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Arsenic in PDB 3a6e: W174F Mutant Creatininase, Type I

Enzymatic activity of W174F Mutant Creatininase, Type I

All present enzymatic activity of W174F Mutant Creatininase, Type I:
3.5.2.10;

Protein crystallography data

The structure of W174F Mutant Creatininase, Type I, PDB code: 3a6e was solved by Y.Nakajima, K.Yamashita, K.Ito, T.Yoshimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 105.900, 59.700, 145.100, 90.00, 99.70, 90.00
R / Rfree (%) 19.6 / 22.9

Other elements in 3a6e:

The structure of W174F Mutant Creatininase, Type I also contains other interesting chemical elements:

Manganese (Mn) 6 atoms
Zinc (Zn) 6 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the W174F Mutant Creatininase, Type I (pdb code 3a6e). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 6 binding sites of Arsenic where determined in the W174F Mutant Creatininase, Type I, PDB code: 3a6e:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6;

Arsenic binding site 1 out of 6 in 3a6e

Go back to Arsenic Binding Sites List in 3a6e
Arsenic binding site 1 out of 6 in the W174F Mutant Creatininase, Type I


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of W174F Mutant Creatininase, Type I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As302

b:27.5
occ:1.00
AS A:CAC302 0.0 27.5 1.0
O2 A:CAC302 1.7 21.6 1.0
O1 A:CAC302 1.7 23.9 1.0
C1 A:CAC302 2.0 22.8 1.0
C2 A:CAC302 2.0 22.3 1.0
MN A:MN300 3.0 29.1 1.0
ZN A:ZN301 3.3 18.0 1.0
O A:HOH1082 3.4 13.2 1.0
N A:TYR121 4.0 14.6 1.0
OE1 A:GLU183 4.1 15.7 1.0
OD2 A:ASP45 4.1 11.9 1.0
OD1 A:ASP45 4.1 11.8 1.0
ND1 A:HIS178 4.2 14.0 1.0
O A:GLY119 4.2 12.7 1.0
CB A:TYR121 4.4 17.6 1.0
CD A:GLU183 4.5 18.9 1.0
CG A:ASP45 4.5 13.0 1.0
OE2 A:GLU183 4.5 15.7 1.0
CA A:HIS120 4.5 14.3 1.0
O A:GLU177 4.5 25.3 1.0
OE1 A:GLU34 4.7 14.5 1.0
O A:SER78 4.8 19.1 1.0
C A:HIS120 4.8 12.9 1.0
ND1 A:HIS120 4.8 13.8 1.0
CA A:TYR121 4.9 15.2 1.0
O A:HOH1165 4.9 18.4 1.0
CZ3 A:TRP154 4.9 20.6 1.0
CH2 A:TRP154 4.9 17.2 1.0
OE1 A:GLU122 5.0 14.9 1.0

Arsenic binding site 2 out of 6 in 3a6e

Go back to Arsenic Binding Sites List in 3a6e
Arsenic binding site 2 out of 6 in the W174F Mutant Creatininase, Type I


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of W174F Mutant Creatininase, Type I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As303

b:27.6
occ:1.00
AS B:CAC303 0.0 27.6 1.0
O2 B:CAC303 1.7 23.9 1.0
O1 B:CAC303 1.7 25.7 1.0
C1 B:CAC303 2.0 25.2 1.0
C2 B:CAC303 2.0 26.4 1.0
MN B:MN300 3.1 30.7 1.0
ZN B:ZN301 3.3 19.9 1.0
O B:HOH1135 3.5 15.1 1.0
OD2 B:ASP45 4.0 13.7 1.0
OE1 B:GLU183 4.0 16.6 1.0
N B:TYR121 4.1 14.8 1.0
ND1 B:HIS178 4.1 14.6 1.0
OD1 B:ASP45 4.2 14.4 1.0
O B:GLY119 4.2 12.3 1.0
CG B:ASP45 4.5 14.5 1.0
CD B:GLU183 4.5 17.8 1.0
CB B:TYR121 4.5 19.2 1.0
OE2 B:GLU183 4.5 16.4 1.0
O B:GLU177 4.6 25.1 1.0
CA B:HIS120 4.6 15.4 1.0
OE2 B:GLU34 4.8 15.5 1.0
ND1 B:HIS120 4.8 12.6 1.0
O B:SER78 4.8 18.5 1.0
O B:HOH1189 4.8 18.3 1.0
O B:HOH1749 4.9 30.4 1.0
C B:HIS120 4.9 15.8 1.0
CH2 B:TRP154 4.9 19.1 1.0
CZ3 B:TRP154 4.9 20.0 1.0
CA B:TYR121 5.0 16.4 1.0
CE1 B:HIS178 5.0 16.9 1.0

