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Arsenic in PDB 3a6f: W174F Mutant Creatininase, Type II

Enzymatic activity of W174F Mutant Creatininase, Type II

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

Protein crystallography data

The structure of W174F Mutant Creatininase, Type II, PDB code: 3a6f 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 / 1.78
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 164.300, 164.300, 163.900, 90.00, 90.00, 120.00
R / Rfree (%) 23.5 / 25.7

Other elements in 3a6f:

The structure of W174F Mutant Creatininase, Type II 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 II (pdb code 3a6f). 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 II, PDB code: 3a6f:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6;

Arsenic binding site 1 out of 6 in 3a6f

Go back to Arsenic Binding Sites List in 3a6f
Arsenic binding site 1 out of 6 in the W174F Mutant Creatininase, Type II


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 II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As303

b:40.5
occ:1.00
 AS A:CAC303 0.0 40.5 1.0
O1 A:CAC303 1.7 39.4 1.0
O2 A:CAC303 1.7 40.9 1.0
C1 A:CAC303 2.0 38.5 1.0
C2 A:CAC303 2.0 38.1 1.0
MN A:MN300 3.1 34.8 1.0
ZN A:ZN301 3.4 27.9 1.0
O A:HOH1001 3.4 21.6 1.0
OE1 A:GLU183 3.9 22.9 1.0
N A:TYR121 4.1 23.4 1.0
OD1 A:ASP45 4.2 24.3 1.0
OD2 A:ASP45 4.2 19.4 1.0
O A:GLY119 4.2 21.8 1.0
ND1 A:HIS178 4.3 25.3 1.0
CB A:TYR121 4.5 27.7 1.0
CG A:ASP45 4.5 19.8 1.0
CD A:GLU183 4.6 24.2 1.0
CA A:HIS120 4.6 22.7 1.0
OE2 A:GLU183 4.7 24.3 1.0
O A:GLU177 4.8 36.9 1.0
OE1 A:GLU34 4.8 23.1 1.0
O A:SER78 4.8 27.2 1.0
ND1 A:HIS120 4.8 22.1 1.0
C A:HIS120 4.9 23.2 1.0
CZ3 A:TRP154 4.9 30.7 1.0
CH2 A:TRP154 4.9 31.4 1.0
CA A:TYR121 4.9 24.3 1.0

Arsenic binding site 2 out of 6 in 3a6f

Go back to Arsenic Binding Sites List in 3a6f
Arsenic binding site 2 out of 6 in the W174F Mutant Creatininase, Type II


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 II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As303

b:35.7
occ:1.00
 AS B:CAC303 0.0 35.7 1.0
O1 B:CAC303 1.7 30.5 1.0
O2 B:CAC303 1.8 30.8 1.0
C1 B:CAC303 2.0 33.8 1.0
C2 B:CAC303 2.0 35.5 1.0
MN B:MN300 3.1 39.6 1.0
ZN B:ZN301 3.3 26.1 1.0
O B:HOH1002 3.4 22.6 1.0
OD1 B:ASP45 4.1 14.6 1.0
N B:TYR121 4.2 22.3 1.0
O B:GLY119 4.2 21.9 1.0
OD2 B:ASP45 4.2 22.6 1.0
ND1 B:HIS178 4.2 20.4 1.0
OE2 B:GLU183 4.3 24.6 1.0
OE1 B:GLU183 4.3 25.2 1.0
CD B:GLU183 4.4 22.1 1.0
CG B:ASP45 4.5 19.0 1.0
CB B:TYR121 4.5 24.6 1.0
O B:GLU177 4.6 32.5 1.0
CA B:HIS120 4.6 22.6 1.0
O B:SER78 4.6 23.5 1.0
OE2 B:GLU34 4.8 17.8 1.0
ND1 B:HIS120 4.9 19.6 1.0
O B:HOH1537 4.9 47.5 1.0
CH2 B:TRP154 4.9 27.8 1.0
C B:HIS120 5.0 22.3 1.0
CZ3 B:TRP154 5.0 28.8 1.0
O B:HOH1100 5.0 22.6 1.0
O B:HOH1674 5.0 37.3 1.0

