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Manganese 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:

Arsenic (As) 6 atoms
Zinc (Zn) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the W174F Mutant Creatininase, Type II (pdb code 3a6f). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the W174F Mutant Creatininase, Type II, PDB code: 3a6f:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3a6f

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of W174F Mutant Creatininase, Type II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn300

b:34.8
occ:1.00
 OD2 A:ASP45 2.2 19.4 1.0
OE1 A:GLU34 2.2 23.1 1.0
ND1 A:HIS120 2.2 22.1 1.0
O A:HOH1001 2.3 21.6 1.0
O2 A:CAC303 2.4 40.9 1.0
O1 A:CAC303 2.6 39.4 1.0
CE1 A:HIS120 2.9 22.6 1.0
AS A:CAC303 3.1 40.5 1.0
CD A:GLU34 3.2 23.7 1.0
CG A:ASP45 3.3 19.8 1.0
CG A:HIS120 3.4 22.1 1.0
OE2 A:GLU34 3.6 24.6 1.0
OD1 A:ASP45 3.8 24.3 1.0
ZN A:ZN301 3.8 27.9 1.0
CA A:HIS120 3.9 22.7 1.0
CB A:HIS120 3.9 21.5 1.0
OE1 A:GLU122 4.1 22.5 1.0
NE2 A:HIS120 4.2 22.4 1.0
C2 A:CAC303 4.3 38.1 1.0
CD2 A:HIS120 4.4 22.1 1.0
N A:TYR121 4.4 23.4 1.0
CB A:ASP45 4.5 17.2 1.0
CE1 A:HIS178 4.5 24.8 1.0
ND1 A:HIS178 4.5 25.3 1.0
CG A:GLU34 4.5 22.1 1.0
CE1 A:HIS36 4.5 18.4 1.0
C A:HIS120 4.5 23.2 1.0
O A:GLY119 4.6 21.8 1.0
C1 A:CAC303 4.6 38.5 1.0
CB A:GLU34 4.7 21.3 1.0
NE2 A:HIS36 4.7 17.5 1.0
CD A:GLU122 5.0 23.9 1.0

Manganese binding site 2 out of 6 in 3a6f

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of W174F Mutant Creatininase, Type II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn300

b:39.6
occ:1.00
 OD2 B:ASP45 2.0 22.6 1.0
O B:HOH1002 2.2 22.6 1.0
ND1 B:HIS120 2.2 19.6 1.0
OE2 B:GLU34 2.2 17.8 1.0
O2 B:CAC303 2.4 30.8 1.0
O1 B:CAC303 2.6 30.5 1.0
CE1 B:HIS120 3.0 19.1 1.0
AS B:CAC303 3.1 35.7 1.0
CG B:ASP45 3.1 19.0 1.0
CD B:GLU34 3.3 19.9 1.0
CG B:HIS120 3.4 20.6 1.0
OD1 B:ASP45 3.6 14.6 1.0
OE1 B:GLU34 3.6 17.6 1.0
ZN B:ZN301 3.7 26.1 1.0
CA B:HIS120 3.8 22.6 1.0
CB B:HIS120 4.0 21.5 1.0
OE1 B:GLU122 4.1 21.0 1.0
NE2 B:HIS120 4.2 19.6 1.0
CB B:ASP45 4.4 17.0 1.0
C2 B:CAC303 4.4 35.5 1.0
N B:TYR121 4.4 22.3 1.0
CD2 B:HIS120 4.4 17.8 1.0
ND1 B:HIS178 4.5 20.4 1.0
O B:GLY119 4.5 21.9 1.0
C1 B:CAC303 4.5 33.8 1.0
C B:HIS120 4.5 22.3 1.0
CE1 B:HIS178 4.5 20.7 1.0
NE2 B:HIS36 4.6 17.5 1.0
CG B:GLU34 4.6 17.5 1.0
CE1 B:HIS36 4.6 18.6 1.0
CB B:GLU34 4.8 16.1 1.0
CD B:GLU122 4.9 22.6 1.0
N B:HIS120 5.0 21.6 1.0