Arsenic binding site 3 out of 6 in 3a6e

Go back to Arsenic Binding Sites List in 3a6e
Arsenic binding site 3 out of 6 in the W174F Mutant Creatininase, Type I


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of W174F Mutant Creatininase, Type I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As304

b:31.8
occ:1.00
AS C:CAC304 0.0 31.8 1.0
O1 C:CAC304 1.7 26.1 1.0
O2 C:CAC304 1.7 31.6 1.0
C1 C:CAC304 2.0 30.0 1.0
C2 C:CAC304 2.0 29.8 1.0
MN C:MN300 3.1 36.6 1.0
ZN C:ZN301 3.3 23.4 1.0
O C:HOH1177 3.4 17.1 1.0
OE1 C:GLU183 4.1 21.9 1.0
N C:TYR121 4.1 16.4 1.0
ND1 C:HIS178 4.1 21.2 1.0
OD2 C:ASP45 4.1 16.9 1.0
OD1 C:ASP45 4.2 18.3 1.0
O C:GLY119 4.2 18.6 1.0
OE2 C:GLU183 4.5 20.2 1.0
CB C:TYR121 4.5 21.6 1.0
O C:GLU177 4.5 27.7 1.0
CG C:ASP45 4.5 19.5 1.0
CD C:GLU183 4.5 21.6 1.0
CA C:HIS120 4.6 17.5 1.0
OE2 C:GLU34 4.7 17.4 1.0
ND1 C:HIS120 4.8 15.5 1.0
O C:SER78 4.8 21.6 1.0
CH2 C:TRP154 4.8 24.9 1.0
O C:HOH1234 4.9 21.2 1.0
CZ3 C:TRP154 4.9 25.0 1.0
C C:HIS120 4.9 18.1 1.0
CE1 C:HIS178 5.0 22.6 1.0
CA C:TYR121 5.0 18.6 1.0
OE1 C:GLU122 5.0 18.0 1.0

Arsenic binding site 4 out of 6 in 3a6e

Go back to Arsenic Binding Sites List in 3a6e
Arsenic binding site 4 out of 6 in the W174F Mutant Creatininase, Type I


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of W174F Mutant Creatininase, Type I within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As305

b:30.8
occ:1.00
AS D:CAC305 0.0 30.8 1.0
O1 D:CAC305 1.7 25.0 1.0
O2 D:CAC305 1.7 29.6 1.0
C1 D:CAC305 2.0 27.1 1.0
C2 D:CAC305 2.0 27.7 1.0
MN D:MN300 3.0 32.8 1.0
ZN D:ZN301 3.3 22.3 1.0
O D:HOH1074 3.4 13.1 1.0
OE1 D:GLU183 4.0 15.9 1.0
OD2 D:ASP45 4.1 14.8 1.0
ND1 D:HIS178 4.1 14.4 1.0
N D:TYR121 4.1 16.3 1.0
OD1 D:ASP45 4.2 14.3 1.0
O D:GLY119 4.2 17.4 1.0
CD D:GLU183 4.4 19.0 1.0
OE2 D:GLU183 4.4 18.0 1.0
CB D:TYR121 4.5 19.7 1.0
CG D:ASP45 4.5 15.2 1.0
O D:GLU177 4.5 26.8 1.0
CA D:HIS120 4.6 16.5 1.0
O D:SER78 4.6 20.1 1.0
OE2 D:GLU34 4.8 19.4 1.0
ND1 D:HIS120 4.8 15.9 1.0
O D:HOH1184 4.9 18.9 1.0
C D:HIS120 4.9 16.0 1.0
CZ3 D:TRP154 4.9 20.9 1.0
CH2 D:TRP154 4.9 19.7 1.0
CE1 D:HIS178 5.0 14.3 1.0
CA D:TYR121 5.0 17.8 1.0
OE1 D:GLU122 5.0 16.6 1.0

