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Zinc in PDB 4rl0: Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins

Enzymatic activity of Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins

All present enzymatic activity of Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins:
3.5.2.6;

Protein crystallography data

The structure of Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins, PDB code: 4rl0 was solved by H.Feng, J.Ding, D.Zhu, X.Liu, X.Xu, Y.Zhang, S.Zang, D.-C.Wang, W.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.36 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.180, 78.890, 133.060, 90.00, 90.00, 90.00
R / Rfree (%) 13.1 / 15.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins (pdb code 4rl0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins, PDB code: 4rl0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4rl0

Go back to Zinc Binding Sites List in 4rl0
Zinc binding site 1 out of 4 in the Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:10.0
occ:1.00
ND1 A:HIS122 2.0 7.9 1.0
O A:HOH426 2.0 12.4 1.0
NE2 A:HIS189 2.0 7.1 1.0
NE2 A:HIS120 2.1 6.4 1.0
O A:3S0303 2.8 17.4 1.0
CE1 A:HIS122 2.9 9.0 1.0
CG A:HIS122 3.0 6.1 1.0
CD2 A:HIS189 3.0 4.7 1.0
CE1 A:HIS189 3.0 7.2 1.0
CE1 A:HIS120 3.1 9.2 1.0
CD2 A:HIS120 3.1 6.1 1.0
HA A:3S0303 3.2 20.0 1.0
CB A:HIS122 3.4 6.0 1.0
C A:3S0303 3.7 16.8 1.0
ZN A:ZN302 3.8 11.3 1.0
CA A:3S0303 3.9 16.7 1.0
NE2 A:HIS122 4.0 8.6 1.0
CD2 A:HIS122 4.1 8.4 1.0
OD1 A:ASP124 4.1 8.1 1.0
OAX A:3S0303 4.1 11.6 1.0
ND1 A:HIS189 4.1 6.6 1.0
CG A:HIS189 4.1 4.8 1.0
ND1 A:HIS120 4.2 7.9 1.0
SG A:CYS208 4.2 7.5 1.0
NAR A:3S0303 4.2 14.1 1.0
CG A:HIS120 4.2 5.8 1.0
CB A:CYS208 4.3 7.0 1.0
CG2 A:THR190 4.5 7.2 1.0
OD2 A:ASP124 4.6 8.7 1.0
CB A:3S0303 4.7 14.5 1.0
CAW A:3S0303 4.8 11.6 1.0
OXT A:3S0303 4.8 23.1 1.0
CG A:ASP124 4.8 7.6 1.0
CA A:HIS122 4.9 6.4 1.0
CAS A:3S0303 4.9 13.0 1.0

Zinc binding site 2 out of 4 in 4rl0

Go back to Zinc Binding Sites List in 4rl0
Zinc binding site 2 out of 4 in the Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:11.3
occ:1.00
OD2 A:ASP124 2.0 8.7 1.0
OAX A:3S0303 2.1 11.6 1.0
NE2 A:HIS250 2.1 8.9 1.0
O A:HOH426 2.2 12.4 1.0
SG A:CYS208 2.3 7.5 1.0
NAR A:3S0303 2.4 14.1 1.0
CAW A:3S0303 3.0 11.6 1.0
CAS A:3S0303 3.1 13.0 1.0
CE1 A:HIS250 3.1 8.4 1.0
CG A:ASP124 3.1 7.6 1.0
CD2 A:HIS250 3.2 7.9 1.0
HB A:3S0303 3.3 17.4 1.0
CB A:CYS208 3.3 7.0 1.0
CB A:3S0303 3.4 14.5 1.0
OD1 A:ASP124 3.5 8.1 1.0
HA A:3S0303 3.6 20.0 1.0
ZN A:ZN301 3.8 10.0 1.0
CA A:3S0303 4.0 16.7 1.0
OAY A:3S0303 4.2 13.0 1.0
O A:3S0303 4.2 17.4 1.0
HAZ A:3S0303 4.2 23.8 1.0
ND1 A:HIS250 4.2 10.2 1.0
CG A:HIS250 4.3 10.2 1.0
CB A:SER249 4.3 7.2 1.0
NE2 A:HIS189 4.4 7.1 1.0
CAT A:3S0303 4.4 18.5 1.0
CB A:ASP124 4.4 7.7 1.0
C A:3S0303 4.5 16.8 1.0
CE1 A:HIS189 4.6 7.2 1.0
CA A:CYS208 4.6 7.4 1.0
CE1 A:HIS120 4.6 9.2 1.0
OG A:SER249 4.7 7.2 1.0
NE2 A:HIS120 4.7 6.4 1.0
CAZ A:3S0303 4.7 19.9 1.0
SAV A:3S0303 4.9 15.8 1.0
HBM A:3S0303 4.9 23.8 1.0