Manganese binding site 3 out of 6 in 3a6f

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of W174F Mutant Creatininase, Type II within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn300

b:31.9
occ:1.00
 OE1 C:GLU34 2.2 25.6 1.0
OD2 C:ASP45 2.2 15.6 1.0
O C:HOH1003 2.2 16.0 1.0
O1 C:CAC303 2.3 40.0 1.0
ND1 C:HIS120 2.3 22.5 1.0
O2 C:CAC303 2.7 37.3 1.0
CE1 C:HIS120 3.0 21.8 1.0
AS C:CAC303 3.1 37.5 1.0
CD C:GLU34 3.2 25.6 1.0
CG C:ASP45 3.2 19.5 1.0
CG C:HIS120 3.5 21.6 1.0
OE2 C:GLU34 3.6 25.5 1.0
OD1 C:ASP45 3.7 18.9 1.0
ZN C:ZN301 3.7 25.3 1.0
CA C:HIS120 3.9 21.9 1.0
CB C:HIS120 4.0 22.1 1.0
OE1 C:GLU122 4.0 22.4 1.0
C1 C:CAC303 4.2 35.4 1.0
NE2 C:HIS120 4.2 23.2 1.0
ND1 C:HIS178 4.4 20.7 1.0
CE1 C:HIS178 4.5 19.4 1.0
CE1 C:HIS36 4.5 18.9 1.0
CD2 C:HIS120 4.5 21.4 1.0
CG C:GLU34 4.5 22.6 1.0
N C:TYR121 4.5 22.3 1.0
NE2 C:HIS36 4.5 20.0 1.0
CB C:ASP45 4.5 17.7 1.0
O C:GLY119 4.5 19.9 1.0
C C:HIS120 4.6 22.9 1.0
C2 C:CAC303 4.7 38.0 1.0
CB C:GLU34 4.7 21.8 1.0
CD C:GLU122 4.9 23.6 1.0

Manganese binding site 4 out of 6 in 3a6f

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of W174F Mutant Creatininase, Type II within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn300

b:40.0
occ:1.00
 ND1 D:HIS120 2.1 18.9 1.0
OD2 D:ASP45 2.2 24.1 1.0
O D:HOH1004 2.2 23.0 1.0
OE2 D:GLU34 2.3 20.5 1.0
O1 D:CAC303 2.4 34.5 1.0
O2 D:CAC303 2.7 32.1 1.0
CE1 D:HIS120 2.9 19.4 1.0
AS D:CAC303 3.1 36.7 1.0
CG D:ASP45 3.2 21.5 1.0
CD D:GLU34 3.3 21.1 1.0
CG D:HIS120 3.3 20.9 1.0
OD1 D:ASP45 3.6 17.5 1.0
OE1 D:GLU34 3.6 22.4 1.0
CA D:HIS120 3.7 20.8 1.0
ZN D:ZN301 3.8 26.7 1.0
CB D:HIS120 3.8 19.9 1.0
OE1 D:GLU122 4.1 20.1 1.0
NE2 D:HIS120 4.1 20.1 1.0
N D:TYR121 4.3 20.6 1.0
CE1 D:HIS178 4.3 23.1 1.0
CD2 D:HIS120 4.3 19.1 1.0
ND1 D:HIS178 4.4 22.3 1.0
CB D:ASP45 4.4 18.8 1.0
C D:HIS120 4.4 20.0 1.0
O D:GLY119 4.5 19.1 1.0
C2 D:CAC303 4.5 33.1 1.0
C1 D:CAC303 4.5 35.1 1.0
NE2 D:HIS36 4.6 18.2 1.0
CG D:GLU34 4.6 19.6 1.0
CE1 D:HIS36 4.7 18.6 1.0
CB D:GLU34 4.8 17.7 1.0
N D:HIS120 4.9 19.3 1.0
CD D:GLU122 5.0 21.8 1.0

