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Manganese in PDB 3a6g: W154F Mutant Creatininase

Enzymatic activity of W154F Mutant Creatininase

All present enzymatic activity of W154F Mutant Creatininase:
3.5.2.10;

Protein crystallography data

The structure of W154F Mutant Creatininase, PDB code: 3a6g 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 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 164.500, 164.500, 164.100, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 21.6

Other elements in 3a6g:

The structure of W154F Mutant Creatininase also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the W154F Mutant Creatininase (pdb code 3a6g). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the W154F Mutant Creatininase, PDB code: 3a6g:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3a6g

Go back to Manganese Binding Sites List in 3a6g
Manganese binding site 1 out of 6 in the W154F Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of W154F Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn300

b:23.7
occ:1.00
 OD2 A:ASP45 2.1 15.1 1.0
OE1 A:GLU34 2.1 16.4 1.0
ND1 A:HIS120 2.3 11.7 1.0
O A:HOH1002 2.3 16.0 1.0
O A:HOH1001 2.3 19.2 1.0
CE1 A:HIS120 3.0 14.7 1.0
O A:HOH1515 3.1 41.3 1.0
CD A:GLU34 3.1 15.4 1.0
CG A:ASP45 3.2 14.9 1.0
CG A:HIS120 3.5 14.5 1.0
OE2 A:GLU34 3.5 17.3 1.0
ZN A:ZN301 3.6 32.1 1.0
OD1 A:ASP45 3.7 13.0 1.0
CA A:HIS120 4.0 13.7 1.0
CB A:HIS120 4.0 12.7 1.0
OE1 A:GLU122 4.2 15.7 1.0
NE2 A:HIS120 4.2 16.0 1.0
ND1 A:HIS178 4.3 17.6 1.0
CE1 A:HIS178 4.4 17.2 1.0
CB A:ASP45 4.4 13.5 1.0
CD2 A:HIS120 4.5 14.3 1.0
CG A:GLU34 4.5 14.3 1.0
CE1 A:HIS36 4.5 14.3 1.0
NE2 A:HIS36 4.6 13.3 1.0
O A:GLY119 4.6 15.9 1.0
N A:TYR121 4.7 14.2 1.0
CB A:GLU34 4.7 13.6 1.0
C A:HIS120 4.7 14.0 1.0
CD A:GLU122 5.0 16.7 1.0

Manganese binding site 2 out of 6 in 3a6g

Go back to Manganese Binding Sites List in 3a6g
Manganese binding site 2 out of 6 in the W154F Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of W154F Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn300

b:23.9
occ:1.00
 OD2 B:ASP45 2.1 15.2 1.0
O B:HOH1004 2.2 17.4 1.0
OE2 B:GLU34 2.2 14.8 1.0
ND1 B:HIS120 2.3 12.0 1.0
O B:HOH1003 2.3 17.1 1.0
O B:HOH1013 2.5 32.9 1.0
CE1 B:HIS120 3.0 12.0 1.0
CD B:GLU34 3.2 13.2 1.0
CG B:ASP45 3.2 15.2 1.0
CG B:HIS120 3.5 15.3 1.0
ZN B:ZN301 3.5 30.1 1.0
OE1 B:GLU34 3.5 15.1 1.0
OD1 B:ASP45 3.7 15.4 1.0
CA B:HIS120 3.9 16.0 1.0
CB B:HIS120 4.0 14.8 1.0
OE1 B:GLU122 4.1 14.2 1.0
NE2 B:HIS120 4.2 13.7 1.0
ND1 B:HIS178 4.3 17.1 1.0
CE1 B:HIS178 4.4 17.2 1.0
CB B:ASP45 4.4 14.4 1.0
CD2 B:HIS120 4.4 13.4 1.0
NE2 B:HIS36 4.5 13.2 1.0
CG B:GLU34 4.5 12.5 1.0
N B:TYR121 4.5 15.2 1.0
CE1 B:HIS36 4.6 15.1 1.0
O B:GLY119 4.6 15.9 1.0
C B:HIS120 4.7 15.5 1.0
CB B:GLU34 4.7 12.1 1.0
CD B:GLU122 5.0 16.2 1.0

Manganese binding site 3 out of 6 in 3a6g

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Manganese binding site 3 out of 6 in the W154F Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of W154F Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn300

b:24.1
occ:1.00
 OD2 C:ASP45 2.1 15.4 1.0
OE1 C:GLU34 2.1 18.8 1.0
ND1 C:HIS120 2.2 14.2 1.0
O C:HOH1006 2.2 19.9 1.0
O C:HOH1005 2.4 21.5 1.0
O C:HOH1014 2.5 32.6 1.0
CE1 C:HIS120 2.9 12.9 1.0
CD C:GLU34 3.1 17.6 1.0
CG C:ASP45 3.2 14.7 1.0
CG C:HIS120 3.4 14.8 1.0
OE2 C:GLU34 3.4 17.8 1.0
ZN C:ZN301 3.7 34.3 1.0
OD1 C:ASP45 3.7 15.3 1.0
CA C:HIS120 3.9 15.7 1.0
CB C:HIS120 4.0 13.7 1.0
OE1 C:GLU122 4.1 16.0 1.0
NE2 C:HIS120 4.2 14.6 1.0
ND1 C:HIS178 4.3 19.4 1.0
CE1 C:HIS178 4.4 18.9 1.0
CD2 C:HIS120 4.4 12.4 1.0
CG C:GLU34 4.5 16.0 1.0
CB C:ASP45 4.5 14.2 1.0
N C:TYR121 4.5 15.8 1.0
CE1 C:HIS36 4.5 16.0 1.0
O C:GLY119 4.5 16.8 1.0
C C:HIS120 4.6 15.3 1.0
NE2 C:HIS36 4.7 15.9 1.0
CB C:GLU34 4.7 14.4 1.0
CD C:GLU122 5.0 18.1 1.0

