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Zinc in PDB 3knr: Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 1 Mm Zn(II)

Enzymatic activity of Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 1 Mm Zn(II)

All present enzymatic activity of Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 1 Mm Zn(II):
3.5.2.6;

Protein crystallography data

The structure of Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 1 Mm Zn(II), PDB code: 3knr 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 / 1.71
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.143, 94.364, 79.898, 90.00, 120.11, 90.00
R / Rfree (%) 17.2 / 21

Zinc Binding Sites:

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

Zinc binding site 1 out of 6 in 3knr

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Zinc binding site 1 out of 6 in the Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 1 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, 1 Mm Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn228

b:23.1
occ:1.00
ND1 A:HIS88 1.9 23.3 1.0
O A:HOH267 2.0 21.4 1.0
NE2 A:HIS149 2.0 18.5 1.0
NE2 A:HIS86 2.1 17.4 1.0
O A:HOH772 2.6 39.0 1.0
CE1 A:HIS88 2.8 23.2 1.0
CG A:HIS88 2.9 23.5 1.0
CD2 A:HIS149 2.9 15.5 1.0
CE1 A:HIS86 3.0 20.2 1.0
CD2 A:HIS86 3.0 19.6 1.0
CE1 A:HIS149 3.1 17.1 1.0
CB A:HIS88 3.2 24.0 1.0
OD1 A:ASP168 3.8 11.3 0.5
NE2 A:HIS88 3.9 26.1 1.0
CD2 A:HIS88 4.0 25.5 1.0
CG A:HIS149 4.1 16.7 1.0
ND1 A:HIS86 4.1 14.9 1.0
ND1 A:HIS149 4.1 15.5 1.0
CG A:HIS86 4.2 16.3 1.0
CG2 A:THR150 4.3 16.2 1.0
CG A:ASP168 4.3 17.2 0.5
OD1 A:ASP90 4.3 28.4 1.0
CB A:ASP168 4.4 14.8 0.5
CG A:ASP168 4.4 16.0 0.5
O A:HOH685 4.4 37.3 1.0
CB A:ASP168 4.4 14.8 0.5
O A:HOH539 4.4 38.9 1.0
OD1 A:ASP168 4.5 19.3 0.5
ZN A:ZN229 4.5 22.7 0.1
OD2 A:ASP168 4.6 18.7 0.5
O A:HOH771 4.7 45.0 1.0
CA A:HIS88 4.7 25.1 1.0
O A:HOH324 4.8 23.0 1.0
OD2 A:ASP90 5.0 23.2 1.0

Zinc binding site 2 out of 6 in 3knr

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Zinc binding site 2 out of 6 in the Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 1 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, 1 Mm Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn229

b:22.7
occ:0.15
OD2 A:ASP90 1.8 23.2 1.0
OD2 A:ASP168 1.9 18.7 0.5
NE2 A:HIS210 2.1 21.2 1.0
O A:HOH771 2.2 45.0 1.0
CG A:ASP168 2.5 17.2 0.5
OD1 A:ASP168 2.5 19.3 0.5
OD1 A:ASP168 2.8 11.3 0.5
CE1 A:HIS210 2.8 21.7 1.0
OD2 A:ASP168 2.9 18.8 0.5
CG A:ASP168 2.9 16.0 0.5
O A:HOH267 3.0 21.4 1.0
CG A:ASP90 3.0 28.7 1.0
CD2 A:HIS210 3.3 22.4 1.0
OD1 A:ASP90 3.6 28.4 1.0
O A:HOH1150 3.9 48.6 1.0
CB A:ASP168 3.9 14.8 0.5
CB A:ASP168 3.9 14.8 0.5
O A:HOH772 4.0 39.0 1.0
ND1 A:HIS210 4.0 23.3 1.0
O A:HOH685 4.1 37.3 1.0
NH2 A:ARG91 4.2 22.2 1.0
CB A:ASP90 4.2 26.3 1.0
O A:HOH364 4.2 31.5 1.0
CG A:HIS210 4.3 22.0 1.0
ZN A:ZN228 4.5 23.1 1.0
NE A:ARG91 4.7 20.6 1.0
CZ A:ARG91 4.8 24.4 1.0
CH2 A:TRP59 4.8 22.4 1.0
O A:HOH318 4.9 36.0 1.0
NE2 A:HIS149 4.9 18.5 1.0
CA A:ASP168 5.0 14.6 0.5