Arsenic binding site 3 out of 6 in 3a6f

Go back to Arsenic Binding Sites List in 3a6f
Arsenic binding site 3 out of 6 in the W174F Mutant Creatininase, Type II


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 II within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As303

b:37.5
occ:1.00
 AS C:CAC303 0.0 37.5 1.0
O2 C:CAC303 1.7 37.3 1.0
O1 C:CAC303 1.7 40.0 1.0
C1 C:CAC303 2.0 35.4 1.0
C2 C:CAC303 2.0 38.0 1.0
MN C:MN300 3.1 31.9 1.0
O C:HOH1003 3.4 16.0 1.0
ZN C:ZN301 3.4 25.3 1.0
OE2 C:GLU183 3.9 18.4 1.0
N C:TYR121 4.1 22.3 1.0
O C:GLY119 4.3 19.9 1.0
OD2 C:ASP45 4.3 15.6 1.0
ND1 C:HIS178 4.3 20.7 1.0
OD1 C:ASP45 4.3 18.9 1.0
CD C:GLU183 4.4 19.9 1.0
CB C:TYR121 4.5 25.9 1.0
CA C:HIS120 4.5 21.9 1.0
OE1 C:GLU183 4.6 19.1 1.0
CG C:ASP45 4.6 19.5 1.0
O C:GLU177 4.7 33.9 1.0
O C:SER78 4.7 26.4 1.0
OE1 C:GLU34 4.8 25.6 1.0
ND1 C:HIS120 4.8 22.5 1.0
CH2 C:TRP154 4.9 30.0 1.0
C C:HIS120 4.9 22.9 1.0
CZ3 C:TRP154 4.9 29.8 1.0
O C:HOH1678 4.9 55.5 1.0
CA C:TYR121 5.0 22.8 1.0
OE1 C:GLU122 5.0 22.4 1.0

Arsenic binding site 4 out of 6 in 3a6f

Go back to Arsenic Binding Sites List in 3a6f
Arsenic binding site 4 out of 6 in the W174F Mutant Creatininase, Type II


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 II within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As303

b:36.7
occ:1.00
 AS D:CAC303 0.0 36.7 1.0
O2 D:CAC303 1.7 32.1 1.0
O1 D:CAC303 1.8 34.5 1.0
C1 D:CAC303 2.0 35.1 1.0
C2 D:CAC303 2.0 33.1 1.0
MN D:MN300 3.1 40.0 1.0
ZN D:ZN301 3.3 26.7 1.0
O D:HOH1004 3.3 23.0 1.0
ND1 D:HIS178 4.0 22.3 1.0
OD1 D:ASP45 4.1 17.5 1.0
N D:TYR121 4.1 20.6 1.0
O D:GLY119 4.2 19.1 1.0
OE1 D:GLU183 4.3 22.4 1.0
OD2 D:ASP45 4.4 24.1 1.0
OE2 D:GLU183 4.4 22.8 1.0
CB D:TYR121 4.5 24.6 1.0
O D:GLU177 4.5 35.0 1.0
CD D:GLU183 4.5 23.2 1.0
CG D:ASP45 4.6 21.5 1.0
CA D:HIS120 4.6 20.8 1.0
O D:HOH1579 4.8 45.0 1.0
O D:SER78 4.8 23.4 1.0
CE1 D:HIS178 4.8 23.1 1.0
ND1 D:HIS120 4.8 18.9 1.0
OE2 D:GLU34 4.9 20.5 1.0
CH2 D:TRP154 4.9 27.1 1.0
CZ3 D:TRP154 4.9 27.4 1.0
C D:HIS120 4.9 20.0 1.0
O D:HOH1149 4.9 25.7 1.0
CA D:TYR121 5.0 22.5 1.0

