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Zinc in PDB 2qin: Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant

Enzymatic activity of Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant

All present enzymatic activity of Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant:
3.5.2.6;

Protein crystallography data

The structure of Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant, PDB code: 2qin was solved by J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.84 / 1.76
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.141, 112.845, 78.352, 90.00, 113.35, 90.00
R / Rfree (%) 17.3 / 21.2

Other elements in 2qin:

The structure of Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant (pdb code 2qin). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant, PDB code: 2qin:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 2qin

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Zinc binding site 1 out of 9 in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:21.8
occ:1.00
O A:HOH2192 1.8 19.0 1.0
NE2 A:HIS121 2.0 15.8 1.0
NE2 A:HIS263 2.1 16.7 1.0
SG A:CYS120 2.4 15.8 1.0
CD2 A:HIS121 2.9 15.7 1.0
CE1 A:HIS263 3.0 16.9 1.0
CE1 A:HIS121 3.0 15.8 1.0
O A:HOH2313 3.1 40.9 1.0
CD2 A:HIS263 3.1 16.5 1.0
CB A:CYS120 3.5 14.0 1.0
ZN A:ZN2002 3.5 17.6 1.0
CG A:HIS121 4.0 14.4 1.0
ND1 A:HIS121 4.0 15.0 1.0
NE2 A:HIS116 4.1 12.9 1.0
ND1 A:HIS263 4.1 16.9 1.0
CG A:HIS263 4.2 16.8 1.0
O A:HOH2203 4.3 29.6 1.0
CE1 A:HIS116 4.3 13.8 1.0
CA A:CYS120 4.6 13.6 1.0
C A:CYS120 4.7 13.6 1.0
OH A:TYR32 4.8 23.3 1.0
CB A:HIS118 4.8 12.3 1.0
O A:CYS120 4.9 14.0 1.0
N A:CYS120 5.0 13.0 1.0

Zinc binding site 2 out of 9 in 2qin

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Zinc binding site 2 out of 9 in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:17.6
occ:1.00
NE2 A:HIS196 2.0 13.5 1.0
O A:HOH2192 2.1 19.0 1.0
ND1 A:HIS118 2.1 12.8 1.0
NE2 A:HIS116 2.1 12.9 1.0
CD2 A:HIS196 2.9 13.9 1.0
CE1 A:HIS118 3.0 12.7 1.0
O A:HOH2313 3.0 40.9 1.0
CD2 A:HIS116 3.0 13.0 1.0
CE1 A:HIS196 3.1 13.8 1.0
CG A:HIS118 3.1 12.2 1.0
CE1 A:HIS116 3.1 13.8 1.0
CB A:HIS118 3.5 12.3 1.0
ZN A:ZN2001 3.5 21.8 1.0
CG A:HIS196 4.1 13.6 1.0
O A:HOH2203 4.1 29.6 1.0
NE2 A:HIS118 4.1 13.0 1.0
CG A:HIS116 4.2 12.0 1.0
ND1 A:HIS196 4.2 13.8 1.0
ND1 A:HIS116 4.2 13.7 1.0
CD2 A:HIS118 4.2 12.8 1.0
CD2 A:HIS121 4.3 15.7 1.0
NE2 A:HIS121 4.3 15.8 1.0
SG A:CYS120 4.6 15.8 1.0
OG A:SER221 4.8 17.9 1.0
CA A:HIS118 5.0 11.9 1.0

Zinc binding site 3 out of 9 in 2qin

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Zinc binding site 3 out of 9 in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:16.5
occ:1.00
O B:HOH4232 1.9 14.3 1.0
NE2 B:HIS121 2.0 11.8 1.0
NE2 B:HIS263 2.1 10.8 1.0
SG B:CYS120 2.5 13.1 1.0
CD2 B:HIS121 2.9 11.5 1.0
CE1 B:HIS121 3.0 11.8 1.0
CE1 B:HIS263 3.0 12.1 1.0
CD2 B:HIS263 3.1 11.2 1.0
O B:HOH4234 3.3 39.3 1.0
CB B:CYS120 3.6 10.7 1.0
ZN B:ZN2002 3.6 13.1 1.0
ND1 B:HIS121 4.0 10.8 1.0
CG B:HIS121 4.0 10.9 1.0
NE2 B:HIS116 4.1 11.3 1.0
O B:HOH4230 4.1 33.4 1.0
ND1 B:HIS263 4.2 10.9 1.0
CG B:HIS263 4.2 10.8 1.0
CE1 B:HIS116 4.3 10.8 1.0
O B:HOH4241 4.5 29.3 1.0
CA B:CYS120 4.6 10.6 1.0
C B:CYS120 4.8 10.5 1.0
CB B:HIS118 4.9 8.9 1.0
OH B:TYR32 4.9 18.1 1.0
O B:CYS120 5.0 10.5 1.0

