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Zinc in PDB 4bp0: Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1

Enzymatic activity of Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1

All present enzymatic activity of Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1, PDB code: 4bp0 was solved by M.A.Mcdonough, J.Brem, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.9428 / 2.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.650, 83.550, 282.410, 90.00, 90.00, 90.00
R / Rfree (%) 15.16 / 19.81

Other elements in 4bp0:

The structure of Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1 also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1 (pdb code 4bp0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1, PDB code: 4bp0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 4bp0

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Zinc binding site 1 out of 10 in the Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1312

b:28.0
occ:1.00
 ND1 A:HIS110 2.0 29.6 1.0
NE2 A:HIS108 2.0 24.5 1.0
NE2 A:HIS197 2.0 25.0 1.0
O A:HOH2056 2.0 27.4 1.0
CE1 A:HIS110 2.9 31.2 1.0
CD2 A:HIS197 3.0 25.6 1.0
CD2 A:HIS108 3.0 35.0 1.0
CG A:HIS110 3.0 30.9 1.0
CE1 A:HIS108 3.0 24.4 1.0
CE1 A:HIS197 3.0 27.5 1.0
O A:HOH2132 3.3 57.6 1.0
ZN A:ZN1313 3.4 37.9 1.0
CB A:HIS110 3.4 25.9 1.0
OD1 A:ASP112 3.8 37.4 1.0
O A:HOH2057 3.9 55.4 1.0
CL A:CL1318 4.0 51.7 1.0
NE2 A:HIS110 4.0 30.6 1.0
CD2 A:HIS110 4.1 27.5 1.0
SG A:CYS216 4.1 32.6 1.0
ND1 A:HIS197 4.1 29.2 1.0
ND1 A:HIS108 4.1 27.1 1.0
CG A:HIS197 4.1 31.1 1.0
CG A:HIS108 4.1 22.9 1.0
CB A:CYS216 4.1 22.5 1.0
OD2 A:ASP112 4.3 28.6 1.0
CG A:ASP112 4.4 20.2 1.0
O A:HOH2177 4.8 55.7 1.0
CA A:HIS110 4.8 26.7 1.0

Zinc binding site 2 out of 10 in 4bp0

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Zinc binding site 2 out of 10 in the Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1313

b:37.9
occ:1.00
 O A:HOH2056 2.0 27.4 1.0
NE2 A:HIS258 2.1 31.5 1.0
OD2 A:ASP112 2.1 28.6 1.0
SG A:CYS216 2.3 32.6 1.0
CL A:CL1318 2.5 51.7 1.0
CD2 A:HIS258 2.9 25.5 1.0
CG A:ASP112 3.1 20.2 1.0
CE1 A:HIS258 3.1 31.4 1.0
CB A:CYS216 3.3 22.5 1.0
ZN A:ZN1312 3.4 28.0 1.0
OD1 A:ASP112 3.4 37.4 1.0
O A:HOH2058 3.5 42.9 1.0
O A:HOH2132 4.0 57.6 1.0
CG A:HIS258 4.1 25.8 1.0
NE2 A:HIS197 4.2 25.0 1.0
ND1 A:HIS258 4.2 28.8 1.0
CE1 A:HIS108 4.2 24.4 1.0
NE2 A:HIS108 4.3 24.5 1.0
CB A:ASP112 4.5 22.7 1.0
CE1 A:HIS197 4.5 27.5 1.0
CA A:CYS216 4.6 25.8 1.0
O A:HOH2057 4.8 55.4 1.0
CD2 A:HIS197 5.0 25.6 1.0
O A:HOH2051 5.0 50.4 1.0

Zinc binding site 3 out of 10 in 4bp0

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Zinc binding site 3 out of 10 in the Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1314

b:38.9
occ:1.00
 OD2 A:ASP35 2.0 40.1 1.0
OD2 C:ASP35 2.0 47.0 1.0
NE2 A:HIS33 2.0 39.6 1.0
NE2 C:HIS33 2.1 45.6 1.0
OD1 C:ASP35 2.3 42.8 1.0
CG C:ASP35 2.5 44.5 1.0
CG A:ASP35 2.7 44.3 1.0
OD1 A:ASP35 2.9 49.5 1.0
CE1 A:HIS33 2.9 43.9 1.0
CD2 C:HIS33 3.0 43.5 1.0
CD2 A:HIS33 3.0 33.0 1.0
CE1 C:HIS33 3.1 61.5 1.0
CB C:ASP35 4.0 44.0 1.0
ND1 A:HIS33 4.1 43.9 1.0
CG A:HIS33 4.1 39.0 1.0
CG C:HIS33 4.2 43.5 1.0
ND1 C:HIS33 4.2 45.7 1.0
CB A:ASP35 4.2 39.7 1.0
C3 C:GOL1312 4.9 65.0 1.0
CA C:ASP35 4.9 41.7 1.0

