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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

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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

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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

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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

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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

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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

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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

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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

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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: Wed Aug 20 22:11:13 2025

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