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Manganese in PDB 3a6k: The E122Q Mutant Creatininase, Mn-Zn Type

Enzymatic activity of The E122Q Mutant Creatininase, Mn-Zn Type

All present enzymatic activity of The E122Q Mutant Creatininase, Mn-Zn Type:
3.5.2.10;

Protein crystallography data

The structure of The E122Q Mutant Creatininase, Mn-Zn Type, PDB code: 3a6k 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 / 2.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 164.200, 164.200, 164.700, 90.00, 90.00, 120.00
R / Rfree (%) 20.7 / 23.7

Other elements in 3a6k:

The structure of The E122Q Mutant Creatininase, Mn-Zn Type 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 The E122Q Mutant Creatininase, Mn-Zn Type (pdb code 3a6k). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the The E122Q Mutant Creatininase, Mn-Zn Type, PDB code: 3a6k:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3a6k

Go back to Manganese Binding Sites List in 3a6k
Manganese binding site 1 out of 6 in the The E122Q Mutant Creatininase, Mn-Zn Type


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The E122Q Mutant Creatininase, Mn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn300

b:40.7
occ:1.00
 OE1 A:GLU34 2.2 39.2 1.0
ND1 A:HIS120 2.2 37.5 1.0
OD2 A:ASP45 2.2 32.8 1.0
CL A:CL302 2.7 46.6 1.0
CE1 A:HIS120 2.9 36.0 1.0
CD A:GLU34 3.1 37.9 1.0
CG A:ASP45 3.3 31.2 1.0
CG A:HIS120 3.4 37.1 1.0
OE2 A:GLU34 3.4 39.8 1.0
ZN A:ZN301 3.7 37.2 1.0
OD1 A:ASP45 3.9 30.6 1.0
CA A:HIS120 3.9 36.9 1.0
CB A:HIS120 3.9 36.7 1.0
NE2 A:HIS120 4.1 36.1 1.0
NE2 A:GLN122 4.1 49.2 1.0
CE1 A:HIS178 4.2 48.9 1.0
ND1 A:HIS178 4.2 51.0 1.0
CD2 A:HIS120 4.4 37.4 1.0
N A:TYR121 4.5 40.9 1.0
CG A:GLU34 4.5 36.9 1.0
O A:GLY119 4.6 35.9 1.0
CB A:ASP45 4.6 31.5 1.0
CE1 A:HIS36 4.6 34.8 1.0
C A:HIS120 4.6 37.8 1.0
CB A:GLU34 4.7 33.7 1.0
NE2 A:HIS36 4.8 33.2 1.0

Manganese binding site 2 out of 6 in 3a6k

Go back to Manganese Binding Sites List in 3a6k
Manganese binding site 2 out of 6 in the The E122Q Mutant Creatininase, Mn-Zn Type


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The E122Q Mutant Creatininase, Mn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn300

b:39.6
occ:1.00
 OD2 B:ASP45 2.2 27.2 1.0
ND1 B:HIS120 2.3 34.1 1.0
OE1 B:GLU34 2.3 37.2 1.0
CL B:CL302 2.8 49.6 1.0
CE1 B:HIS120 3.0 31.8 1.0
CD B:GLU34 3.3 33.6 1.0
CG B:ASP45 3.3 25.9 1.0
CG B:HIS120 3.5 33.7 1.0
OE2 B:GLU34 3.6 35.2 1.0
ZN B:ZN301 3.7 33.0 1.0
OD1 B:ASP45 3.8 23.9 1.0
CA B:HIS120 3.9 36.8 1.0
CB B:HIS120 4.0 33.7 1.0
NE2 B:GLN122 4.1 49.7 1.0
CE1 B:HIS178 4.2 43.9 1.0
NE2 B:HIS120 4.2 33.7 1.0
ND1 B:HIS178 4.3 45.0 1.0
O B:GLY119 4.4 40.1 1.0
N B:TYR121 4.4 40.7 1.0
CD2 B:HIS120 4.5 34.1 1.0
CB B:ASP45 4.6 24.8 1.0
C B:HIS120 4.6 36.8 1.0
CG B:GLU34 4.6 29.9 1.0
NE2 B:HIS36 4.6 29.9 1.0
CE1 B:HIS36 4.8 32.3 1.0
CB B:GLU34 4.8 25.0 1.0
N B:HIS120 5.0 36.5 1.0