Zinc binding site 4 out of 10 in 4bp0

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Zinc binding site 4 out of 10 in the Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1311

b:38.9
occ:1.00
 ND1 B:HIS110 2.0 37.8 1.0
NE2 B:HIS197 2.0 44.6 1.0
NE2 B:HIS108 2.1 46.6 1.0
O B:HOH2028 2.2 36.5 1.0
CE1 B:HIS110 2.8 42.8 1.0
CD2 B:HIS108 3.0 34.9 1.0
CE1 B:HIS197 3.0 43.1 1.0
CG B:HIS110 3.0 35.5 1.0
CD2 B:HIS197 3.1 44.3 1.0
CE1 B:HIS108 3.1 51.7 1.0
ZN B:ZN1312 3.3 49.3 1.0
CB B:HIS110 3.5 38.5 1.0
OD1 B:ASP112 3.9 51.1 1.0
NE2 B:HIS110 3.9 38.5 1.0
CL B:CL1315 4.0 61.9 1.0
CD2 B:HIS110 4.1 39.5 1.0
ND1 B:HIS197 4.1 48.3 1.0
CB B:CYS216 4.1 59.9 1.0
SG B:CYS216 4.1 57.5 1.0
CG B:HIS108 4.1 36.2 1.0
CG B:HIS197 4.2 42.1 1.0
ND1 B:HIS108 4.2 45.8 1.0
OD2 B:ASP112 4.4 47.6 1.0
CG B:ASP112 4.5 42.2 1.0
CA B:HIS110 4.9 45.0 1.0

Zinc binding site 5 out of 10 in 4bp0

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Zinc binding site 5 out of 10 in the Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1312

b:49.3
occ:1.00
 O B:HOH2028 2.0 36.5 1.0
NE2 B:HIS258 2.1 54.8 1.0
OD2 B:ASP112 2.1 47.6 1.0
SG B:CYS216 2.2 57.5 1.0
CL B:CL1315 2.5 61.9 1.0
CD2 B:HIS258 3.0 51.7 1.0
CE1 B:HIS258 3.0 44.5 1.0
CG B:ASP112 3.1 42.2 1.0
ZN B:ZN1311 3.3 38.9 1.0
CB B:CYS216 3.4 59.9 1.0
OD1 B:ASP112 3.4 51.1 1.0
NE2 B:HIS108 4.1 46.6 1.0
ND1 B:HIS258 4.1 51.9 1.0
CG B:HIS258 4.2 53.1 1.0
CE1 B:HIS108 4.2 51.7 1.0
NE2 B:HIS197 4.2 44.6 1.0
CE1 B:HIS197 4.5 43.1 1.0
CB B:ASP112 4.5 42.5 1.0
CA B:CYS216 4.7 54.8 1.0
ND1 B:HIS110 4.9 37.8 1.0

Zinc binding site 6 out of 10 in 4bp0

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Zinc binding site 6 out of 10 in the Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1313

b:48.4
occ:1.00
 NE2 B:HIS33 2.0 63.7 1.0
OD2 B:ASP35 2.1 73.4 1.0
OD1 B:ASP35 2.2 59.8 1.0
CG B:ASP35 2.5 61.0 1.0
CE1 B:HIS33 3.0 66.0 1.0
CD2 B:HIS33 3.0 59.7 1.0
CB B:ASP35 4.0 58.6 1.0
ND1 B:HIS33 4.1 63.7 1.0
CG B:HIS33 4.2 64.6 1.0
N B:ASP35 4.8 55.1 1.0
CA B:ASP35 4.9 58.0 1.0

Zinc binding site 7 out of 10 in 4bp0

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Zinc binding site 7 out of 10 in the Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1310

b:35.0
occ:1.00
 ND1 C:HIS110 2.0 27.8 1.0
O C:HOH2029 2.1 36.0 1.0
NE2 C:HIS197 2.1 38.7 1.0
NE2 C:HIS108 2.1 34.0 1.0
CD2 C:HIS108 3.0 29.0 1.0
CE1 C:HIS110 3.0 43.3 1.0
CG C:HIS110 3.0 35.8 1.0
CD2 C:HIS197 3.0 37.0 1.0
CE1 C:HIS197 3.1 42.1 1.0
CE1 C:HIS108 3.2 36.8 1.0
CB C:HIS110 3.4 27.1 1.0
ZN C:ZN1311 3.4 43.1 1.0
OD1 C:ASP112 3.9 38.2 1.0
CL C:CL1314 3.9 64.5 1.0
NE2 C:HIS110 4.1 39.3 1.0
SG C:CYS216 4.1 45.3 1.0
CD2 C:HIS110 4.1 35.4 1.0
CG C:HIS108 4.2 31.9 1.0
CB C:CYS216 4.2 35.1 1.0
CG C:HIS197 4.2 40.3 1.0
ND1 C:HIS197 4.2 48.4 1.0
ND1 C:HIS108 4.2 34.2 1.0
OD2 C:ASP112 4.4 38.0 1.0
CG C:ASP112 4.6 39.1 1.0
CA C:HIS110 4.8 33.0 1.0