Zinc binding site 4 out of 9 in 2qin

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Zinc binding site 4 out of 9 in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2002

b:13.1
occ:1.00
O B:HOH4232 1.9 14.3 1.0
NE2 B:HIS196 2.0 9.7 1.0
ND1 B:HIS118 2.1 9.6 1.0
NE2 B:HIS116 2.1 11.3 1.0
O B:HOH4241 2.9 29.3 1.0
CD2 B:HIS196 2.9 9.4 1.0
CE1 B:HIS118 3.0 10.2 1.0
CE1 B:HIS116 3.0 10.8 1.0
CD2 B:HIS116 3.1 9.9 1.0
CE1 B:HIS196 3.1 10.2 1.0
CG B:HIS118 3.1 9.0 1.0
O B:HOH4234 3.4 39.3 1.0
CB B:HIS118 3.5 8.9 1.0
ZN B:ZN2001 3.6 16.5 1.0
O B:HOH4230 4.0 33.4 1.0
ND1 B:HIS116 4.1 11.4 1.0
CG B:HIS196 4.1 9.4 1.0
NE2 B:HIS118 4.1 9.0 1.0
CG B:HIS116 4.1 10.1 1.0
ND1 B:HIS196 4.2 9.3 1.0
CD2 B:HIS118 4.2 9.7 1.0
CD2 B:HIS121 4.3 11.5 1.0
NE2 B:HIS121 4.3 11.8 1.0
SG B:CYS120 4.7 13.1 1.0
OG B:SER221 4.9 8.8 0.5
CA B:HIS118 4.9 9.2 1.0

Zinc binding site 5 out of 9 in 2qin

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Zinc binding site 5 out of 9 in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2001

b:24.8
occ:1.00
O C:HOH2241 1.9 20.0 1.0
NE2 C:HIS121 2.0 18.7 1.0
NE2 C:HIS263 2.3 20.8 1.0
SG C:CYS120 2.4 18.8 1.0
CD2 C:HIS121 2.8 17.5 1.0
CE1 C:HIS121 2.9 18.5 1.0
CE1 C:HIS263 3.1 21.8 1.0
O C:HOH2252 3.2 40.9 1.0
CD2 C:HIS263 3.3 21.7 1.0
CB C:CYS120 3.5 17.5 1.0
ZN C:ZN2002 3.6 20.3 1.0
CG C:HIS121 3.9 18.0 1.0
ND1 C:HIS121 3.9 18.6 1.0
NE2 C:HIS116 4.1 16.6 1.0
ND1 C:HIS263 4.2 20.9 1.0
CE1 C:HIS116 4.3 16.4 1.0
CG C:HIS263 4.4 22.0 1.0
CA C:CYS120 4.5 17.1 1.0
C C:CYS120 4.6 17.2 1.0
O C:CYS120 4.8 17.4 1.0
O C:HOH2251 4.8 41.3 1.0
OH C:TYR32 4.8 23.3 1.0
CB C:HIS118 4.9 15.3 1.0
N C:CYS120 4.9 16.7 1.0

Zinc binding site 6 out of 9 in 2qin

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Zinc binding site 6 out of 9 in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2002

b:20.3
occ:1.00
NE2 C:HIS196 2.0 17.0 1.0
O C:HOH2241 2.1 20.0 1.0
NE2 C:HIS116 2.1 16.6 1.0
ND1 C:HIS118 2.2 16.1 1.0
CD2 C:HIS196 3.0 16.3 1.0
O C:HOH2252 3.0 40.9 1.0
CD2 C:HIS116 3.0 16.2 1.0
CE1 C:HIS116 3.1 16.4 1.0
CE1 C:HIS196 3.1 17.1 1.0
CE1 C:HIS118 3.1 16.2 1.0
CG C:HIS118 3.2 15.9 1.0
O C:HOH2251 3.4 41.3 1.0
CB C:HIS118 3.5 15.3 1.0
ZN C:ZN2001 3.6 24.8 1.0
ND1 C:HIS116 4.1 17.0 1.0
CG C:HIS116 4.1 15.8 1.0
CG C:HIS196 4.1 15.8 1.0
ND1 C:HIS196 4.1 16.7 1.0
NE2 C:HIS118 4.2 16.4 1.0
CD2 C:HIS121 4.3 17.5 1.0
NE2 C:HIS121 4.3 18.7 1.0
CD2 C:HIS118 4.3 15.2 1.0
SG C:CYS120 4.7 18.8 1.0
OG C:SER221 5.0 22.1 1.0
CA C:HIS118 5.0 15.2 1.0
O C:HOH2200 5.0 44.3 1.0

