Atomistry » Zinc » PDB 4rm5-4rvn » 4rm5
Atomistry »
  Zinc »
    PDB 4rm5-4rvn »
      4rm5 »

Zinc in PDB 4rm5: 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: 4rm5 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) 35.02 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.100, 68.120, 68.910, 87.62, 88.34, 77.42
R / Rfree (%) 15.9 / 19.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins (pdb code 4rm5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins, PDB code: 4rm5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4rm5

Go back to Zinc Binding Sites List in 4rm5
Zinc binding site 1 out of 8 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:Zn300

b:20.9
occ:1.00
ND1 A:HIS122 2.0 15.4 1.0
NE2 A:HIS189 2.1 16.2 1.0
CE1 A:HIS120 2.2 13.5 1.0
O A:HOH401 2.6 13.2 1.0
CE1 A:HIS122 3.0 18.9 1.0
ND1 A:HIS120 3.0 18.7 1.0
CG A:HIS122 3.0 16.5 1.0
CD2 A:HIS189 3.1 13.2 1.0
CE1 A:HIS189 3.1 12.5 1.0
NE2 A:HIS120 3.2 21.8 1.0
CB A:HIS122 3.4 11.6 1.0
SG A:CYS208 3.9 16.6 1.0
ZN A:ZN301 4.0 52.2 1.0
NE2 A:HIS122 4.1 17.0 1.0
CD2 A:HIS122 4.1 17.8 1.0
CB A:CYS208 4.2 12.6 1.0
CG A:HIS120 4.2 15.2 1.0
CG A:HIS189 4.2 14.0 1.0
ND1 A:HIS189 4.2 16.6 1.0
CD2 A:HIS120 4.3 13.8 1.0
OD1 A:ASN124 4.3 21.5 1.0
CG2 A:THR190 4.5 13.6 1.0
CA A:HIS122 4.9 13.4 1.0

Zinc binding site 2 out of 8 in 4rm5

Go back to Zinc Binding Sites List in 4rm5
Zinc binding site 2 out of 8 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:Zn301

b:52.2
occ:1.00
O A:HOH410 2.4 16.0 1.0
NE2 A:HIS250 2.4 40.5 1.0
SG A:CYS208 2.4 16.6 1.0
O A:HOH401 2.6 13.2 1.0
CD2 A:HIS250 3.0 41.5 1.0
CE1 A:HIS250 3.3 39.1 1.0
CB A:CYS208 3.4 12.6 1.0
ND2 A:ASN124 3.9 18.2 1.0
CE1 A:HIS189 4.0 12.5 1.0
ZN A:ZN300 4.0 20.9 1.0
CG A:HIS250 4.0 39.3 1.0
NE2 A:HIS189 4.1 16.2 1.0
ND1 A:HIS250 4.2 39.8 1.0
CA A:CYS208 4.4 14.8 1.0
NZ A:LYS211 4.5 32.8 1.0
CB A:SER249 4.5 20.3 1.0
CG A:ASN124 4.8 20.8 1.0
ND1 A:HIS189 4.8 16.6 1.0
OG A:SER249 4.9 18.3 1.0
OD1 A:ASN124 5.0 21.5 1.0

Zinc binding site 3 out of 8 in 4rm5

Go back to Zinc Binding Sites List in 4rm5
Zinc binding site 3 out of 8 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:Zn300

