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Zinc in PDB 3kns: Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II)

Enzymatic activity of Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II)

All present enzymatic activity of Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II):
3.5.2.6;

Protein crystallography data

The structure of Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II), PDB code: 3kns was solved by F.J.Medrano Martin, J.M.Gonzalez, A.J.Vila, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.30 / 1.58
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.784, 94.341, 79.776, 90.00, 119.62, 90.00
R / Rfree (%) 16.1 / 19.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II) (pdb code 3kns). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II), PDB code: 3kns:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3kns

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Zinc binding site 1 out of 8 in the Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn228

b:17.4
occ:1.00
 ND1 A:HIS88 1.9 17.9 1.0
NE2 A:HIS149 2.0 13.9 1.0
O A:HOH267 2.0 16.4 1.0
NE2 A:HIS86 2.1 11.9 1.0
O A:HOH737 2.4 21.0 1.0
CE1 A:HIS88 2.9 17.1 1.0
CG A:HIS88 2.9 15.8 1.0
CE1 A:HIS149 3.0 14.2 1.0
CD2 A:HIS149 3.0 13.0 1.0
CE1 A:HIS86 3.0 12.5 1.0
CD2 A:HIS86 3.1 13.9 1.0
CB A:HIS88 3.3 16.2 1.0
NE2 A:HIS88 4.0 20.2 1.0
OXT A:ACY233 4.0 25.9 1.0
CD2 A:HIS88 4.0 19.5 1.0
ND1 A:HIS149 4.1 13.4 1.0
CG A:HIS149 4.1 11.8 1.0
ND1 A:HIS86 4.1 11.6 1.0
CG A:ASP168 4.2 15.8 1.0
OD2 A:ASP168 4.2 17.4 1.0
CG A:HIS86 4.2 11.7 1.0
OD1 A:ASP90 4.2 16.7 1.0
CG2 A:THR150 4.3 15.2 1.0
OD1 A:ASP168 4.4 18.6 1.0
O A:HOH535 4.4 40.5 1.0
CB A:ASP168 4.5 11.7 1.0
ZN A:ZN229 4.5 17.8 1.0
C A:ACY233 4.7 25.4 1.0
CA A:HIS88 4.8 15.7 1.0
O A:ACY233 4.8 23.3 1.0
O A:HOH320 4.8 25.2 1.0
O A:HOH671 4.8 35.5 1.0

Zinc binding site 2 out of 8 in 3kns

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Zinc binding site 2 out of 8 in the Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn229

b:17.8
occ:1.00
 OD2 A:ASP90 1.9 15.3 1.0
OD2 A:ASP168 1.9 17.4 1.0
O A:ACY233 2.0 23.3 1.0
NE2 A:HIS210 2.0 13.1 1.0
CG A:ASP168 2.6 15.8 1.0
OD1 A:ASP168 2.7 18.6 1.0
O A:HOH267 2.9 16.4 1.0
CE1 A:HIS210 2.9 15.6 1.0
C A:ACY233 2.9 25.4 1.0
CG A:ASP90 3.0 16.1 1.0
CD2 A:HIS210 3.1 13.9 1.0
OXT A:ACY233 3.4 25.9 1.0
OD1 A:ASP90 3.5 16.7 1.0
NH2 A:ARG91 3.8 16.1 1.0
CB A:ASP168 4.0 11.7 1.0
ND1 A:HIS210 4.1 15.5 1.0
O A:HOH363 4.1 24.1 1.0
O A:HOH1139 4.1 42.5 1.0
CG A:HIS210 4.2 12.7 1.0
CB A:ASP90 4.2 14.8 1.0
CH3 A:ACY233 4.2 25.1 1.0
NE A:ARG91 4.4 13.5 1.0
ZN A:ZN228 4.5 17.4 1.0
CZ A:ARG91 4.6 15.4 1.0
O A:HOH737 4.6 21.0 1.0
CH2 A:TRP59 4.9 15.3 1.0
O A:HOH671 4.9 35.5 1.0
CE1 A:HIS86 5.0 12.5 1.0
NE2 A:HIS149 5.0 13.9 1.0
CA A:ASP168 5.0 12.2 1.0

Zinc binding site 3 out of 8 in 3kns

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Zinc binding site 3 out of 8 in the Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn228

b:17.7
occ:1.00
 ND1 B:HIS88 1.9 15.2 1.0
O B:HOH743 1.9 18.5 1.0
NE2 B:HIS149 2.0 14.8 1.0
NE2 B:HIS86 2.1 12.8 1.0
O B:HOH279 2.5 26.0 1.0
CE1 B:HIS88 2.9 15.9 1.0
CG B:HIS88 2.9 15.0 1.0
CD2 B:HIS149 3.0 13.3 1.0
CE1 B:HIS86 3.0 12.6 1.0
CE1 B:HIS149 3.0 14.3 1.0
CD2 B:HIS86 3.1 13.9 1.0
OD1 B:ASP168 3.2 14.1 0.3
CB B:HIS88 3.2 16.7 1.0
OD1 B:ASP168 3.8 21.9 0.7
CG B:ASP168 4.0 17.8 0.7
NE2 B:HIS88 4.0 18.8 1.0
CD2 B:HIS88 4.0 19.9 1.0
ND1 B:HIS86 4.1 12.7 1.0
ND1 B:HIS149 4.1 14.1 1.0
CG B:HIS149 4.1 11.6 1.0
OD1 B:ASP90 4.1 25.0 1.0
CG B:HIS86 4.2 12.1 1.0
ZN B:ZN229 4.2 21.9 0.7
CG B:ASP168 4.2 14.3 0.3
OD2 B:ASP168 4.3 15.8 0.7
O B:HOH681 4.3 44.8 1.0
CG2 B:THR150 4.3 13.9 1.0
CB B:ASP168 4.4 14.3 0.7
CB B:ASP168 4.5 12.3 0.3
O B:HOH383 4.5 37.1 1.0
O B:HOH744 4.6 36.2 1.0
CA B:HIS88 4.7 17.9 1.0
O B:HOH233 4.9 19.9 1.0
OD2 B:ASP90 4.9 28.8 1.0
CG B:ASP90 4.9 22.6 1.0

Zinc binding site 4 out of 8 in 3kns

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Zinc binding site 4 out of 8 in the Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn229

b:21.9
occ:0.70
 OD1 B:ASP168 1.9 21.9 0.7
OD2 B:ASP90 1.9 28.8 1.0
NE2 B:HIS210 2.0 22.3 1.0
OD1 B:ASP168 2.0 14.1 0.3
O B:HOH744 2.2 36.2 1.0
O B:HOH743 2.6 18.5 1.0
CG B:ASP168 2.6 17.8 0.7
CG B:ASP168 2.7 14.3 0.3
OD2 B:ASP168 2.7 15.8 0.7
OD2 B:ASP168 2.9 16.6 0.3
CE1 B:HIS210 2.9 23.2 1.0
CG B:ASP90 3.0 22.6 1.0
CD2 B:HIS210 3.0 19.8 1.0
OD1 B:ASP90 3.5 25.0 1.0
O B:HOH1232 3.7 36.4 1.0
NH2 B:ARG91 3.9 23.0 1.0
CB B:ASP168 4.0 12.3 0.3
ND1 B:HIS210 4.1 21.0 1.0
CB B:ASP168 4.1 14.3 0.7
CG B:HIS210 4.1 19.9 1.0
O B:HOH279 4.2 26.0 1.0
ZN B:ZN228 4.2 17.7 1.0
CB B:ASP90 4.2 21.3 1.0
NE B:ARG91 4.5 20.6 1.0
O B:HOH383 4.5 37.1 1.0
O B:HOH1231 4.6 29.4 1.0
CZ B:ARG91 4.7 23.1 1.0
NE2 B:HIS149 4.8 14.8 1.0
CH2 B:TRP59 4.8 32.8 1.0
CE1 B:HIS86 4.9 12.6 1.0
CE1 B:HIS149 5.0 14.3 1.0

