
|
5.0
|
22.5
|
1.0
|
OG
|
D:SER249
|
5.0
|
20.3
|
1.0
|
|
Zinc binding site 3 out
of 4 in 7z16
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Zinc Binding Sites List in 7z16
Zinc binding site 3 out
of 4 in the E. Coli C-P Lyase Bound to Phnk/Phnl Dual Abc Dimer with Amppnp and Phnk E171Q Mutation
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of E. Coli C-P Lyase Bound to Phnk/Phnl Dual Abc Dimer with Amppnp and Phnk E171Q Mutation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn1000
b:61.0
occ:1.00
|
NE2
|
G:HIS328
|
2.3
|
14.4
|
1.0
|
NE2
|
G:HIS333
|
2.3
|
15.3
|
1.0
|
CD2
|
G:HIS333
|
3.0
|
15.3
|
1.0
|
HD2
|
G:HIS333
|
3.1
|
15.3
|
1.0
|
CE1
|
G:HIS328
|
3.1
|
14.4
|
1.0
|
HE1
|
G:HIS328
|
3.2
|
14.4
|
1.0
|
CD2
|
G:HIS328
|
3.3
|
14.4
|
1.0
|
CE1
|
G:HIS333
|
3.3
|
15.3
|
1.0
|
HD2
|
G:HIS328
|
3.5
|
14.4
|
1.0
|
HE1
|
G:HIS333
|
3.6
|
15.3
|
1.0
|
HD23
|
G:LEU329
|
3.7
|
15.3
|
1.0
|
HE1
|
H:HIS108
|
3.8
|
14.6
|
1.0
|
HH21
|
H:ARG107
|
4.0
|
15.0
|
1.0
|
CG
|
G:HIS333
|
4.2
|
15.3
|
1.0
|
ND1
|
G:HIS328
|
4.3
|
14.4
|
1.0
|
ND1
|
G:HIS333
|
4.3
|
15.3
|
1.0
|
HG3
|
H:PRO126
|
4.4
|
14.6
|
1.0
|
CG
|
G:HIS328
|
4.4
|
14.4
|
1.0
|
CD2
|
G:LEU329
|
4.5
|
15.3
|
1.0
|
HD21
|
G:LEU329
|
4.5
|
15.3
|
1.0
|
HA
|
G:LEU329
|
4.6
|
15.3
|
1.0
|
NH2
|
H:ARG107
|
4.6
|
15.0
|
1.0
|
CE1
|
H:HIS108
|
4.7
|
14.6
|
1.0
|
HH22
|
H:ARG107
|
4.7
|
15.0
|
1.0
|
HD22
|
G:LEU329
|
4.8
|
15.3
|
1.0
|
HE2
|
H:HIS108
|
4.9
|
14.6
|
1.0
|
|
Zinc binding site 4 out
of 4 in 7z16
Go back to
Zinc Binding Sites List in 7z16
Zinc binding site 4 out
of 4 in the E. Coli C-P Lyase Bound to Phnk/Phnl Dual Abc Dimer with Amppnp and Phnk E171Q Mutation
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of E. Coli C-P Lyase Bound to Phnk/Phnl Dual Abc Dimer with Amppnp and Phnk E171Q Mutation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn1000
b:34.2
occ:1.00
|
SG
|
H:CYS241
|
2.3
|
23.4
|
1.0
|
SG
|
H:CYS266
|
2.3
|
20.8
|
1.0
|
SG
|
H:CYS244
|
2.3
|
24.4
|
1.0
|
SG
