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Zinc in PDB 5n0h: Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement

Enzymatic activity of Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement

All present enzymatic activity of Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement, PDB code: 5n0h was solved by J.E.Raczynska, I.G.Shabalin, M.Jaskolski, W.Minor, A.Wlodawer, D.T.King, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.19 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 106.000, 106.000, 92.580, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 20

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement (pdb code 5n0h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement, PDB code: 5n0h:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5n0h

Go back to Zinc Binding Sites List in 5n0h
Zinc binding site 1 out of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement


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 Hydrolyzed Meropenem - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:21.7
occ:0.70
NE2 A:HIS250 2.1 23.8 1.0
NAN A:8YL301 2.1 23.6 0.6
OD2 A:ASP124 2.2 22.7 1.0
OAH A:8YL301 2.2 20.5 0.6
SG A:CYS208 2.3 23.8 1.0
O A:HOH535 2.5 8.3 0.4
OAF A:8YL301 2.7 20.8 0.6
CAS A:8YL301 2.9 23.8 0.6
CE1 A:HIS250 2.9 25.1 1.0
CAP A:8YL301 3.0 23.1 0.6
CD2 A:HIS250 3.2 26.2 1.0
CG A:ASP124 3.2 20.7 1.0
CAZ A:8YL301 3.3 23.7 0.6
CB A:CYS208 3.4 19.9 1.0
OD1 A:ASP124 3.5 26.0 1.0
CAQ A:8YL301 3.7 23.0 0.6
ZN A:ZN303 4.0 19.3 1.0
CBA A:8YL301 4.1 23.3 0.6
ND1 A:HIS250 4.1 26.0 1.0
CAT A:8YL301 4.1 26.3 0.6
CAV A:8YL301 4.2 25.3 0.6
CB A:SER249 4.2 21.5 1.0
OAE A:8YL301 4.2 21.6 0.6
OAJ A:8YL301 4.2 23.4 0.6
CG A:HIS250 4.2 25.1 1.0
NE2 A:HIS189 4.5 17.8 1.0
CB A:ASP124 4.5 18.4 1.0
CA A:CYS208 4.6 17.9 1.0
O A:HOH441 4.6 27.3 0.4
OG A:SER249 4.6 19.7 1.0
OAI A:8YL301 4.6 20.2 0.6
CE1 A:HIS189 4.7 17.1 1.0
CAU A:8YL301 4.8 24.0 0.6
CE1 A:HIS120 4.8 16.8 1.0
NE2 A:HIS120 4.9 16.1 1.0

Zinc binding site 2 out of 4 in 5n0h

Go back to Zinc Binding Sites List in 5n0h
Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement


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 Hydrolyzed Meropenem - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:19.3
occ:1.00
ND1 A:HIS122 2.0 15.3 1.0
OAF A:8YL301 2.0 20.8 0.6
NE2 A:HIS120 2.1 16.1 1.0
NE2 A:HIS189 2.1 17.8 1.0
O A:HOH535 2.2 8.3 0.4
CAQ A:8YL301 2.8 23.0 0.6
OAI A:8YL301 3.0 20.2 0.6
CG A:HIS122 3.0 15.3 1.0
CD2 A:HIS189 3.0 16.4 1.0
CD2 A:HIS120 3.0 15.0 1.0
CE1 A:HIS120 3.0 16.8 1.0
CE1 A:HIS122 3.0 18.3 1.0
CE1 A:HIS189 3.1 17.1 1.0
CB A:HIS122 3.3 13.3 1.0
ZN A:ZN302 4.0 21.7 0.7
ND1 A:HIS120 4.1 16.6 1.0
SG A:CYS208 4.1 23.8 1.0
NE2 A:HIS122 4.1 18.2 1.0
CD2 A:HIS122 4.1 17.5 1.0
CBA A:8YL301 4.1 23.3 0.6
CG A:HIS120 4.2 14.4 1.0
OD1 A:ASP124 4.2 26.0 1.0
CG A:HIS189 4.2 16.9 1.0
ND1 A:HIS189 4.2 15.9 1.0
CB A:CYS208 4.2 19.9 1.0
NAN A:8YL301 4.3 23.6 0.6
CAU A:8YL301 4.4 24.0 0.6
OAJ A:8YL301 4.4 23.4 0.6
CG2 A:THR190 4.4 18.3 1.0
OAH A:8YL301 4.6 20.5 0.6
CA A:HIS122 4.8 13.6 1.0
CAZ A:8YL301 4.9 23.7 0.6
CAP A:8YL301 4.9 23.1 0.6
CAS A:8YL301 4.9 23.8 0.6
OD2 A:ASP124 5.0 22.7 1.0

