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Copper in PDB 2fu7: Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form)

Enzymatic activity of Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form)

All present enzymatic activity of Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form):
3.5.2.6;

Protein crystallography data

The structure of Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form), PDB code: 2fu7 was solved by L.Nauton, G.Garau, R.Kahn, O.Dideberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.37 / 1.85
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 105.350, 105.350, 196.280, 90.00, 90.00, 120.00
R / Rfree (%) 16.3 / 19.5

Copper Binding Sites:

The binding sites of Copper atom in the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form) (pdb code 2fu7). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form), PDB code: 2fu7:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2fu7

Go back to Copper Binding Sites List in 2fu7
Copper binding site 1 out of 6 in the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:14.1
occ:1.00
 NE2 A:HIS116 2.0 10.3 1.0
ND1 A:HIS118 2.0 13.1 1.0
NE2 A:HIS196 2.2 10.8 1.0
CE1 A:HIS116 2.9 13.9 1.0
CD2 A:HIS196 3.0 12.2 1.0
CE1 A:HIS118 3.0 13.0 1.0
CD2 A:HIS116 3.0 11.7 1.0
CG A:HIS118 3.1 11.7 1.0
O A:HOH411 3.1 24.0 1.0
CE1 A:HIS196 3.3 11.8 1.0
CB A:HIS118 3.4 10.8 1.0
CU A:CU402 3.5 17.0 1.0
ND1 A:HIS116 4.0 11.3 1.0
OD1 A:ASP120 4.0 13.4 1.0
CG A:HIS116 4.1 9.8 1.0
NE2 A:HIS118 4.1 11.7 1.0
CD2 A:HIS118 4.2 10.5 1.0
CG A:HIS196 4.2 11.7 1.0
CD2 A:HIS121 4.2 12.1 1.0
NE2 A:HIS121 4.3 9.8 1.0
ND1 A:HIS196 4.3 10.4 1.0
OD2 A:ASP120 4.7 15.3 1.0
CG A:ASP120 4.8 14.4 1.0
CA A:HIS118 4.9 11.0 1.0
CE2 A:PHE156 5.0 25.0 1.0

Copper binding site 2 out of 6 in 2fu7

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Copper binding site 2 out of 6 in the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:17.0
occ:1.00
 NE2 A:HIS121 2.0 9.8 1.0
OD2 A:ASP120 2.1 15.3 1.0
NE2 A:HIS263 2.1 15.0 1.0
O A:HOH411 2.4 24.0 1.0
CG A:ASP120 2.9 14.4 1.0
CE1 A:HIS121 3.0 11.2 1.0
CD2 A:HIS263 3.0 16.4 1.0
CD2 A:HIS121 3.1 12.1 1.0
CE1 A:HIS263 3.1 15.5 1.0
OD1 A:ASP120 3.1 13.4 1.0
CU A:CU401 3.5 14.1 1.0
CE1 A:HIS116 4.0 13.9 1.0
NE2 A:HIS116 4.0 10.3 1.0
ND1 A:HIS121 4.1 10.2 1.0
CG A:HIS121 4.2 11.9 1.0
ND1 A:HIS263 4.2 15.3 1.0
CG A:HIS263 4.2 12.2 1.0
CB A:ASP120 4.3 14.1 1.0
O A:HOH420 4.3 24.9 1.0
OG A:SER221 4.5 16.4 1.0
NE2 A:HIS196 4.7 10.8 1.0

Copper binding site 3 out of 6 in 2fu7

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Copper binding site 3 out of 6 in the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:5.7
occ:0.25
 N10 A:PHN410 1.8 18.6 0.5
NE2 A:HIS51 1.9 20.6 1.0
N1 A:PHN410 2.3 19.8 0.5
C10 A:PHN410 2.7 18.9 0.5
C1A A:PHN410 2.9 19.3 0.5
C9 A:PHN410 2.9 19.6 0.5
CE1 A:HIS51 2.9 24.0 1.0
CD2 A:HIS51 3.0 18.3 1.0
C2 A:PHN410 3.4 19.0 0.5
ND1 A:HIS51 4.0 23.5 1.0
CG A:HIS51 4.1 18.5 1.0
C6A A:PHN410 4.1 19.7 0.5
C8 A:PHN410 4.2 19.3 0.5
OG1 A:THR208 4.3 15.4 1.0
C4A A:PHN410 4.3 19.6 0.5
C3 A:PHN410 4.6 19.9 0.5
C7 A:PHN410 4.7 20.4 0.5