Zinc binding site 7 out of 9 in 2qin

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Zinc binding site 7 out of 9 in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:18.1
occ:1.00
O D:HOH4261 2.0 13.3 1.0
NE2 D:HIS121 2.0 13.1 1.0
NE2 D:HIS263 2.1 11.1 1.0
SG D:CYS120 2.4 14.5 1.0
CE1 D:HIS121 3.0 12.5 1.0
CD2 D:HIS121 3.0 11.8 1.0
CE1 D:HIS263 3.0 11.5 1.0
CD2 D:HIS263 3.2 11.8 1.0
O D:HOH4378 3.2 41.0 1.0
ZN D:ZN2002 3.6 13.4 1.0
CB D:CYS120 3.7 12.1 1.0
ND1 D:HIS121 4.0 11.7 1.0
CG D:HIS121 4.0 12.0 1.0
NE2 D:HIS116 4.1 9.9 1.0
ND1 D:HIS263 4.1 11.6 1.0
O D:HOH4207 4.2 32.0 1.0
CG D:HIS263 4.2 10.6 1.0
CE1 D:HIS116 4.3 10.4 1.0
O D:HOH4347 4.5 29.9 1.0
CA D:CYS120 4.7 11.8 1.0
C D:CYS120 4.8 11.6 1.0
O D:CYS120 4.9 11.9 1.0
CB D:HIS118 4.9 10.2 1.0
OH D:TYR32 4.9 23.1 1.0
NE2 D:HIS196 5.0 9.9 1.0

Zinc binding site 8 out of 9 in 2qin

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Zinc binding site 8 out of 9 in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:13.4
occ:1.00
O D:HOH4261 1.9 13.3 1.0
NE2 D:HIS196 2.0 9.9 1.0
ND1 D:HIS118 2.0 10.6 1.0
NE2 D:HIS116 2.1 9.9 1.0
O D:HOH4347 2.8 29.9 1.0
CD2 D:HIS196 2.9 8.4 1.0
CE1 D:HIS118 2.9 11.1 1.0
CD2 D:HIS116 3.0 9.6 1.0
CE1 D:HIS116 3.0 10.4 1.0
CG D:HIS118 3.1 10.7 1.0
CE1 D:HIS196 3.1 10.4 1.0
O D:HOH4378 3.3 41.0 1.0
CB D:HIS118 3.5 10.2 1.0
ZN D:ZN2001 3.6 18.1 1.0
NE2 D:HIS118 4.1 10.8 1.0
CG D:HIS196 4.1 9.3 1.0
ND1 D:HIS116 4.1 11.1 1.0
CG D:HIS116 4.1 9.9 1.0
ND1 D:HIS196 4.2 9.3 1.0
CD2 D:HIS118 4.2 11.4 1.0
O D:HOH4207 4.2 32.0 1.0
NE2 D:HIS121 4.3 13.1 1.0
CD2 D:HIS121 4.3 11.8 1.0
SG D:CYS120 4.6 14.5 1.0
CA D:HIS118 5.0 10.3 1.0
OG D:SER221 5.0 12.6 1.0

Zinc binding site 9 out of 9 in 2qin

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Zinc binding site 9 out of 9 in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Cys Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3001

b:10.7
occ:0.50
O B:HOH4240 2.2 7.0 1.0
NE2 B:HIS51 2.2 13.3 1.0
CD2 B:HIS51 3.0 12.8 1.0
CE1 B:HIS51 3.3 14.0 1.0
CD B:PRO76 3.9 16.8 1.0
CG B:HIS51 4.3 12.8 1.0
ND1 B:HIS51 4.4 13.8 1.0
CG B:PRO76 4.5 17.3 1.0
CA B:THR75 4.8 15.8 1.0
O B:GLN74 4.9 14.8 1.0
CB B:THR75 5.0 15.9 1.0

Reference:

J.Crisp, R.Conners, J.D.Garrity, A.L.Carenbauer, M.W.Crowder, J.Spencer. Structural Basis For the Role of Asp-120 in Metallo-Beta-Lactamases. Biochemistry V. 46 10664 2007.
ISSN: ISSN 0006-2960
PubMed: 17715946
DOI: 10.1021/BI700707U
Page generated: Wed Dec 16 03:50:29 2020

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