|
H:CYS272
|
2.3
|
23.1
|
1.0
|
HB3
|
H:CYS241
|
2.9
|
23.4
|
1.0
|
H
|
H:CYS244
|
3.0
|
24.4
|
1.0
|
HB2
|
H:CYS241
|
3.0
|
23.4
|
1.0
|
CB
|
H:CYS241
|
3.0
|
23.4
|
1.0
|
HB3
|
H:CYS244
|
3.0
|
24.4
|
1.0
|
H
|
H:CYS266
|
3.1
|
20.8
|
1.0
|
HB2
|
H:CYS266
|
3.1
|
20.8
|
1.0
|
CB
|
H:CYS244
|
3.3
|
24.4
|
1.0
|
HA
|
H:CYS272
|
3.3
|
23.1
|
1.0
|
CB
|
H:CYS266
|
3.3
|
20.8
|
1.0
|
HB2
|
H:CYS272
|
3.4
|
23.1
|
1.0
|
CB
|
H:CYS272
|
3.4
|
23.1
|
1.0
|
N
|
H:CYS244
|
3.7
|
24.4
|
1.0
|
HB
|
H:ILE243
|
3.8
|
25.2
|
1.0
|
N
|
H:CYS266
|
3.8
|
20.8
|
1.0
|
CA
|
H:CYS272
|
3.9
|
23.1
|
1.0
|
H
|
H:SER246
|
4.0
|
22.9
|
1.0
|
HB3
|
H:SER246
|
4.0
|
22.9
|
1.0
|
CA
|
H:CYS244
|
4.0
|
24.4
|
1.0
|
HB2
|
H:CYS244
|
4.1
|
24.4
|
1.0
|
HB3
|
H:CYS266
|
4.1
|
20.8
|
1.0
|
H
|
H:GLY245
|
4.2
|
23.1
|
1.0
|
HG
|
H:SER249
|
4.2
|
20.3
|
1.0
|
CA
|
H:CYS266
|
4.2
|
20.8
|
1.0
|
HB3
|
H:CYS272
|
4.2
|
23.1
|
1.0
|
H
|
H:ILE243
|
4.3
|
25.2
|
1.0
|
CA
|
H:CYS241
|
4.5
|
23.4
|
1.0
|
HA
|
H:VAL265
|
4.6
|
22.5
|
1.0
|
HB2
|
H:SER246
|
4.6
|
22.9
|
1.0
|
HG22
|
H:ILE243
|
4.6
|
25.2
|
1.0
|
N
|
H:GLY245
|
4.6
|
23.1
|
1.0
|
HA
|
H:CYS266
|
4.7
|
20.8
|
1.0
|
C
|
H:CYS244
|
4.7
|
24.4
|
1.0
|
HB2
|
H:GLN275
|
4.7
|
25.5
|
1.0
|
CB
|
H:ILE243
|
4.7
|
25.2
|
1.0
|
CB
|
H:SER246
|
4.7
|
22.9
|
1.0
|
N
|
H:SER246
|
4.8
|
22.9
|
1.0
|
HA
|
H:CYS241
|
4.8
|
23.4
|
1.0
|
C
|
H:ILE243
|
4.8
|
25.2
|
1.0
|
O
|
H:CYS272
|
4.8
|
23.1
|
1.0
|
C
|
H:CYS272
|
4.8
|
23.1
|
1.0
|
HA
|
H:CYS244
|
4.9
|
24.4
|
1.0
|
HD2
|
H:TYR271
|
4.9
|
22.0
|
1.0
|
N
|
H:CYS272
|
4.9
|
23.1
|
1.0
|
HB
|
H:VAL265
|
4.9
|
22.5
|
1.0
|
HG
|
H:SER276
|
5.0
|
27.8
|
1.0
|
C
|
H:VAL265
|
5.0
|
22.5
|
1.0
|
OG
|
H:SER249
|
5.0
|
20.3
|
1.0
|
|
Reference:
S.K.Amstrup,
N.Sofos,
J.L.Karlsen,
R.B.Skjerning,
T.Boesen,
J.J.Enghild,
B.Hove-Jensen,
D.E.Brodersen.
Structural Remodelling of the Carbon-Phosphorus Lyase Machinery By A Dual Abc Atpase Biorxiv 2022.
DOI: 10.1101/2022.06.09.495270
Page generated: Wed Oct 30 16:09:47 2024
|