Zinc binding site 3 out of 4 in 5n0h

Go back to Zinc Binding Sites List in 5n0h
Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:22.7
occ:0.60
NE2 B:HIS250 2.0 29.4 1.0
O B:HOH542 2.2 24.2 1.0
OD2 B:ASP124 2.2 23.4 1.0
SG B:CYS208 2.3 25.6 1.0
CE1 B:HIS250 2.9 27.2 1.0
O B:HOH534 2.9 45.3 1.0
CD2 B:HIS250 3.1 28.1 1.0
CG B:ASP124 3.2 19.3 1.0
CB B:CYS208 3.4 18.9 1.0
OD1 B:ASP124 3.6 22.1 1.0
O B:HOH528 3.8 41.9 1.0
ZN B:ZN302 3.8 18.3 0.9
ND1 B:HIS250 4.1 30.9 1.0
CG B:HIS250 4.1 28.4 1.0
CB B:SER249 4.2 21.7 1.0
O B:HOH504 4.3 30.1 1.0
NE2 B:HIS189 4.5 16.7 1.0
CB B:ASP124 4.5 16.4 1.0
OG B:SER249 4.6 19.1 1.0
CE1 B:HIS120 4.6 16.7 1.0
CE1 B:HIS189 4.7 15.3 1.0
NE2 B:HIS120 4.7 16.6 1.0
CA B:CYS208 4.7 15.8 1.0

Zinc binding site 4 out of 4 in 5n0h

Go back to Zinc Binding Sites List in 5n0h
Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:18.3
occ:0.90
NE2 B:HIS120 2.1 16.6 1.0
ND1 B:HIS122 2.1 18.5 1.0
O B:HOH542 2.1 24.2 1.0
NE2 B:HIS189 2.1 16.7 1.0
O B:HOH528 2.7 41.9 1.0
CD2 B:HIS120 3.0 15.3 1.0
CE1 B:HIS120 3.0 16.7 1.0
CE1 B:HIS122 3.0 16.9 1.0
CD2 B:HIS189 3.0 15.3 1.0
CG B:HIS122 3.0 15.7 1.0
CE1 B:HIS189 3.1 15.3 1.0
CB B:HIS122 3.4 14.2 1.0
ZN B:ZN301 3.8 22.7 0.6
SG B:CYS208 4.0 25.6 1.0
NE2 B:HIS122 4.1 17.8 1.0
ND1 B:HIS120 4.1 16.3 1.0
CG B:HIS120 4.1 14.6 1.0
CD2 B:HIS122 4.2 17.3 1.0
CG B:HIS189 4.2 15.6 1.0
ND1 B:HIS189 4.2 14.6 1.0
OD1 B:ASP124 4.2 22.1 1.0
CB B:CYS208 4.3 18.9 1.0
CG2 B:THR190 4.5 17.9 1.0
O B:HOH534 4.7 45.3 1.0
OD2 B:ASP124 4.8 23.4 1.0
CA B:HIS122 4.8 13.7 1.0
ND2 B:ASN220 4.9 51.5 1.0
CG B:ASP124 5.0 19.3 1.0

Reference:

J.E.Raczynska, I.G.Shabalin, W.Minor, A.Wlodawer, M.Jaskolski. A Close Look Onto Structural Models and Primary Ligands of Metallo-Beta-Lactamases. Drug Resist. Updat. V. 40 1 2018.
ISSN: ESSN 1532-2084
PubMed: 30466711
DOI: 10.1016/J.DRUP.2018.08.001
Page generated: Wed Dec 16 06:34:06 2020

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