b:24.2
occ:1.00
ND1 B:HIS122 2.1 21.2 1.0
NE2 B:HIS120 2.2 14.4 1.0
CE1 B:HIS189 2.3 14.8 1.0
O B:HOH401 2.5 15.3 1.0
ND1 B:HIS189 3.0 15.8 1.0
CD2 B:HIS120 3.0 13.0 1.0
CG B:HIS122 3.0 24.4 1.0
CE1 B:HIS122 3.0 20.3 1.0
O B:HOH539 3.1 48.2 1.0
CE1 B:HIS120 3.2 16.2 1.0
CB B:HIS122 3.3 14.8 1.0
NE2 B:HIS189 3.5 23.2 1.0
SG B:CYS208 4.0 18.0 1.0
ZN B:ZN301 4.1 65.2 1.0
NE2 B:HIS122 4.1 18.7 1.0
CD2 B:HIS122 4.2 21.4 1.0
CG B:HIS120 4.2 14.1 1.0
ND1 B:HIS120 4.2 14.4 1.0
CB B:CYS208 4.3 10.4 1.0
OD1 B:ASN124 4.3 24.1 1.0
CG B:HIS189 4.3 15.2 1.0
CG2 B:THR190 4.5 14.4 1.0
CD2 B:HIS189 4.5 15.9 1.0
CA B:HIS122 4.8 14.0 1.0
O B:HOH468 5.0 25.3 1.0

Zinc binding site 4 out of 8 in 4rm5

Go back to Zinc Binding Sites List in 4rm5
Zinc binding site 4 out of 8 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:Zn301

b:65.2
occ:1.00
NE2 B:HIS250 2.1 33.8 1.0
O B:HOH468 2.3 25.3 1.0
SG B:CYS208 2.5 18.0 1.0
O B:HOH401 2.7 15.3 1.0
CD2 B:HIS250 2.9 28.0 1.0
CE1 B:HIS250 3.3 31.5 1.0
CB B:CYS208 3.3 10.4 1.0
O B:HOH534 3.4 43.7 1.0
ND2 B:ASN124 3.9 20.2 1.0
O B:HOH539 3.9 48.2 1.0
NE2 B:HIS189 4.0 23.2 1.0
CE1 B:HIS189 4.0 14.8 1.0
ZN B:ZN300 4.1 24.2 1.0
CG B:HIS250 4.1 32.8 1.0
ND1 B:HIS250 4.3 30.2 1.0
CA B:CYS208 4.4 17.9 1.0
CB B:SER249 4.5 20.6 1.0
CG B:ASN124 4.7 23.6 1.0
NZ B:LYS211 4.8 30.0 1.0
OD1 B:ASN124 4.8 24.1 1.0
ND1 B:HIS189 4.9 15.8 1.0
CD2 B:HIS189 4.9 15.9 1.0
OG B:SER249 4.9 20.1 1.0

Zinc binding site 5 out of 8 in 4rm5

Go back to Zinc Binding Sites List in 4rm5
Zinc binding site 5 out of 8 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 5 of Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn300

b:24.4
occ:1.00
ND1 C:HIS122 2.1 22.1 1.0
NE2 C:HIS189 2.1 21.6 1.0
CE1 C:HIS120 2.3 16.5 1.0
O C:HOH401 2.9 27.0 1.0
CD2 C:HIS189 3.0 11.2 1.0
ND1 C:HIS120 3.1 19.7 1.0
CG C:HIS122 3.1 19.8 1.0
CE1 C:HIS122 3.1 21.1 1.0
CE1 C:HIS189 3.2 21.7 1.0
NE2 C:HIS120 3.3 22.8 1.0
CB C:HIS122 3.4 15.5 1.0
ZN C:ZN301 4.1 54.9 1.0
SG C:CYS208 4.1 18.0 1.0
CG C:HIS189 4.2 14.8 1.0
NE2 C:HIS122 4.2 21.3 1.0
CD2 C:HIS122 4.2 20.2 1.0
ND1 C:HIS189 4.3 15.5 1.0
OD1 C:ASN124 4.3 20.1 1.0
CG C:HIS120 4.3 14.3 1.0
CB C:CYS208 4.4 20.1 1.0
CD2 C:HIS120 4.4 15.0 1.0
CG2 C:THR190 4.5 14.0 1.0
CA C:HIS122 4.8 17.9 1.0
ND2 C:ASN124 5.0 21.9 1.0

