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Zinc in PDB 2f4l: Crystal Structure of A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution, PDB code: 2f4l was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.70 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.257, 104.068, 154.945, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 24.2

Other elements in 2f4l:

The structure of Crystal Structure of A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution (pdb code 2f4l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution, PDB code: 2f4l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2f4l

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Zinc binding site 1 out of 8 in the Crystal Structure of A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution


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 A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1400

b:37.0
occ:1.00
 NE2 A:HIS175 2.1 29.0 1.0
OE1 A:GLU189 2.1 27.7 1.0
OD1 A:ASP173 2.2 25.9 1.0
OE2 A:GLU189 2.2 19.2 1.0
CD A:GLU189 2.4 27.7 1.0
CE1 A:HIS175 3.0 34.5 1.0
O A:HOH1450 3.0 30.1 1.0
CG A:ASP173 3.0 19.5 1.0
CD2 A:HIS175 3.1 26.4 1.0
OD2 A:ASP173 3.2 26.3 1.0
ZN A:ZN1401 3.3 48.7 1.0
CG A:GLU189 3.9 32.9 1.0
CB A:ALA36 3.9 28.4 1.0
ND1 A:HIS175 4.1 26.9 1.0
OE2 A:GLU182 4.1 55.4 1.0
CG A:HIS175 4.2 26.1 1.0
OD1 A:ASP148 4.3 34.6 1.0
O A:HOH1405 4.4 18.5 1.0
CB A:ASP173 4.4 23.5 1.0
O A:ASP173 4.6 22.7 1.0
N A:ALA187 4.8 26.0 1.0
CB A:GLU189 4.9 31.1 1.0
CA A:ASP173 4.9 22.7 1.0
C A:ASP173 5.0 21.8 1.0

Zinc binding site 2 out of 8 in 2f4l

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Zinc binding site 2 out of 8 in the Crystal Structure of A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution


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 A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1401

b:48.7
occ:1.00
 OD1 A:ASN146 2.1 29.8 1.0
OD1 A:ASP148 2.2 34.6 1.0
OD2 A:ASP173 2.3 26.3 1.0
OD2 A:ASP148 2.7 37.7 1.0
CG A:ASP148 2.8 33.4 1.0
CG A:ASN146 3.0 28.0 1.0
O A:HOH1450 3.0 30.1 1.0
ND2 A:ASN146 3.2 31.1 1.0
CG A:ASP173 3.2 19.5 1.0
ZN A:ZN1400 3.3 37.0 1.0
OD1 A:ASP173 3.6 25.9 1.0
OE2 A:GLU182 4.0 55.4 1.0
CE1 A:HIS175 4.1 34.5 1.0
NE2 A:HIS175 4.2 29.0 1.0
CB A:ASP148 4.3 29.4 1.0
OE1 A:GLU182 4.4 47.5 1.0
CB A:ASN146 4.4 27.6 1.0
CB A:ASP173 4.5 23.5 1.0
CD A:GLU182 4.6 35.9 1.0
ND2 A:ASN50 4.6 37.2 1.0
O A:GLY124 4.8 26.2 1.0
ND2 A:ASN268 4.8 29.4 1.0
OD1 A:ASN268 4.9 28.2 1.0
CG2 A:VAL125 4.9 22.0 1.0
CA A:ASN146 4.9 28.0 1.0
C A:GLY124 4.9 25.4 1.0
CA A:ASP148 5.0 29.5 1.0
N A:ASP148 5.0 29.3 1.0

Zinc binding site 3 out of 8 in 2f4l

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Zinc binding site 3 out of 8 in the Crystal Structure of A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution


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 A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2400

b:38.3
occ:1.00
 OD1 B:ASP173 2.1 22.7 1.0
OE1 B:GLU189 2.2 25.0 1.0
NE2 B:HIS175 2.2 27.5 1.0
OE2 B:GLU189 2.5 27.1 1.0
O B:HOH2435 2.6 21.3 1.0
CD B:GLU189 2.7 27.4 1.0
CG B:ASP173 3.0 20.0 1.0
CD2 B:HIS175 3.1 26.8 1.0
OD2 B:ASP173 3.2 26.1 1.0
CE1 B:HIS175 3.3 34.4 1.0
ZN B:ZN2401 3.3 48.1 1.0
CB B:ALA36 4.0 29.6 1.0
OE2 B:GLU182 4.1 55.8 1.0
CG B:GLU189 4.2 29.5 1.0
CG B:HIS175 4.3 26.8 1.0
O B:HOH2413 4.3 20.4 1.0
ND1 B:HIS175 4.3 27.0 1.0
CB B:ASP173 4.4 23.4 1.0
O B:ASP173 4.4 22.6 1.0
OD1 B:ASP148 4.5 36.7 1.0
N B:ALA187 4.6 30.0 1.0
C B:ASP173 4.8 22.6 1.0
CA B:ASP173 4.8 22.7 1.0
CB B:ALA187 4.9 29.3 1.0
CB B:GLU189 5.0 27.7 1.0