Zinc binding site 8 out of 10 in 4bp0

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Zinc binding site 8 out of 10 in the Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1311

b:43.1
occ:1.00
 O C:HOH2029 2.0 36.0 1.0
NE2 C:HIS258 2.1 40.4 1.0
OD2 C:ASP112 2.1 38.0 1.0
CL C:CL1314 2.3 64.5 1.0
SG C:CYS216 2.3 45.3 1.0
CD2 C:HIS258 3.0 40.9 1.0
CE1 C:HIS258 3.0 48.6 1.0
CG C:ASP112 3.1 39.1 1.0
OD1 C:ASP112 3.4 38.2 1.0
O C:HOH2030 3.4 52.5 1.0
ZN C:ZN1310 3.4 35.0 1.0
CB C:CYS216 3.5 35.1 1.0
ND1 C:HIS258 4.1 43.7 1.0
CG C:HIS258 4.2 41.2 1.0
CE1 C:HIS108 4.2 36.8 1.0
NE2 C:HIS108 4.2 34.0 1.0
NE2 C:HIS197 4.3 38.7 1.0
CB C:ASP112 4.5 36.3 1.0
CA C:CYS216 4.7 40.6 1.0
CE1 C:HIS197 4.7 42.1 1.0
O C:ASP112 5.0 40.8 1.0

Zinc binding site 9 out of 10 in 4bp0

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Zinc binding site 9 out of 10 in the Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1310

b:35.0
occ:1.00
 ND1 D:HIS110 1.9 30.7 1.0
NE2 D:HIS197 2.0 34.1 1.0
O D:HOH2027 2.1 33.8 1.0
NE2 D:HIS108 2.1 27.8 1.0
CE1 D:HIS110 2.8 35.0 1.0
CD2 D:HIS197 2.9 34.0 1.0
CG D:HIS110 2.9 39.8 1.0
CD2 D:HIS108 3.0 31.8 1.0
CE1 D:HIS197 3.1 34.1 1.0
CE1 D:HIS108 3.1 37.7 1.0
CB D:HIS110 3.4 32.1 1.0
ZN D:ZN1311 3.4 44.4 1.0
OD1 D:ASP112 3.8 40.8 1.0
NE2 D:HIS110 3.9 44.1 1.0
CD2 D:HIS110 4.0 44.9 1.0
SG D:CYS216 4.1 44.5 1.0
CG D:HIS197 4.1 37.1 1.0
CB D:CYS216 4.1 37.6 1.0
ND1 D:HIS197 4.1 35.4 1.0
CG D:HIS108 4.2 33.8 1.0
ND1 D:HIS108 4.2 33.8 1.0
CL D:CL1315 4.2 56.4 1.0
OD2 D:ASP112 4.3 37.3 1.0
CG D:ASP112 4.5 38.6 1.0
CA D:HIS110 4.8 32.8 1.0

Zinc binding site 10 out of 10 in 4bp0

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Zinc binding site 10 out of 10 in the Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Closed Form of Pseudomonas Aeruginosa Spm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1311

b:44.4
occ:1.00
 O D:HOH2027 2.0 33.8 1.0
NE2 D:HIS258 2.1 50.5 1.0
OD2 D:ASP112 2.1 37.3 1.0
SG D:CYS216 2.4 44.5 1.0
CL D:CL1315 2.5 56.4 1.0
CD2 D:HIS258 3.0 45.1 1.0
CE1 D:HIS258 3.1 41.4 1.0
CG D:ASP112 3.1 38.6 1.0
ZN D:ZN1310 3.4 35.0 1.0
OD1 D:ASP112 3.5 40.8 1.0
CB D:CYS216 3.5 37.6 1.0
O D:HOH2008 3.8 56.4 1.0
ND1 D:HIS258 4.1 39.3 1.0
CG D:HIS258 4.2 42.0 1.0
NE2 D:HIS197 4.2 34.1 1.0
CE1 D:HIS108 4.4 37.7 1.0
NE2 D:HIS108 4.4 27.8 1.0
CB D:ASP112 4.5 34.9 1.0
CE1 D:HIS197 4.6 34.1 1.0
CA D:CYS216 4.7 30.8 1.0
O D:HOH2079 4.9 46.2 1.0
CD2 D:HIS197 5.0 34.0 1.0

Reference:

M.A.Mcdonough, J.Brem, C.J.Schofield. The Crystal Structure of the Closed Form or Pseudomonas Aeruginosa Spm-1 To Be Published.
Page generated: Sat Oct 26 19:52:31 2024

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