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Manganese in PDB 3a6h: W154A Mutant Creatininase

Enzymatic activity of W154A Mutant Creatininase

All present enzymatic activity of W154A Mutant Creatininase:
3.5.2.10;

Protein crystallography data

The structure of W154A Mutant Creatininase, PDB code: 3a6h 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 (°) 106.800, 60.240, 146.200, 90.00, 100.30, 90.00
R / Rfree (%) 19.9 / 23.1

Other elements in 3a6h:

The structure of W154A Mutant Creatininase also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Zinc (Zn) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the W154A Mutant Creatininase (pdb code 3a6h). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the W154A Mutant Creatininase, PDB code: 3a6h:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3a6h

Go back to Manganese Binding Sites List in 3a6h
Manganese binding site 1 out of 6 in the W154A Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of W154A Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn300

b:36.3
occ:1.00
 OD2 A:ASP45 2.2 18.5 1.0
O A:HOH1001 2.2 19.7 1.0
ND1 A:HIS120 2.3 26.7 1.0
OE2 A:GLU34 2.3 21.3 1.0
CE1 A:HIS120 3.1 27.6 1.0
CL A:CL302 3.2 33.3 1.0
CG A:ASP45 3.2 17.4 1.0
CD A:GLU34 3.3 19.6 1.0
CG A:HIS120 3.4 28.1 1.0
ZN A:ZN301 3.5 33.1 1.0
OE1 A:GLU34 3.5 18.6 1.0
OD1 A:ASP45 3.6 17.0 1.0
CA A:HIS120 3.7 27.8 1.0
CB A:HIS120 3.8 26.7 1.0
OE1 A:GLU122 4.1 23.9 1.0
NE2 A:HIS120 4.3 28.4 1.0
N A:TYR121 4.4 26.3 1.0
O A:GLY119 4.4 23.6 1.0
ND1 A:HIS178 4.5 19.7 1.0
C A:HIS120 4.5 27.5 1.0
CD2 A:HIS120 4.5 27.3 1.0
CE1 A:HIS178 4.5 18.0 1.0
CB A:ASP45 4.5 17.8 1.0
NE2 A:HIS36 4.6 13.9 1.0
CE1 A:HIS36 4.6 16.7 1.0
CG A:GLU34 4.6 16.7 1.0
CB A:GLU34 4.9 17.7 1.0
N A:HIS120 4.9 25.4 1.0
CD A:GLU122 4.9 24.6 1.0

Manganese binding site 2 out of 6 in 3a6h

Go back to Manganese Binding Sites List in 3a6h
Manganese binding site 2 out of 6 in the W154A Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of W154A Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn300

b:39.0
occ:1.00
 OD2 B:ASP45 2.2 18.0 1.0
OE2 B:GLU34 2.2 21.3 1.0
O B:HOH1002 2.3 17.8 1.0
ND1 B:HIS120 2.3 23.2 1.0
CE1 B:HIS120 3.1 22.1 1.0
CL B:CL303 3.2 32.0 1.0
CD B:GLU34 3.2 20.8 1.0
CG B:ASP45 3.2 18.7 1.0
CG B:HIS120 3.5 21.8 1.0
OE1 B:GLU34 3.5 18.8 1.0
ZN B:ZN301 3.6 33.8 1.0
OD1 B:ASP45 3.7 18.6 1.0
CA B:HIS120 3.8 25.9 1.0
CB B:HIS120 3.9 24.6 1.0
OE1 B:GLU122 4.1 25.8 1.0
NE2 B:HIS120 4.3 23.2 1.0
O B:GLY119 4.4 27.4 1.0
N B:TYR121 4.4 25.1 1.0
CE1 B:HIS178 4.5 21.3 1.0
NE2 B:HIS36 4.5 16.2 1.0
ND1 B:HIS178 4.5 22.5 1.0
CD2 B:HIS120 4.5 22.6 1.0
CB B:ASP45 4.5 18.0 1.0
C B:HIS120 4.5 25.7 1.0
CE1 B:HIS36 4.6 18.0 1.0
CG B:GLU34 4.6 18.5 1.0
CB B:GLU34 4.8 16.7 1.0
N B:HIS120 4.9 26.4 1.0
CD B:GLU122 4.9 24.7 1.0

Manganese binding site 3 out of 6 in 3a6h

Go back to Manganese Binding Sites List in 3a6h
Manganese binding site 3 out of 6 in the W154A Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of W154A Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn300

b:44.6
occ:1.00
 OD1 C:ASP45 2.1 23.2 1.0
OE2 C:GLU34 2.3 23.6 1.0
ND1 C:HIS120 2.3 25.9 1.0
O C:HOH1003 2.3 20.3 1.0
CE1 C:HIS120 3.1 25.2 1.0
CL C:CL304 3.1 29.4 1.0
CG C:ASP45 3.2 23.4 1.0
CD C:GLU34 3.3 20.9 1.0
CG C:HIS120 3.5 26.2 1.0
ZN C:ZN301 3.5 37.7 1.0
OD2 C:ASP45 3.6 23.2 1.0
OE1 C:GLU34 3.7 22.1 1.0
CA C:HIS120 3.8 28.7 1.0
CB C:HIS120 3.9 27.1 1.0
OE1 C:GLU122 4.2 25.7 1.0
O C:GLY119 4.3 32.3 1.0
NE2 C:HIS120 4.3 24.6 1.0
ND1 C:HIS178 4.5 27.3 1.0
CB C:ASP45 4.5 21.2 1.0
CE1 C:HIS36 4.5 22.3 1.0
N C:TYR121 4.5 27.7 1.0
CD2 C:HIS120 4.5 24.9 1.0
CE1 C:HIS178 4.5 26.9 1.0
NE2 C:HIS36 4.6 21.9 1.0
C C:HIS120 4.6 28.7 1.0
CG C:GLU34 4.6 20.6 1.0
CB C:GLU34 4.8 19.2 1.0
N C:HIS120 4.9 30.4 1.0