Zinc binding site 3 out of 6 in 3knr

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Zinc binding site 3 out of 6 in the Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 1 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, 1 Mm Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn228

b:21.9
occ:1.00
ND1 B:HIS88 1.8 18.1 1.0
O B:HOH767 2.0 25.7 1.0
NE2 B:HIS149 2.0 19.9 1.0
NE2 B:HIS86 2.1 17.2 1.0
O B:HOH282 2.6 28.9 1.0
CE1 B:HIS88 2.8 20.9 1.0
CG B:HIS88 2.9 18.4 1.0
CD2 B:HIS149 2.9 18.6 1.0
CE1 B:HIS149 3.0 18.8 1.0
CD2 B:HIS86 3.1 19.7 1.0
CE1 B:HIS86 3.1 18.2 1.0
CB B:HIS88 3.3 21.2 1.0
OD1 B:ASP168 3.9 23.7 1.0
NE2 B:HIS88 3.9 23.2 1.0
CD2 B:HIS88 4.0 22.0 1.0
CG B:HIS149 4.1 16.4 1.0
ND1 B:HIS149 4.1 16.8 1.0
ND1 B:HIS86 4.2 16.6 1.0
OD1 B:ASP90 4.2 41.5 1.0
CG2 B:THR150 4.2 17.0 1.0
CG B:HIS86 4.2 14.8 1.0
O B:HOH266 4.2 36.2 1.0
O B:HOH775 4.2 43.0 1.0
CG B:ASP168 4.4 23.1 1.0
CB B:ASP168 4.4 17.5 1.0
CA B:HIS88 4.7 22.5 1.0
O B:HOH385 4.8 38.0 1.0
OD2 B:ASP90 4.9 40.7 1.0
CG B:ASP90 4.9 33.5 1.0

Zinc binding site 4 out of 6 in 3knr

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Zinc binding site 4 out of 6 in the Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 1 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, 1 Mm Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn228

b:23.1
occ:1.00
ND1 C:HIS88 1.8 25.4 1.0
O C:HOH522 2.0 21.4 1.0
NE2 C:HIS149 2.0 18.7 1.0
NE2 C:HIS86 2.1 18.6 1.0
O C:HOH776 2.5 39.2 1.0
CE1 C:HIS88 2.8 22.7 1.0
CG C:HIS88 2.9 23.7 1.0
CD2 C:HIS149 2.9 16.9 1.0
CE1 C:HIS86 3.0 19.7 1.0
CE1 C:HIS149 3.1 19.6 1.0
CD2 C:HIS86 3.1 17.5 1.0
CB C:HIS88 3.3 25.2 1.0
OD1 C:ASP168 3.7 15.9 0.5
NE2 C:HIS88 3.9 25.5 1.0
CD2 C:HIS88 3.9 26.3 1.0
CG C:HIS149 4.1 17.9 1.0
ND1 C:HIS149 4.1 16.6 1.0
ND1 C:HIS86 4.1 14.0 1.0
CG C:HIS86 4.2 14.6 1.0
CG2 C:THR150 4.2 16.5 1.0
CG C:ASP168 4.3 17.0 0.5
OD2 C:ASP90 4.3 30.2 1.0
O C:HOH282 4.3 39.8 1.0
CG C:ASP168 4.4 17.1 0.5
CB C:ASP168 4.4 15.2 0.5
CB C:ASP168 4.5 14.9 0.5
OD1 C:ASP168 4.5 18.6 0.5
O C:HOH496 4.5 36.4 1.0
OD2 C:ASP168 4.5 21.8 0.5
ZN C:ZN229 4.6 20.5 0.1
O C:HOH546 4.6 49.8 1.0
CA C:HIS88 4.8 26.3 1.0
O C:HOH300 4.8 23.2 1.0
OD1 C:ASP90 4.9 22.7 1.0