Zinc binding site 6 out of 8 in 4rm5

Go back to Zinc Binding Sites List in 4rm5
Zinc binding site 6 out of 8 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 6 of Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:54.9
occ:1.00
NE2 C:HIS250 2.3 35.1 1.0
O C:HOH518 2.4 32.5 1.0
SG C:CYS208 2.6 18.0 1.0
O C:HOH401 2.7 27.0 1.0
CD2 C:HIS250 2.8 30.4 1.0
CB C:CYS208 3.3 20.1 1.0
CE1 C:HIS250 3.6 29.0 1.0
ND2 C:ASN124 3.7 21.9 1.0
ZN C:ZN300 4.1 24.4 1.0
CG C:HIS250 4.1 38.5 1.0
CE1 C:HIS189 4.1 21.7 1.0
NE2 C:HIS189 4.2 21.6 1.0
CA C:CYS208 4.4 16.8 1.0
ND1 C:HIS250 4.4 37.0 1.0
CG C:ASN124 4.6 24.1 1.0
CB C:SER249 4.6 20.7 1.0
OD1 C:ASN124 4.9 20.1 1.0
ND1 C:HIS189 5.0 15.5 1.0

Zinc binding site 7 out of 8 in 4rm5

Go back to Zinc Binding Sites List in 4rm5
Zinc binding site 7 out of 8 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 7 of Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn300

b:22.8
occ:1.00
ND1 D:HIS122 2.0 16.9 1.0
NE2 D:HIS120 2.1 13.4 1.0
NE2 D:HIS189 2.2 19.2 1.0
O D:HOH483 2.6 15.4 1.0
CE1 D:HIS122 2.9 17.2 1.0
CE1 D:HIS120 3.0 15.2 1.0
CD2 D:HIS189 3.0 12.8 1.0
CG D:HIS122 3.0 20.2 1.0
CD2 D:HIS120 3.1 14.2 1.0
CE1 D:HIS189 3.2 18.0 1.0
CB D:HIS122 3.4 13.8 1.0
SG D:CYS208 3.9 19.0 1.0
NE2 D:HIS122 4.1 18.3 1.0
ND1 D:HIS120 4.1 16.6 1.0
ZN D:ZN301 4.1 44.3 1.0
CD2 D:HIS122 4.1 20.1 1.0
CG D:HIS120 4.2 15.2 1.0
CG D:HIS189 4.2 15.1 1.0
CB D:CYS208 4.2 18.1 1.0
ND1 D:HIS189 4.3 20.2 1.0
OD1 D:ASN124 4.3 20.8 1.0
CG2 D:THR190 4.6 20.2 1.0
CA D:HIS122 4.8 13.9 1.0
O D:HOH426 4.9 22.6 1.0

Zinc binding site 8 out of 8 in 4rm5

Go back to Zinc Binding Sites List in 4rm5
Zinc binding site 8 out of 8 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 8 of Structural and Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis of Cephalosporins within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:44.3
occ:1.00
O D:HOH426 2.1 22.6 1.0
NE2 D:HIS250 2.1 30.4 1.0
SG D:CYS208 2.5 19.0 1.0
O D:HOH483 2.6 15.4 1.0
CD2 D:HIS250 2.7 25.0 1.0
CE1 D:HIS250 3.3 27.6 1.0
CB D:CYS208 3.3 18.1 1.0
ND2 D:ASN124 3.9 21.3 1.0
CG D:HIS250 3.9 31.4 1.0
CE1 D:HIS189 4.1 18.0 1.0
ZN D:ZN300 4.1 22.8 1.0
ND1 D:HIS250 4.1 25.4 1.0
NE2 D:HIS189 4.2 19.2 1.0
CA D:CYS208 4.3 18.7 1.0
CB D:SER249 4.4 14.2 1.0
NZ D:LYS211 4.7 28.8 1.0
CG D:ASN124 4.8 17.2 1.0
ND1 D:HIS189 4.9 20.2 1.0
OG D:SER249 4.9 20.3 1.0
OD1 D:ASN124 5.0 20.8 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: Sun Oct 27 07:17:17 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy