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Zinc in PDB 2qjs: Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Asn Mutant

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

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

Protein crystallography data

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

Resolution Low / High (Å) 10.00 / 2.25
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 86.382, 86.382, 227.363, 90.00, 90.00, 120.00
R / Rfree (%) n/a / 28.3

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 2qjs

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Zinc binding site 1 out of 8 in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Asn 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 Asn Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:52.4
occ:1.00
 NE2 A:HIS121 2.1 41.9 1.0
NE2 A:HIS263 2.1 48.9 1.0
O A:HOH2096 2.2 26.4 1.0
O A:HOH2108 2.3 47.2 1.0
O A:HOH2095 2.5 27.1 1.0
CD2 A:HIS263 3.0 43.1 1.0
CE1 A:HIS121 3.0 43.9 1.0
CD2 A:HIS121 3.1 44.3 1.0
CE1 A:HIS263 3.1 48.9 1.0
ZN A:ZN2002 3.7 43.5 1.0
O A:HOH2101 3.9 30.9 1.0
ND1 A:HIS121 4.2 42.6 1.0
CG A:HIS263 4.2 47.2 1.0
ND1 A:HIS263 4.2 46.5 1.0
CG A:HIS121 4.2 39.6 1.0
CE1 A:HIS116 4.6 38.9 1.0
CB A:ASN120 4.6 40.4 0.5
OG A:SER221 4.7 58.4 1.0
NE2 A:HIS116 4.7 33.2 1.0
NE2 A:HIS196 4.8 19.9 1.0

Zinc binding site 2 out of 8 in 2qjs

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Zinc binding site 2 out of 8 in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Asn 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 Asn Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:43.5
occ:1.00
 O A:HOH2095 2.0 27.1 1.0
NE2 A:HIS196 2.1 19.9 1.0
NE2 A:HIS116 2.1 33.2 1.0
ND1 A:HIS118 2.1 37.6 1.0
CE1 A:HIS196 2.9 21.5 1.0
CE1 A:HIS116 2.9 38.9 1.0
CE1 A:HIS118 3.0 34.5 1.0
CG A:HIS118 3.0 35.3 1.0
CD2 A:HIS116 3.2 39.8 1.0
CD2 A:HIS196 3.2 18.8 1.0
O A:HOH2096 3.2 26.4 1.0
CB A:HIS118 3.4 37.4 1.0
O A:HOH2101 3.6 30.9 1.0
ZN A:ZN2001 3.7 52.4 1.0
CD2 A:HIS121 3.9 44.3 1.0
ND1 A:HIS116 4.0 41.7 1.0
NE2 A:HIS118 4.1 38.4 1.0
ND1 A:HIS196 4.1 18.2 1.0
CD2 A:HIS118 4.1 36.0 1.0
NE2 A:HIS121 4.2 41.9 1.0
CG A:HIS116 4.2 42.0 1.0
CG A:HIS196 4.2 15.1 1.0
CG2 A:THR197 4.8 32.5 1.0
CA A:HIS118 4.9 39.2 1.0
O A:HOH2065 4.9 43.5 1.0
OG A:SER221 5.0 58.4 1.0

Zinc binding site 3 out of 8 in 2qjs

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Zinc binding site 3 out of 8 in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Asn 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 Asn Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:53.8
occ:1.00
 O B:HOH2085 2.1 37.1 1.0
NE2 B:HIS263 2.1 54.7 1.0
NE2 B:HIS121 2.1 43.0 1.0
O B:HOH2084 2.2 40.8 1.0
CD2 B:HIS263 2.9 50.7 1.0
CE1 B:HIS121 3.0 41.2 1.0
CD2 B:HIS121 3.1 46.9 1.0
CE1 B:HIS263 3.2 54.2 1.0
ZN B:ZN2002 3.8 42.9 1.0
ND1 B:HIS121 4.1 42.1 1.0
CG B:HIS263 4.2 52.8 1.0
CG B:HIS121 4.2 42.7 1.0
ND1 B:HIS263 4.2 53.4 1.0
OG B:SER221 4.6 41.3 1.0
CE1 B:HIS116 4.7 36.8 1.0
NE2 B:HIS116 4.8 31.5 1.0
CB B:ASN120 4.8 34.9 0.5
NE2 B:HIS196 4.8 19.9 1.0

Zinc binding site 4 out of 8 in 2qjs

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Zinc binding site 4 out of 8 in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Asn 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 Asn Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2002

b:42.9
occ:1.00
 O B:HOH2084 1.8 40.8 1.0
NE2 B:HIS196 2.0 19.9 1.0
NE2 B:HIS116 2.1 31.5 1.0
ND1 B:HIS118 2.1 41.0 1.0
CD2 B:HIS196 2.8 24.5 1.0
CE1 B:HIS116 2.9 36.8 1.0
CE1 B:HIS118 3.0 39.7 1.0
CG B:HIS118 3.1 38.4 1.0
CD2 B:HIS116 3.1 38.4 1.0
CE1 B:HIS196 3.2 26.7 1.0
O B:HOH2085 3.2 37.1 1.0
CB B:HIS118 3.5 42.1 1.0
ZN B:ZN2001 3.8 53.8 1.0
CG B:HIS196 4.0 27.1 1.0
CD2 B:HIS121 4.0 46.9 1.0
ND1 B:HIS116 4.1 43.6 1.0
NE2 B:HIS118 4.1 44.9 1.0
ND1 B:HIS196 4.2 30.7 1.0
CD2 B:HIS118 4.2 41.3 1.0
CG B:HIS116 4.2 43.7 1.0
NE2 B:HIS121 4.3 43.0 1.0
CA B:HIS118 4.9 44.1 1.0