Arsenic binding site 5 out of 6 in 3a6f

Go back to Arsenic Binding Sites List in 3a6f
Arsenic binding site 5 out of 6 in the W174F Mutant Creatininase, Type II


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 II within 5.0Å range:
probe atom residue distance (Å) B Occ
E:As303

b:36.3
occ:1.00
 AS E:CAC303 0.0 36.3 1.0
O2 E:CAC303 1.7 34.6 1.0
O1 E:CAC303 1.7 37.4 1.0
C1 E:CAC303 2.0 34.2 1.0
C2 E:CAC303 2.0 34.9 1.0
MN E:MN300 3.1 33.8 1.0
ZN E:ZN301 3.4 25.7 1.0
O E:HOH1005 3.5 17.1 1.0
OE1 E:GLU183 3.9 19.2 1.0
N E:TYR121 4.1 24.1 1.0
OD2 E:ASP45 4.1 16.3 1.0
OD1 E:ASP45 4.2 14.9 1.0
O E:GLY119 4.3 18.6 1.0
ND1 E:HIS178 4.4 19.0 1.0
CB E:TYR121 4.5 27.9 1.0
CG E:ASP45 4.5 15.5 1.0
CD E:GLU183 4.5 20.6 1.0
CA E:HIS120 4.6 22.0 1.0
OE2 E:GLU183 4.6 19.0 1.0
OE1 E:GLU34 4.8 19.4 1.0
O E:SER78 4.8 25.8 1.0
ND1 E:HIS120 4.8 25.0 1.0
O E:GLU177 4.8 31.7 1.0
O E:HOH1624 4.8 41.5 1.0
CZ3 E:TRP154 4.9 25.1 1.0
C E:HIS120 4.9 22.9 1.0
CH2 E:TRP154 4.9 25.9 1.0
O E:HOH1118 4.9 22.0 1.0
CA E:TYR121 4.9 23.7 1.0
O E:HOH1462 5.0 41.3 1.0

Arsenic binding site 6 out of 6 in 3a6f

Go back to Arsenic Binding Sites List in 3a6f
Arsenic binding site 6 out of 6 in the W174F Mutant Creatininase, Type II


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 II within 5.0Å range:
probe atom residue distance (Å) B Occ
F:As303

b:35.0
occ:1.00
 AS F:CAC303 0.0 35.0 1.0
O2 F:CAC303 1.7 26.7 1.0
O1 F:CAC303 1.8 31.7 1.0
C1 F:CAC303 2.0 32.9 1.0
C2 F:CAC303 2.0 30.6 1.0
MN F:MN300 3.0 36.1 1.0
O F:HOH1006 3.2 19.5 1.0
ZN F:ZN301 3.3 24.2 1.0
OD1 F:ASP45 4.1 17.7 1.0
OD2 F:ASP45 4.1 18.8 1.0
N F:TYR121 4.1 20.5 1.0
OE1 F:GLU183 4.2 18.6 1.0
ND1 F:HIS178 4.2 18.3 1.0
O F:GLY119 4.2 18.8 1.0
OE2 F:GLU183 4.4 19.1 1.0
CD F:GLU183 4.5 19.1 1.0
CG F:ASP45 4.5 17.1 1.0
CB F:TYR121 4.5 23.1 1.0
O F:SER78 4.5 22.1 1.0
CA F:HIS120 4.6 19.4 1.0
O F:GLU177 4.7 36.4 1.0
OE2 F:GLU34 4.7 18.0 1.0
CD2 F:HIS120 4.9 13.1 1.0
C F:HIS120 4.9 18.9 1.0
CA F:TYR121 5.0 19.9 1.0
CH2 F:TRP154 5.0 25.2 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: Wed Jul 10 11:35:23 2024

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