Manganese binding site 4 out of 6 in 3a6h

Go back to Manganese Binding Sites List in 3a6h
Manganese binding site 4 out of 6 in the W154A Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of W154A Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn300

b:38.7
occ:1.00
 OD2 D:ASP45 2.2 20.4 1.0
O D:HOH1004 2.3 17.8 1.0
ND1 D:HIS120 2.3 25.1 1.0
OE2 D:GLU34 2.3 22.9 1.0
CE1 D:HIS120 3.1 25.5 1.0
CL D:CL305 3.2 35.1 1.0
CG D:ASP45 3.2 19.5 1.0
CD D:GLU34 3.3 20.4 1.0
CG D:HIS120 3.4 25.9 1.0
ZN D:ZN301 3.5 35.2 1.0
OD1 D:ASP45 3.6 20.1 1.0
OE1 D:GLU34 3.6 21.1 1.0
CA D:HIS120 3.8 27.2 1.0
CB D:HIS120 3.8 26.2 1.0
OE1 D:GLU122 4.2 23.7 1.0
NE2 D:HIS120 4.3 27.1 1.0
ND1 D:HIS178 4.3 22.0 1.0
CE1 D:HIS178 4.4 23.1 1.0
O D:GLY119 4.4 26.2 1.0
N D:TYR121 4.5 26.4 1.0
CD2 D:HIS120 4.5 24.7 1.0
NE2 D:HIS36 4.5 15.3 1.0
CB D:ASP45 4.5 19.7 1.0
C D:HIS120 4.5 26.8 1.0
CE1 D:HIS36 4.6 17.4 1.0
CG D:GLU34 4.6 18.3 1.0
CB D:GLU34 4.8 17.3 1.0
N D:HIS120 4.9 25.2 1.0

Manganese binding site 5 out of 6 in 3a6h

Go back to Manganese Binding Sites List in 3a6h
Manganese binding site 5 out of 6 in the W154A Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of W154A Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn300

b:54.9
occ:1.00
 OD2 E:ASP45 2.3 28.6 1.0
ND1 E:HIS120 2.3 30.1 1.0
OE2 E:GLU34 2.3 26.4 1.0
O E:HOH1005 2.5 30.4 1.0
CL E:CL306 3.0 37.7 1.0
CE1 E:HIS120 3.2 30.2 1.0
CG E:ASP45 3.2 27.9 1.0
CG E:HIS120 3.4 31.8 1.0
CD E:GLU34 3.4 27.2 1.0
ZN E:ZN301 3.6 45.4 1.0
CA E:HIS120 3.6 31.5 1.0
OD1 E:ASP45 3.6 30.3 1.0
CB E:HIS120 3.7 31.6 1.0
OE1 E:GLU34 3.8 28.1 1.0
OE1 E:GLU122 4.1 31.3 1.0
O E:GLY119 4.2 30.5 1.0
N E:TYR121 4.3 33.4 1.0
NE2 E:HIS120 4.3 30.9 1.0
C E:HIS120 4.4 32.3 1.0
CB E:ASP45 4.4 27.4 1.0
CD2 E:HIS120 4.5 30.4 1.0
CE1 E:HIS178 4.6 35.1 1.0
ND1 E:HIS178 4.7 36.7 1.0
CE1 E:HIS36 4.7 29.9 1.0
CG E:GLU34 4.7 27.2 1.0
N E:HIS120 4.7 30.4 1.0
NE2 E:HIS36 4.7 29.9 1.0
CB E:GLU34 4.9 26.1 1.0
C E:GLY119 4.9 30.7 1.0
CD E:GLU122 5.0 30.4 1.0

Manganese binding site 6 out of 6 in 3a6h

Go back to Manganese Binding Sites List in 3a6h
Manganese binding site 6 out of 6 in the W154A Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of W154A Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn300

b:52.1
occ:1.00
 OD1 F:ASP45 2.2 29.5 1.0
OE2 F:GLU34 2.4 28.7 1.0
ND1 F:HIS120 2.4 31.6 1.0
O F:HOH1006 2.4 24.1 1.0
CL F:CL307 2.9 47.7 1.0
CE1 F:HIS120 3.2 31.0 1.0
CG F:ASP45 3.2 28.7 1.0
CD F:GLU34 3.5 26.1 1.0
CG F:HIS120 3.5 32.6 1.0
ZN F:ZN301 3.6 45.7 1.0
OD2 F:ASP45 3.7 29.1 1.0
CA F:HIS120 3.7 33.5 1.0
CB F:HIS120 3.9 32.8 1.0
OE1 F:GLU34 3.9 28.8 1.0
OE1 F:GLU122 4.1 30.0 1.0
O F:GLY119 4.2 32.4 1.0
N F:TYR121 4.3 33.7 1.0
NE2 F:HIS120 4.4 32.0 1.0
C F:HIS120 4.4 33.6 1.0
CB F:ASP45 4.5 27.1 1.0
CD2 F:HIS120 4.5 31.9 1.0
CE1 F:HIS36 4.6 27.1 1.0
ND1 F:HIS178 4.7 35.1 1.0
CE1 F:HIS178 4.7 32.5 1.0
CG F:GLU34 4.8 26.3 1.0
NE2 F:HIS36 4.8 27.9 1.0
N F:HIS120 4.8 31.7 1.0
CB F:GLU34 4.9 25.7 1.0
C F:GLY119 4.9 32.3 1.0
CD F:GLU122 5.0 29.9 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 15:41:25 2024

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