Zinc binding site 5 out of 8 in 3kns

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Zinc binding site 5 out of 8 in the Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn228

b:17.4
occ:1.00
 ND1 C:HIS88 1.9 19.4 1.0
NE2 C:HIS149 2.0 14.5 1.0
O C:HOH519 2.0 16.5 1.0
NE2 C:HIS86 2.1 12.9 1.0
O C:HOH915 2.3 21.0 1.0
CE1 C:HIS88 2.9 18.6 1.0
CG C:HIS88 2.9 17.0 1.0
CE1 C:HIS149 3.0 13.9 1.0
CD2 C:HIS149 3.0 11.7 1.0
CE1 C:HIS86 3.0 13.1 1.0
CD2 C:HIS86 3.1 14.8 1.0
CB C:HIS88 3.3 17.2 1.0
OXT C:ACY230 4.0 25.5 1.0
NE2 C:HIS88 4.0 20.2 1.0
CD2 C:HIS88 4.0 19.7 1.0
ND1 C:HIS149 4.1 14.4 1.0
OD2 C:ASP168 4.1 18.0 1.0
CG C:HIS149 4.1 12.8 1.0
ND1 C:HIS86 4.1 12.1 1.0
CG C:ASP168 4.1 15.7 1.0
CG C:HIS86 4.2 11.6 1.0
OD1 C:ASP90 4.2 16.8 1.0
CG2 C:THR150 4.3 15.5 1.0
O C:HOH494 4.4 36.0 1.0
OD1 C:ASP168 4.4 17.5 1.0
CB C:ASP168 4.5 12.7 1.0
ZN C:ZN229 4.5 17.6 1.0
O C:HOH300 4.7 23.6 1.0
C C:ACY230 4.7 25.1 1.0
CA C:HIS88 4.8 16.6 1.0
O C:ACY230 4.8 23.9 1.0
O C:HOH276 4.9 34.0 1.0

Zinc binding site 6 out of 8 in 3kns

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Zinc binding site 6 out of 8 in the Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn229

b:17.6
occ:1.00
 OD2 C:ASP90 1.9 15.1 1.0
OD2 C:ASP168 1.9 18.0 1.0
O C:ACY230 2.0 23.9 1.0
NE2 C:HIS210 2.0 13.9 1.0
CG C:ASP168 2.6 15.7 1.0
OD1 C:ASP168 2.7 17.5 1.0
O C:HOH519 2.9 16.5 1.0
CE1 C:HIS210 2.9 15.6 1.0
C C:ACY230 2.9 25.1 1.0
CG C:ASP90 3.0 16.3 1.0
CD2 C:HIS210 3.1 14.2 1.0
OXT C:ACY230 3.3 25.5 1.0
OD1 C:ASP90 3.5 16.8 1.0
NH2 C:ARG91 3.8 16.6 1.0
CB C:ASP168 4.0 12.7 1.0
ND1 C:HIS210 4.0 15.1 1.0
O C:HOH318 4.1 23.5 1.0
O C:HOH1101 4.1 41.2 1.0
CG C:HIS210 4.1 13.5 1.0
CB C:ASP90 4.2 14.6 1.0
CH3 C:ACY230 4.2 24.2 1.0
NE C:ARG91 4.4 13.2 1.0
ZN C:ZN228 4.5 17.4 1.0
CZ C:ARG91 4.6 16.1 1.0
O C:HOH915 4.6 21.0 1.0
O C:HOH1099 4.9 39.1 1.0
CH2 C:TRP59 4.9 15.5 1.0
O C:HOH276 4.9 34.0 1.0
CE1 C:HIS86 5.0 13.1 1.0
NE2 C:HIS149 5.0 14.5 1.0