Copper binding site 4 out of 6 in 2fu7

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Copper binding site 4 out of 6 in the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:14.2
occ:1.00
 NE2 B:HIS116 2.1 8.1 1.0
NE2 B:HIS196 2.1 13.4 1.0
ND1 B:HIS118 2.1 12.5 1.0
O B:HOH411 2.8 31.6 1.0
CE1 B:HIS116 3.0 11.2 1.0
CD2 B:HIS196 3.0 10.3 1.0
CE1 B:HIS118 3.0 12.0 1.0
CD2 B:HIS116 3.1 10.0 1.0
CG B:HIS118 3.1 11.2 1.0
CE1 B:HIS196 3.2 14.1 1.0
O B:HOH587 3.3 27.3 1.0
CB B:HIS118 3.5 11.1 1.0
CU B:CU402 3.6 16.9 1.0
OD1 B:ASP120 4.1 14.6 1.0
ND1 B:HIS116 4.1 11.0 1.0
CG B:HIS116 4.2 10.2 1.0
NE2 B:HIS118 4.2 10.6 1.0
CG B:HIS196 4.2 9.6 1.0
CD2 B:HIS121 4.2 14.5 1.0
CD2 B:HIS118 4.2 13.0 1.0
ND1 B:HIS196 4.2 12.0 1.0
NE2 B:HIS121 4.3 12.1 1.0
OD2 B:ASP120 4.7 16.6 1.0
CG B:ASP120 4.9 12.7 1.0
CA B:HIS118 4.9 10.8 1.0

Copper binding site 5 out of 6 in 2fu7

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Copper binding site 5 out of 6 in the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu402

b:16.9
occ:1.00
 NE2 B:HIS121 2.0 12.1 1.0
OD2 B:ASP120 2.1 16.6 1.0
NE2 B:HIS263 2.1 13.5 1.0
O B:HOH587 2.5 27.3 1.0
CE1 B:HIS121 2.9 13.9 1.0
CG B:ASP120 2.9 12.7 1.0
CD2 B:HIS121 3.0 14.5 1.0
CD2 B:HIS263 3.0 16.4 1.0
CE1 B:HIS263 3.1 13.7 1.0
OD1 B:ASP120 3.2 14.6 1.0
CU B:CU401 3.6 14.2 1.0
ND1 B:HIS121 4.0 11.7 1.0
CE1 B:HIS116 4.1 11.2 1.0
CG B:HIS121 4.1 13.4 1.0
NE2 B:HIS116 4.1 8.1 1.0
ND1 B:HIS263 4.2 13.0 1.0
CG B:HIS263 4.2 14.8 1.0
CB B:ASP120 4.3 12.5 1.0
O B:HOH411 4.3 31.6 1.0
O B:HOH416 4.5 30.3 1.0
OG B:SER221 4.6 18.0 1.0
NE2 B:HIS196 4.8 13.4 1.0

Copper binding site 6 out of 6 in 2fu7

Go back to Copper Binding Sites List in 2fu7
Copper binding site 6 out of 6 in the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Cu- Substituted Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu403

b:33.0
occ:0.50
 N1 B:PHN410 1.9 15.2 0.2
NE2 B:HIS51 1.9 26.7 1.0
C2 B:PHN410 2.7 17.0 0.2
N10 B:PHN410 2.8 18.3 0.2
CD2 B:HIS51 2.8 24.7 1.0
C1A B:PHN410 2.8 17.3 0.2
CE1 B:HIS51 3.0 27.9 1.0
C10 B:PHN410 3.2 17.5 0.2
C9 B:PHN410 3.9 17.4 0.2
CG B:HIS51 4.0 21.8 1.0
C3 B:PHN410 4.0 16.6 0.2
ND1 B:HIS51 4.0 26.3 1.0
C4A B:PHN410 4.2 17.0 0.2
C4 B:PHN410 4.6 17.9 0.2
C6A B:PHN410 4.6 18.0 0.2
O B:HOH544 4.9 26.9 0.5

Reference:

L.Nauton, R.Kahn, G.Garau, J.F.Hernandez, O.Dideberg. Structural Insights Into the Design of Inhibitors For the L1 Metallo-Beta-Lactamase From Stenotrophomonas Maltophilia. J.Mol.Biol. V. 375 257 2008.
ISSN: ISSN 0022-2836
PubMed: 17999929
DOI: 10.1016/J.JMB.2007.10.036
Page generated: Sun Dec 13 11:04:50 2020

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