Manganese binding site 4 out of 6 in 3a6g

Go back to Manganese Binding Sites List in 3a6g
Manganese binding site 4 out of 6 in the W154F Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of W154F Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn300

b:25.4
occ:1.00
 OD2 D:ASP45 2.1 16.6 1.0
OE2 D:GLU34 2.2 16.4 1.0
O D:HOH1008 2.2 16.0 1.0
O D:HOH1007 2.3 19.4 1.0
ND1 D:HIS120 2.3 13.9 1.0
O D:HOH1015 2.4 32.7 1.0
CE1 D:HIS120 3.0 13.5 1.0
CG D:ASP45 3.2 15.4 1.0
CD D:GLU34 3.2 15.2 1.0
CG D:HIS120 3.5 15.0 1.0
OE1 D:GLU34 3.6 18.2 1.0
ZN D:ZN301 3.6 31.9 1.0
OD1 D:ASP45 3.6 15.2 1.0
CA D:HIS120 4.0 16.5 1.0
CB D:HIS120 4.0 16.2 1.0
OE1 D:GLU122 4.2 15.7 1.0
ND1 D:HIS178 4.2 16.5 1.0
NE2 D:HIS120 4.3 14.7 1.0
CE1 D:HIS178 4.4 15.7 1.0
CE1 D:HIS36 4.5 17.3 1.0
CB D:ASP45 4.5 12.3 1.0
O D:GLY119 4.5 17.2 1.0
CD2 D:HIS120 4.5 12.6 1.0
CG D:GLU34 4.5 13.8 1.0
NE2 D:HIS36 4.5 15.0 1.0
N D:TYR121 4.6 15.6 1.0
C D:HIS120 4.7 16.6 1.0
CB D:GLU34 4.7 12.0 1.0
CD D:GLU122 5.0 15.9 1.0

Manganese binding site 5 out of 6 in 3a6g

Go back to Manganese Binding Sites List in 3a6g
Manganese binding site 5 out of 6 in the W154F Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of W154F Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn300

b:22.7
occ:1.00
 OD2 E:ASP45 2.1 17.0 1.0
OE1 E:GLU34 2.2 16.8 1.0
O E:HOH1010 2.2 15.2 1.0
O E:HOH1009 2.3 17.4 1.0
ND1 E:HIS120 2.3 14.1 1.0
O E:HOH1016 2.4 26.2 1.0
CE1 E:HIS120 3.1 14.2 1.0
CD E:GLU34 3.2 18.6 1.0
CG E:ASP45 3.2 16.9 1.0
CG E:HIS120 3.5 14.2 1.0
OE2 E:GLU34 3.5 18.9 1.0
ZN E:ZN301 3.6 30.4 1.0
OD1 E:ASP45 3.6 15.9 1.0
CA E:HIS120 3.9 14.4 1.0
CB E:HIS120 3.9 14.3 1.0
OE1 E:GLU122 4.1 15.0 1.0
ND1 E:HIS178 4.2 18.5 1.0
NE2 E:HIS120 4.3 14.4 1.0
CE1 E:HIS178 4.4 16.3 1.0
O E:GLY119 4.5 17.1 1.0
CB E:ASP45 4.5 15.1 1.0
CG E:GLU34 4.5 16.8 1.0
CD2 E:HIS120 4.5 12.8 1.0
CE1 E:HIS36 4.5 16.1 1.0
N E:TYR121 4.6 14.1 1.0
NE2 E:HIS36 4.6 14.9 1.0
C E:HIS120 4.6 14.1 1.0
CB E:GLU34 4.8 16.3 1.0
CD E:GLU122 5.0 16.6 1.0

Manganese binding site 6 out of 6 in 3a6g

Go back to Manganese Binding Sites List in 3a6g
Manganese binding site 6 out of 6 in the W154F Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of W154F Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn300

b:26.7
occ:1.00
 OD2 F:ASP45 2.1 18.7 1.0
OE2 F:GLU34 2.2 15.4 1.0
O F:HOH1012 2.2 16.1 1.0
ND1 F:HIS120 2.2 14.0 1.0
O F:HOH1011 2.4 22.7 1.0
CE1 F:HIS120 2.9 12.9 1.0
CD F:GLU34 3.1 16.2 1.0
CG F:ASP45 3.2 16.5 1.0
OE1 F:GLU34 3.4 15.5 1.0
CG F:HIS120 3.4 15.6 1.0
O F:HOH1017 3.5 44.5 1.0
OD1 F:ASP45 3.7 16.6 1.0
ZN F:ZN301 3.7 30.7 1.0
CA F:HIS120 3.9 13.2 1.0
CB F:HIS120 3.9 14.3 1.0
OE1 F:GLU122 4.1 17.0 1.0
NE2 F:HIS120 4.2 12.6 1.0
ND1 F:HIS178 4.3 18.7 1.0
CE1 F:HIS178 4.3 18.8 1.0
CD2 F:HIS120 4.4 12.3 1.0
CB F:ASP45 4.5 15.0 1.0
N F:TYR121 4.5 13.7 1.0
O F:GLY119 4.5 16.2 1.0
CG F:GLU34 4.5 15.1 1.0
CE1 F:HIS36 4.6 17.0 1.0
C F:HIS120 4.6 14.0 1.0
NE2 F:HIS36 4.7 16.3 1.0
CB F:GLU34 4.7 14.9 1.0
CD F:GLU122 4.9 18.2 1.0
N F:HIS120 5.0 14.5 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 15:41:12 2024

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