Zinc binding site 5 out of 6 in 3knr

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Zinc binding site 5 out of 6 in the Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 1 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, 1 Mm Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn229

b:20.5
occ:0.15
OD1 C:ASP90 1.9 22.7 1.0
OD2 C:ASP168 1.9 21.8 0.5
NE2 C:HIS210 2.1 20.4 1.0
O C:HOH546 2.2 49.8 1.0
CG C:ASP168 2.5 17.0 0.5
OD1 C:ASP168 2.7 18.6 0.5
OD1 C:ASP168 2.8 15.9 0.5
OD2 C:ASP168 2.8 18.7 0.5
CE1 C:HIS210 2.8 20.1 1.0
CG C:ASP168 2.8 17.1 0.5
O C:HOH522 3.1 21.4 1.0
CG C:ASP90 3.1 29.3 1.0
CD2 C:HIS210 3.3 22.0 1.0
OD2 C:ASP90 3.7 30.2 1.0
O C:HOH1152 3.9 50.8 1.0
CB C:ASP168 3.9 15.2 0.5
CB C:ASP168 4.0 14.9 0.5
ND1 C:HIS210 4.1 21.4 1.0
O C:HOH282 4.1 39.8 1.0
O C:HOH318 4.1 37.8 1.0
O C:HOH776 4.2 39.2 1.0
O C:HOH1154 4.2 56.6 1.0
NH2 C:ARG91 4.2 24.5 1.0
CB C:ASP90 4.2 27.1 1.0
CG C:HIS210 4.3 21.2 1.0
O C:HOH1146 4.4 45.1 1.0
ZN C:ZN228 4.6 23.1 1.0
NE C:ARG91 4.6 21.4 1.0
O C:HOH404 4.8 33.2 1.0
CH2 C:TRP59 4.8 21.6 1.0
CZ C:ARG91 4.8 25.4 1.0
NE2 C:HIS149 4.9 18.7 1.0

Zinc binding site 6 out of 6 in 3knr

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Zinc binding site 6 out of 6 in the Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 1 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, 1 Mm Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn228

b:22.4
occ:1.00
O D:HOH652 1.9 26.6 1.0
ND1 D:HIS88 1.9 20.4 1.0
NE2 D:HIS149 2.0 17.9 1.0
NE2 D:HIS86 2.1 15.6 1.0
O D:HOH265 2.5 29.8 1.0
CE1 D:HIS88 2.9 19.8 1.0
CD2 D:HIS149 2.9 18.1 1.0
CG D:HIS88 2.9 18.4 1.0
CE1 D:HIS149 3.0 20.2 1.0
CD2 D:HIS86 3.1 17.5 1.0
CE1 D:HIS86 3.1 17.9 1.0
CB D:HIS88 3.3 20.5 1.0
OD1 D:ASP168 3.8 24.7 1.0
NE2 D:HIS88 4.0 22.5 1.0
CD2 D:HIS88 4.1 23.0 1.0
ND1 D:HIS149 4.1 16.6 1.0
CG D:HIS149 4.1 16.6 1.0
OD1 D:ASP90 4.1 42.3 1.0
ND1 D:HIS86 4.2 16.0 1.0
CG D:HIS86 4.2 14.6 1.0
O D:HOH778 4.2 44.8 1.0
CG2 D:THR150 4.2 17.8 1.0
O D:HOH248 4.2 35.1 1.0
CG D:ASP168 4.3 21.9 1.0
CB D:ASP168 4.4 18.2 1.0
CA D:HIS88 4.7 22.2 1.0
O D:HOH463 4.8 34.9 1.0
OD2 D:ASP90 4.9 42.1 1.0
CG D:ASP90 4.9 33.5 1.0
O D:HOH230 5.0 23.4 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 04:30:34 2020

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