Zinc binding site 5 out of 8 in 2qjs

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Zinc binding site 5 out of 8 in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Asn 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 Asn Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2001

b:55.3
occ:1.00
 O C:HOH2070 1.8 32.5 1.0
NE2 C:HIS263 2.1 33.6 1.0
NE2 C:HIS121 2.2 60.0 1.0
O C:HOH2069 2.6 33.5 1.0
CD2 C:HIS121 3.0 54.3 1.0
CE1 C:HIS263 3.1 35.3 1.0
CD2 C:HIS263 3.1 37.4 1.0
CE1 C:HIS121 3.3 53.1 1.0
ZN C:ZN2002 3.9 47.5 1.0
ND1 C:HIS263 4.2 35.9 1.0
CG C:HIS121 4.2 48.9 1.0
CG C:HIS263 4.3 38.5 1.0
ND1 C:HIS121 4.3 50.6 1.0
O C:HOH2086 4.3 51.5 1.0
NE2 C:HIS116 4.4 23.8 1.0
CE1 C:HIS116 4.5 21.4 1.0
OG C:SER221 4.6 57.0 1.0
CB C:ASN120 4.8 37.6 0.5
NE2 C:HIS196 4.9 44.0 1.0

Zinc binding site 6 out of 8 in 2qjs

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Zinc binding site 6 out of 8 in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Asn 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 Asn Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2002

b:47.5
occ:1.00
 NE2 C:HIS196 2.0 44.0 1.0
ND1 C:HIS118 2.0 44.6 1.0
NE2 C:HIS116 2.1 23.8 1.0
O C:HOH2069 2.4 33.5 1.0
CD2 C:HIS116 2.9 27.4 1.0
CD2 C:HIS196 3.0 40.2 1.0
CE1 C:HIS118 3.0 49.7 1.0
CG C:HIS118 3.0 46.6 1.0
CE1 C:HIS196 3.1 46.2 1.0
CE1 C:HIS116 3.1 21.4 1.0
CB C:HIS118 3.3 44.5 1.0
O C:HOH2070 3.9 32.5 1.0
O C:HOH2086 3.9 51.5 1.0
ZN C:ZN2001 3.9 55.3 1.0
CG C:HIS116 4.0 26.6 1.0
ND1 C:HIS116 4.0 22.0 1.0
NE2 C:HIS118 4.1 49.0 1.0
CD2 C:HIS118 4.1 46.5 1.0
ND1 C:HIS196 4.1 45.2 1.0
CG C:HIS196 4.1 43.9 1.0
CD2 C:HIS121 4.4 54.3 1.0
NE2 C:HIS121 4.7 60.0 1.0
CA C:HIS118 4.8 37.0 1.0

Zinc binding site 7 out of 8 in 2qjs

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Zinc binding site 7 out of 8 in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Asn 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 Asn Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:54.4
occ:1.00
 NE2 D:HIS263 2.1 49.8 1.0
NE2 D:HIS121 2.1 48.1 1.0
O D:HOH2093 2.2 32.6 1.0
CD2 D:HIS263 2.9 51.8 1.0
CD2 D:HIS121 3.0 45.9 1.0
CE1 D:HIS121 3.1 42.4 1.0
CE1 D:HIS263 3.3 47.6 1.0
O D:HOH2105 3.8 39.1 1.0
ZN D:ZN2002 4.1 44.8 1.0
CG D:HIS121 4.1 43.5 1.0
CG D:HIS263 4.1 50.7 1.0
ND1 D:HIS121 4.1 44.8 1.0
ND1 D:HIS263 4.3 47.9 1.0
O D:HOH2053 4.5 53.5 1.0
CE1 D:HIS116 4.6 34.4 1.0
O D:HOH2095 4.6 43.9 1.0
OG D:SER221 4.6 49.2 1.0
NE2 D:HIS116 4.8 34.6 1.0
CB D:ASN120 4.8 36.5 0.5
NE2 D:HIS196 5.0 54.5 1.0

Zinc binding site 8 out of 8 in 2qjs

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Zinc binding site 8 out of 8 in the Stenotrophomonas Maltophilia L1 Metallo-Beta-Lactamase Asp-120 Asn 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 Asn Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:44.8
occ:1.00
 NE2 D:HIS196 2.1 54.5 1.0
ND1 D:HIS118 2.1 45.9 1.0
NE2 D:HIS116 2.1 34.6 1.0
CE1 D:HIS118 3.0 52.4 1.0
CE1 D:HIS196 3.0 49.2 1.0
CD2 D:HIS196 3.0 53.5 1.0
CE1 D:HIS116 3.1 34.4 1.0
CD2 D:HIS116 3.1 29.1 1.0
CG D:HIS118 3.2 45.9 1.0
O D:HOH2093 3.5 32.6 1.0
CB D:HIS118 3.5 42.7 1.0
ZN D:ZN2001 4.1 54.4 1.0
NE2 D:HIS118 4.1 48.3 1.0
ND1 D:HIS196 4.1 43.7 1.0
ND1 D:HIS116 4.1 34.6 1.0
CG D:HIS196 4.2 45.9 1.0
CG D:HIS116 4.2 29.8 1.0
CD2 D:HIS118 4.2 42.4 1.0
O D:HOH2095 4.6 43.9 1.0
CD2 D:HIS121 4.6 45.9 1.0
O D:HOH2105 4.7 39.1 1.0
CG2 D:THR197 4.8 23.2 1.0
CA D:HIS118 5.0 36.2 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: Thu Oct 17 03:28:33 2024

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