Arsenic binding site 5 out of 6 in 3a6e

Go back to Arsenic Binding Sites List in 3a6e
Arsenic binding site 5 out of 6 in the W174F Mutant Creatininase, Type I


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of W174F Mutant Creatininase, Type I within 5.0Å range:
probe atom residue distance (Å) B Occ
E:As306

b:40.5
occ:1.00
AS E:CAC306 0.0 40.5 1.0
O2 E:CAC306 1.7 35.5 1.0
O1 E:CAC306 1.7 40.4 1.0
C2 E:CAC306 2.0 39.6 1.0
C1 E:CAC306 2.0 38.4 1.0
MN E:MN300 3.1 41.4 1.0
O E:HOH1289 3.4 18.7 1.0
ZN E:ZN301 3.4 27.2 1.0
OE1 E:GLU183 4.0 31.8 1.0
OD1 E:ASP45 4.1 23.7 1.0
N E:TYR121 4.1 24.2 1.0
O E:GLY119 4.2 19.6 1.0
ND1 E:HIS178 4.2 29.8 1.0
OD2 E:ASP45 4.3 22.6 1.0
CB E:TYR121 4.5 28.5 1.0
CG E:ASP45 4.5 22.1 1.0
CA E:HIS120 4.6 23.4 1.0
O E:GLU177 4.7 39.5 1.0
CD E:GLU183 4.7 31.5 1.0
O E:SER78 4.7 26.9 1.0
CH2 E:TRP154 4.8 35.7 1.0
OE2 E:GLU183 4.8 30.5 1.0
OE2 E:GLU34 4.8 22.0 1.0
CZ3 E:TRP154 4.8 37.3 1.0
ND1 E:HIS120 4.8 24.3 1.0
C E:HIS120 4.9 24.9 1.0
CA E:TYR121 5.0 25.8 1.0
O E:HOH1305 5.0 23.0 1.0

Arsenic binding site 6 out of 6 in 3a6e

Go back to Arsenic Binding Sites List in 3a6e
Arsenic binding site 6 out of 6 in the W174F Mutant Creatininase, Type I


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of W174F Mutant Creatininase, Type I within 5.0Å range:
probe atom residue distance (Å) B Occ
F:As307

b:39.5
occ:1.00
AS F:CAC307 0.0 39.5 1.0
O2 F:CAC307 1.7 35.3 1.0
O1 F:CAC307 1.7 39.1 1.0
C2 F:CAC307 2.0 37.3 1.0
C1 F:CAC307 2.0 37.8 1.0
MN F:MN300 3.1 45.8 1.0
ZN F:ZN301 3.4 26.1 1.0
O F:HOH1246 3.5 23.8 1.0
OD1 F:ASP45 4.1 23.0 1.0
N F:TYR121 4.1 23.7 1.0
OE2 F:GLU183 4.2 27.0 1.0
ND1 F:HIS178 4.2 23.3 1.0
O F:GLY119 4.2 21.0 1.0
OD2 F:ASP45 4.4 21.5 1.0
CB F:TYR121 4.4 27.9 1.0
CG F:ASP45 4.6 22.2 1.0
O F:GLU177 4.6 37.5 1.0
OE1 F:GLU183 4.6 25.1 1.0
CA F:HIS120 4.6 21.8 1.0
CD F:GLU183 4.6 26.2 1.0
CH2 F:TRP154 4.7 37.2 1.0
ND1 F:HIS120 4.8 21.3 1.0
OE2 F:GLU34 4.8 21.9 1.0
CZ3 F:TRP154 4.8 37.8 1.0
O F:SER78 4.9 26.4 1.0
C F:HIS120 4.9 23.2 1.0
CA F:TYR121 4.9 24.9 1.0
OE1 F:GLU122 4.9 22.1 1.0

Reference:

K.Yamashita, Y.Nakajima, H.Matsushita, Y.Nishiya, R.Yamazawa, Y.F.Wu, F.Matsubara, H.Oyama, K.Ito, T.Yoshimoto. Substitution of GLU122 By Glutamine Revealed the Function of the Second Water Molecule As A Proton Donor in the Binuclear Metal Enzyme Creatininase J.Mol.Biol. V. 396 1081 2010.
ISSN: ISSN 0022-2836
PubMed: 20043918
DOI: 10.1016/J.JMB.2009.12.045
Page generated: Tue Oct 27 16:49:51 2020

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