Manganese binding site 5 out of 6 in 3a6f

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of W174F Mutant Creatininase, Type II within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn300

b:33.8
occ:1.00
 OD2 E:ASP45 2.1 16.3 1.0
OE1 E:GLU34 2.2 19.4 1.0
ND1 E:HIS120 2.2 25.0 1.0
O1 E:CAC303 2.3 37.4 1.0
O E:HOH1005 2.3 17.1 1.0
O2 E:CAC303 2.8 34.6 1.0
CE1 E:HIS120 2.9 25.5 1.0
AS E:CAC303 3.1 36.3 1.0
CD E:GLU34 3.1 19.5 1.0
CG E:ASP45 3.2 15.5 1.0
OE2 E:GLU34 3.4 20.7 1.0
CG E:HIS120 3.4 25.0 1.0
OD1 E:ASP45 3.8 14.9 1.0
ZN E:ZN301 3.8 25.7 1.0
CA E:HIS120 3.9 22.0 1.0
CB E:HIS120 4.0 22.9 1.0
OE1 E:GLU122 4.1 22.5 1.0
NE2 E:HIS120 4.2 25.6 1.0
C1 E:CAC303 4.2 34.2 1.0
CB E:ASP45 4.4 14.5 1.0
CD2 E:HIS120 4.4 23.4 1.0
N E:TYR121 4.4 24.1 1.0
CG E:GLU34 4.5 18.6 1.0
ND1 E:HIS178 4.5 19.0 1.0
CE1 E:HIS178 4.5 18.6 1.0
CE1 E:HIS36 4.5 15.9 1.0
C E:HIS120 4.6 22.9 1.0
O E:GLY119 4.6 18.6 1.0
NE2 E:HIS36 4.7 17.0 1.0
C2 E:CAC303 4.7 34.9 1.0
CB E:GLU34 4.8 17.4 1.0
CD E:GLU122 4.9 23.4 1.0

Manganese binding site 6 out of 6 in 3a6f

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of W174F Mutant Creatininase, Type II within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn300

b:36.1
occ:1.00
 O F:HOH1006 2.1 19.5 1.0
OD2 F:ASP45 2.1 18.8 1.0
OE2 F:GLU34 2.3 18.0 1.0
CD2 F:HIS120 2.3 13.1 1.0
O1 F:CAC303 2.3 31.7 1.0
O2 F:CAC303 2.5 26.7 1.0
AS F:CAC303 3.0 35.0 1.0
NE2 F:HIS120 3.2 18.6 1.0
CG F:ASP45 3.2 17.1 1.0
CD F:GLU34 3.3 17.9 1.0
CG F:HIS120 3.4 18.6 1.0
OE1 F:GLU34 3.6 17.3 1.0
OD1 F:ASP45 3.7 17.7 1.0
ZN F:ZN301 3.7 24.2 1.0
CA F:HIS120 3.8 19.4 1.0
CB F:HIS120 4.0 18.6 1.0
OE1 F:GLU122 4.0 20.1 1.0
N F:TYR121 4.3 20.5 1.0
CE1 F:HIS120 4.4 16.1 1.0
C2 F:CAC303 4.4 30.6 1.0
ND1 F:HIS178 4.4 18.3 1.0
C1 F:CAC303 4.4 32.9 1.0
CB F:ASP45 4.4 17.6 1.0
ND1 F:HIS120 4.5 19.1 1.0
C F:HIS120 4.5 18.9 1.0
CE1 F:HIS178 4.5 19.9 1.0
O F:GLY119 4.5 18.8 1.0
CG F:GLU34 4.6 15.8 1.0
NE2 F:HIS36 4.7 15.8 1.0
CE1 F:HIS36 4.7 18.8 1.0
CB F:GLU34 4.8 14.2 1.0
CD F:GLU122 4.9 21.1 1.0
N F:HIS120 5.0 18.9 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: Sat Oct 5 15:41:05 2024

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