Zinc binding site 4 out of 8 in 2f4l

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Zinc binding site 4 out of 8 in the Crystal Structure of A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution


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 A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2401

b:48.1
occ:1.00
 OD1 B:ASP148 2.2 36.7 1.0
OD2 B:ASP173 2.2 26.1 1.0
OD1 B:ASN146 2.2 29.4 1.0
OD2 B:ASP148 2.5 37.2 1.0
CG B:ASP148 2.7 33.5 1.0
CG B:ASN146 3.1 27.9 1.0
CG B:ASP173 3.2 20.0 1.0
ND2 B:ASN146 3.3 29.9 1.0
ZN B:ZN2400 3.3 38.3 1.0
O B:HOH2435 3.5 21.3 1.0
OD1 B:ASP173 3.6 22.7 1.0
OE2 B:GLU182 4.0 55.8 1.0
OE1 B:GLU182 4.1 41.3 1.0
NE2 B:HIS175 4.1 27.5 1.0
CB B:ASP148 4.2 29.0 1.0
CE1 B:HIS175 4.2 34.4 1.0
CD B:GLU182 4.5 36.8 1.0
CB B:ASP173 4.5 23.4 1.0
CB B:ASN146 4.5 27.0 1.0
ND2 B:ASN268 4.6 29.5 1.0
ND2 B:ASN50 4.8 37.9 1.0
OD1 B:ASN268 4.8 29.0 1.0
CG2 B:VAL125 4.8 21.8 1.0
O B:GLY124 4.8 25.0 1.0
C B:GLY124 4.8 25.0 1.0
CA B:GLY124 4.8 25.7 1.0
CA B:ASP148 4.9 29.5 1.0
CA B:ASN146 5.0 27.2 1.0

Zinc binding site 5 out of 8 in 2f4l

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Zinc binding site 5 out of 8 in the Crystal Structure of A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution


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 A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3400

b:49.4
occ:1.00
 OD1 C:ASP148 2.0 35.8 1.0
OD2 C:ASP173 2.1 27.7 1.0
OD1 C:ASN146 2.2 30.6 1.0
OD2 C:ASP148 2.5 35.4 1.0
CG C:ASP148 2.6 33.9 1.0
CG C:ASN146 3.2 27.5 1.0
CG C:ASP173 3.2 20.6 1.0
ZN C:ZN3401 3.4 40.9 1.0
ND2 C:ASN146 3.5 30.7 1.0
O C:HOH3444 3.6 21.2 1.0
OD1 C:ASP173 3.7 24.9 1.0
OE2 C:GLU182 3.9 45.9 1.0
OE1 C:GLU182 4.1 44.1 1.0
CB C:ASP148 4.1 30.2 1.0
CE1 C:HIS175 4.3 33.7 1.0
NE2 C:HIS175 4.3 29.1 1.0
CD C:GLU182 4.4 33.3 1.0
CB C:ASP173 4.5 23.1 1.0
ND2 C:ASN268 4.5 28.0 1.0
CB C:ASN146 4.6 27.6 1.0
ND2 C:ASN50 4.6 35.5 1.0
CA C:GLY124 4.7 25.1 1.0
C C:GLY124 4.7 25.7 1.0
O C:GLY124 4.7 25.8 1.0
CA C:ASP148 4.8 29.7 1.0
CG2 C:VAL125 4.8 22.3 1.0
OD1 C:ASN268 4.9 28.9 1.0
N C:ASP148 4.9 28.5 1.0
CA C:ASN146 4.9 27.3 1.0

Zinc binding site 6 out of 8 in 2f4l

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Zinc binding site 6 out of 8 in the Crystal Structure of A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution


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 A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3401

b:40.9
occ:1.00
 OD1 C:ASP173 2.1 24.9 1.0
OE1 C:GLU189 2.3 34.6 1.0
NE2 C:HIS175 2.3 29.1 1.0
OE2 C:GLU189 2.4 39.0 1.0
CD C:GLU189 2.6 32.1 1.0
O C:HOH3444 2.6 21.2 1.0
CG C:ASP173 3.0 20.6 1.0
CE1 C:HIS175 3.2 33.7 1.0
OD2 C:ASP173 3.2 27.7 1.0
CD2 C:HIS175 3.2 27.4 1.0
ZN C:ZN3400 3.4 49.4 1.0
OE2 C:GLU182 3.8 45.9 1.0
CB C:ALA36 4.0 33.0 1.0
CG C:GLU189 4.1 28.5 1.0
OD1 C:ASP148 4.2 35.8 1.0
ND1 C:HIS175 4.3 26.1 1.0
CG C:HIS175 4.4 26.3 1.0
CB C:ASP173 4.4 23.1 1.0
O C:ASP173 4.6 21.4 1.0
N C:ALA187 4.6 29.2 1.0
CA C:ASP173 4.9 21.8 1.0
C C:ASP173 4.9 22.1 1.0
CD C:GLU182 4.9 33.3 1.0
CB C:GLU189 5.0 28.4 1.0

Zinc binding site 7 out of 8 in 2f4l

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Zinc binding site 7 out of 8 in the Crystal Structure of A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution


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 A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4400

b:49.4
occ:1.00
 OD2 D:ASP173 2.2 28.7 1.0
OD1 D:ASP148 2.3 36.3 1.0
OD1 D:ASN146 2.3 29.6 1.0
OD2 D:ASP148 2.6 36.2 1.0
CG D:ASP148 2.8 33.4 1.0
O D:HOH4439 3.1 31.9 1.0
CG D:ASN146 3.1 27.9 1.0
CG D:ASP173 3.1 21.4 1.0
ND2 D:ASN146 3.2 30.7 1.0
ZN D:ZN4401 3.3 42.3 1.0
OD1 D:ASP173 3.5 22.7 1.0
OE2 D:GLU182 3.9 48.5 1.0
CE1 D:HIS175 4.1 33.5 1.0
OE1 D:GLU182 4.1 38.7 1.0
NE2 D:HIS175 4.2 29.1 1.0
CB D:ASP148 4.3 29.8 1.0
CD D:GLU182 4.4 35.4 1.0
CB D:ASP173 4.5 23.1 1.0
ND2 D:ASN50 4.5 38.2 1.0
CB D:ASN146 4.5 27.5 1.0
ND2 D:ASN268 4.6 27.9 1.0
O D:GLY124 4.8 24.4 1.0
CG2 D:VAL125 4.9 22.3 1.0
OD1 D:ASN268 4.9 29.0 1.0
C D:GLY124 5.0 25.5 1.0

Zinc binding site 8 out of 8 in 2f4l

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Zinc binding site 8 out of 8 in the Crystal Structure of A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution


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 A Putative Acetamidase (TM0119) From Thermotoga Maritima MSB8 at 2.50 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4401

b:42.3
occ:1.00
 OE1 D:GLU189 2.0 33.6 1.0
OD1 D:ASP173 2.1 22.7 1.0
NE2 D:HIS175 2.1 29.1 1.0
OE2 D:GLU189 2.4 29.0 1.0
CD D:GLU189 2.5 27.9 1.0
CE1 D:HIS175 3.0 33.5 1.0
CG D:ASP173 3.1 21.4 1.0
CD2 D:HIS175 3.2 25.0 1.0
O D:HOH4439 3.3 31.9 1.0
OD2 D:ASP173 3.3 28.7 1.0
ZN D:ZN4400 3.3 49.4 1.0
OE2 D:GLU182 3.7 48.5 1.0
CG D:GLU189 4.0 28.2 1.0
CB D:ALA36 4.0 29.7 1.0
ND1 D:HIS175 4.2 26.4 1.0
CG D:HIS175 4.3 26.1 1.0
OD1 D:ASP148 4.4 36.3 1.0
O D:ASP173 4.4 22.0 1.0
CB D:ASP173 4.5 23.1 1.0
N D:ALA187 4.6 31.0 1.0
C D:ASP173 4.8 22.4 1.0
CA D:ASP173 4.9 22.8 1.0
CB D:GLU189 4.9 24.7 1.0
CD D:GLU182 4.9 35.4 1.0
CB D:ALA187 5.0 30.2 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Wed Oct 16 23:37:14 2024

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