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:

Magnesium (Mg) 2 atoms

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

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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 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 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: Sat Apr 8 06:26:36 2023

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