Zinc binding site 7 out of 8 in 3kns

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Zinc binding site 7 out of 8 in the Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn228

b:17.9
occ:1.00
 ND1 D:HIS88 1.9 15.8 1.0
O D:HOH640 2.0 18.4 1.0
NE2 D:HIS149 2.0 14.7 1.0
NE2 D:HIS86 2.1 13.0 1.0
O D:HOH265 2.6 26.8 1.0
CG D:HIS88 2.9 15.7 1.0
CE1 D:HIS88 2.9 15.8 1.0
CD2 D:HIS149 3.0 14.2 1.0
CE1 D:HIS149 3.0 13.7 1.0
CE1 D:HIS86 3.0 13.0 1.0
CD2 D:HIS86 3.1 13.2 1.0
CB D:HIS88 3.2 16.1 1.0
OD2 D:ASP168 3.5 12.7 0.3
OD2 D:ASP168 3.8 20.1 0.7
CG D:ASP168 4.0 17.1 0.7
NE2 D:HIS88 4.0 18.8 1.0
CD2 D:HIS88 4.0 19.1 1.0
ND1 D:HIS149 4.1 13.5 1.0
ND1 D:HIS86 4.1 13.0 1.0
CG D:HIS149 4.1 11.3 1.0
CG D:HIS86 4.2 12.4 1.0
OD1 D:ASP90 4.2 25.3 1.0
ZN D:ZN229 4.2 21.9 0.7
CG D:ASP168 4.3 14.1 0.3
CG2 D:THR150 4.3 13.3 1.0
O D:HOH729 4.3 42.3 1.0
CB D:ASP168 4.4 14.3 0.7
CB D:ASP168 4.4 12.8 0.3
O D:HOH461 4.5 38.6 1.0
OD1 D:ASP168 4.5 18.7 0.7
O D:HOH968 4.5 36.7 1.0
CA D:HIS88 4.7 17.2 1.0
O D:HOH1053 4.9 20.0 1.0
OD2 D:ASP90 4.9 28.9 1.0
CG D:ASP90 5.0 22.3 1.0

Zinc binding site 8 out of 8 in 3kns

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Zinc binding site 8 out of 8 in the Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 20 Mm Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn229

b:21.9
occ:0.70
 OD2 D:ASP168 1.9 20.1 0.7
OD2 D:ASP90 2.0 28.9 1.0
NE2 D:HIS210 2.0 22.7 1.0
O D:HOH968 2.1 36.7 1.0
OD2 D:ASP168 2.4 12.7 0.3
O D:HOH640 2.6 18.4 1.0
CG D:ASP168 2.7 17.1 0.7
CG D:ASP168 2.8 14.1 0.3
OD1 D:ASP168 2.8 18.7 0.7
OD1 D:ASP168 2.8 16.1 0.3
CE1 D:HIS210 2.9 22.9 1.0
CD2 D:HIS210 3.0 19.1 1.0
CG D:ASP90 3.0 22.3 1.0
OD1 D:ASP90 3.4 25.3 1.0
NH2 D:ARG91 3.8 22.6 1.0
O D:HOH1233 3.9 36.6 1.0
CB D:ASP168 4.0 12.8 0.3
ND1 D:HIS210 4.1 21.5 1.0
CB D:ASP168 4.1 14.3 0.7
CG D:HIS210 4.1 19.3 1.0
O D:HOH265 4.2 26.8 1.0
ZN D:ZN228 4.2 17.9 1.0
CB D:ASP90 4.3 21.4 1.0
NE D:ARG91 4.4 19.8 1.0
O D:HOH461 4.4 38.6 1.0
O D:HOH1230 4.6 29.6 1.0
CZ D:ARG91 4.6 23.5 1.0
CH2 D:TRP59 4.8 30.8 1.0
NE2 D:HIS149 4.8 14.7 1.0
CE1 D:HIS86 4.9 13.0 1.0
CE1 D:HIS149 5.0 13.7 1.0

Reference:

J.M.Gonzalez, M.R.Meini, P.E.Tomatis, F.J.Medrano Martin, J.A.Cricco, A.J.Vila. Metallo-Beta-Lactamases Withstand Low Zn(II) Conditions By Tuning Metal-Ligand Interactions. Nat.Chem.Biol. V. 8 698 2012.
ISSN: ISSN 1552-4450
PubMed: 22729148
DOI: 10.1038/NCHEMBIO.1005
Page generated: Wed Dec 16 04:30:36 2020

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