Zinc binding site 3 out of 4 in 4rl0

Go back to Zinc Binding Sites List in 4rl0
Zinc binding site 3 out of 4 in the Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:9.2
occ:1.00
ND1 B:HIS122 2.0 8.7 1.0
NE2 B:HIS189 2.0 6.6 1.0
O B:HOH419 2.0 12.1 1.0
NE2 B:HIS120 2.1 6.3 1.0
OXT B:3S0303 2.9 18.2 1.0
CE1 B:HIS122 2.9 9.8 1.0
CD2 B:HIS189 3.0 4.9 1.0
CE1 B:HIS189 3.0 6.2 1.0
CG B:HIS122 3.0 7.3 1.0
CE1 B:HIS120 3.0 6.7 1.0
CD2 B:HIS120 3.1 5.7 1.0
HA B:3S0303 3.3 23.4 1.0
CB B:HIS122 3.4 5.9 1.0
C B:3S0303 3.8 19.7 1.0
ZN B:ZN302 3.8 9.9 1.0
NE2 B:HIS122 4.0 9.4 1.0
CA B:3S0303 4.1 19.5 1.0
CD2 B:HIS122 4.1 7.8 1.0
OD1 B:ASP124 4.1 7.7 1.0
ND1 B:HIS189 4.1 5.8 1.0
CG B:HIS189 4.1 4.1 1.0
ND1 B:HIS120 4.1 6.4 1.0
SG B:CYS208 4.2 6.5 1.0
OAY B:3S0303 4.2 11.9 1.0
CG B:HIS120 4.2 4.4 1.0
CB B:CYS208 4.3 6.7 1.0
NAR B:3S0303 4.3 12.6 1.0
CG2 B:THR190 4.5 6.6 1.0
O B:HOH592 4.5 24.8 1.0
OD2 B:ASP124 4.7 7.8 1.0
CAW B:3S0303 4.8 11.0 1.0
CG B:ASP124 4.8 7.0 1.0
CA B:HIS122 4.8 5.3 1.0
CB B:3S0303 4.9 13.7 1.0
O B:3S0303 5.0 22.1 1.0
CAS B:3S0303 5.0 12.1 1.0

Zinc binding site 4 out of 4 in 4rl0

Go back to Zinc Binding Sites List in 4rl0
Zinc binding site 4 out of 4 in the Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:9.9
occ:1.00
OD2 B:ASP124 2.0 7.8 1.0
NE2 B:HIS250 2.1 7.3 1.0
OAY B:3S0303 2.2 11.9 1.0
O B:HOH419 2.2 12.1 1.0
NAR B:3S0303 2.3 12.6 1.0
SG B:CYS208 2.3 6.5 1.0
CAW B:3S0303 3.0 11.0 1.0
CAS B:3S0303 3.1 12.1 1.0
CE1 B:HIS250 3.1 7.5 1.0
CG B:ASP124 3.1 7.0 1.0
CD2 B:HIS250 3.2 6.5 1.0
HB B:3S0303 3.2 16.5 1.0
CB B:3S0303 3.3 13.7 1.0
CB B:CYS208 3.3 6.7 1.0
HA B:3S0303 3.5 23.4 1.0
OD1 B:ASP124 3.5 7.7 1.0
ZN B:ZN301 3.8 9.2 1.0
CA B:3S0303 3.9 19.5 1.0
OAX B:3S0303 4.2 11.3 1.0
HAZ B:3S0303 4.2 20.3 1.0
ND1 B:HIS250 4.2 6.7 1.0
OXT B:3S0303 4.2 18.2 1.0
CG B:HIS250 4.3 7.1 1.0
NE2 B:HIS189 4.3 6.6 1.0
CB B:SER249 4.4 5.6 1.0
CB B:ASP124 4.4 5.7 1.0
CAT B:3S0303 4.4 17.6 1.0
C B:3S0303 4.5 19.7 1.0
CE1 B:HIS189 4.6 6.2 1.0
CA B:CYS208 4.6 6.3 1.0
CE1 B:HIS120 4.6 6.7 1.0
OG B:SER249 4.7 6.0 1.0
CAZ B:3S0303 4.7 16.9 1.0
NE2 B:HIS120 4.8 6.3 1.0
HBM B:3S0303 4.8 20.3 1.0
SAV B:3S0303 4.9 16.6 1.0

Reference:

H.Feng, J.Ding, D.Zhu, X.Liu, X.Xu, Y.Zhang, S.Zang, D.C.Wang, W.Liu. Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins. J.Am.Chem.Soc. V. 136 14694 2014.
ISSN: ISSN 0002-7863
PubMed: 25268575
DOI: 10.1021/JA508388E
Page generated: Wed Dec 16 05:45:56 2020

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