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Zinc in PDB 5zj8: Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative CY32

Enzymatic activity of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative CY32

All present enzymatic activity of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative CY32:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative CY32, PDB code: 5zj8 was solved by H.Zhang, Q.Hao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.53 / 0.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.491, 59.949, 41.946, 90.00, 98.11, 90.00
R / Rfree (%) 11.8 / 13

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative CY32 (pdb code 5zj8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative CY32, PDB code: 5zj8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5zj8

Go back to Zinc Binding Sites List in 5zj8
Zinc binding site 1 out of 2 in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative CY32


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative CY32 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:18.5
occ:1.00
ND1 A:HIS122 2.0 18.8 1.0
NE2 A:HIS189 2.1 19.2 1.0
NE2 A:HIS120 2.1 17.9 1.0
SAA A:9DC303 2.3 19.2 1.0
CE1 A:HIS122 3.0 19.5 1.0
CE1 A:HIS189 3.0 19.2 1.0
CE1 A:HIS120 3.0 18.7 1.0
CG A:HIS122 3.0 18.4 1.0
CD2 A:HIS120 3.1 17.9 1.0
CD2 A:HIS189 3.1 18.7 1.0
CAB A:9DC303 3.3 21.3 1.0
CB A:HIS122 3.4 17.9 1.0
ZN A:ZN302 3.7 18.9 1.0
SG A:CYS208 4.0 18.7 1.0
NE2 A:HIS122 4.1 20.4 1.0
OD1 A:ASP124 4.1 19.1 1.0
ND1 A:HIS120 4.1 19.3 1.0
ND1 A:HIS189 4.1 19.5 1.0
CD2 A:HIS122 4.1 20.0 1.0
CG A:HIS120 4.2 17.5 1.0
CB A:CYS208 4.2 19.0 1.0
CG A:HIS189 4.2 18.8 1.0
CG2 A:THR190 4.5 19.7 1.0
CAC A:9DC303 4.6 28.8 1.0
OD2 A:ASP124 4.8 19.5 1.0
CA A:HIS122 4.8 17.4 1.0
CG A:ASP124 4.9 17.5 1.0

Zinc binding site 2 out of 2 in 5zj8

Go back to Zinc Binding Sites List in 5zj8
Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative CY32


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative CY32 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:18.9
occ:1.00
OD2 A:ASP124 1.9 19.5 1.0
NE2 A:HIS250 2.0 18.5 1.0
SAA A:9DC303 2.3 19.2 1.0
SG A:CYS208 2.3 18.7 1.0
CG A:ASP124 2.9 17.5 1.0
CE1 A:HIS250 3.0 19.1 1.0
CD2 A:HIS250 3.1 18.9 1.0
OD1 A:ASP124 3.3 19.1 1.0
CAB A:9DC303 3.3 21.3 1.0
CB A:CYS208 3.5 19.0 1.0
ZN A:ZN301 3.7 18.5 1.0
SAF A:9DC303 3.9 37.1 1.0
ND1 A:HIS250 4.1 19.4 1.0
CG A:HIS250 4.2 18.8 1.0
CAC A:9DC303 4.2 28.8 1.0
CB A:ASP124 4.2 17.2 1.0
CB A:SER249 4.3 18.3 1.0
O A:HOH592 4.3 26.4 1.0
CE1 A:HIS120 4.5 18.7 1.0
NE2 A:HIS189 4.5 19.2 1.0
NE2 A:HIS120 4.5 17.9 1.0
OG A:SER249 4.6 18.7 1.0
CA A:CYS208 4.7 18.5 1.0
CE1 A:HIS189 4.7 19.2 1.0
CE A:LYS125 4.8 19.2 1.0
CD A:LYS125 5.0 19.8 1.0

Reference:

H.Zhang, Q.Hao. Crystal Structure of Ndm-1 To Be Published.
Page generated: Wed Dec 16 11:27:00 2020

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