Manganese binding site 3 out of 6 in 3a6k

Go back to Manganese Binding Sites List in 3a6k
Manganese binding site 3 out of 6 in the The E122Q Mutant Creatininase, Mn-Zn Type


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The E122Q Mutant Creatininase, Mn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn300

b:38.1
occ:1.00
 OD1 C:ASP45 2.2 29.8 1.0
OE1 C:GLU34 2.2 33.9 1.0
ND1 C:HIS120 2.3 38.7 1.0
CL C:CL302 2.8 48.9 1.0
CE1 C:HIS120 3.0 37.9 1.0
CD C:GLU34 3.2 34.6 1.0
CG C:ASP45 3.3 28.6 1.0
CG C:HIS120 3.5 37.8 1.0
OE2 C:GLU34 3.6 36.7 1.0
ZN C:ZN301 3.6 30.2 1.0
OD2 C:ASP45 3.8 26.6 1.0
NE2 C:GLN122 3.9 50.1 1.0
CA C:HIS120 4.0 37.4 1.0
CB C:HIS120 4.0 36.5 1.0
ND1 C:HIS178 4.2 45.0 1.0
CE1 C:HIS178 4.2 44.4 1.0
NE2 C:HIS120 4.2 40.2 1.0
CD2 C:HIS120 4.5 38.8 1.0
NE2 C:HIS36 4.5 30.4 1.0
CG C:GLU34 4.5 33.9 1.0
O C:GLY119 4.5 35.4 1.0
N C:TYR121 4.5 41.5 1.0
CB C:ASP45 4.6 27.5 1.0
CE1 C:HIS36 4.6 31.5 1.0
C C:HIS120 4.7 38.0 1.0
CB C:GLU34 4.8 31.6 1.0
CD C:GLN122 4.9 50.1 1.0

Manganese binding site 4 out of 6 in 3a6k

Go back to Manganese Binding Sites List in 3a6k
Manganese binding site 4 out of 6 in the The E122Q Mutant Creatininase, Mn-Zn Type


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The E122Q Mutant Creatininase, Mn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn300

b:44.7
occ:1.00
 OE2 D:GLU34 2.3 36.5 1.0
ND1 D:HIS120 2.3 39.5 1.0
OD1 D:ASP45 2.3 34.1 1.0
CE1 D:HIS120 2.9 37.1 1.0
CL D:CL302 3.0 55.6 1.0
CD D:GLU34 3.2 37.6 1.0
CG D:ASP45 3.4 30.5 1.0
CG D:HIS120 3.4 37.3 1.0
OE1 D:GLU34 3.6 41.1 1.0
ZN D:ZN301 3.7 35.9 1.0
OD2 D:ASP45 3.8 33.6 1.0
CA D:HIS120 3.9 36.8 1.0
CB D:HIS120 4.0 36.7 1.0
NE2 D:GLN122 4.1 54.8 1.0
CE1 D:HIS178 4.1 55.9 1.0
NE2 D:HIS120 4.2 38.0 1.0
ND1 D:HIS178 4.3 56.5 1.0
CD2 D:HIS120 4.4 38.6 1.0
N D:TYR121 4.4 41.2 1.0
NE2 D:HIS36 4.5 34.7 1.0
CG D:GLU34 4.5 37.5 1.0
O D:GLY119 4.5 33.6 1.0
C D:HIS120 4.6 38.5 1.0
CB D:ASP45 4.6 32.0 1.0
CB D:GLU34 4.7 35.6 1.0
CE1 D:HIS36 4.7 35.9 1.0

Manganese binding site 5 out of 6 in 3a6k

Go back to Manganese Binding Sites List in 3a6k
Manganese binding site 5 out of 6 in the The E122Q Mutant Creatininase, Mn-Zn Type


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The E122Q Mutant Creatininase, Mn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn300

b:38.0
occ:1.00
 OE1 E:GLU34 2.2 33.2 1.0
OD2 E:ASP45 2.2 29.4 1.0
ND1 E:HIS120 2.3 40.5 1.0
CL E:CL302 2.9 51.9 1.0
CE1 E:HIS120 2.9 39.4 1.0
CD E:GLU34 3.1 34.2 1.0
OE2 E:GLU34 3.3 34.3 1.0
CG E:ASP45 3.3 31.6 1.0
CG E:HIS120 3.5 38.6 1.0
ZN E:ZN301 3.6 34.6 1.0
OD1 E:ASP45 3.9 28.2 1.0
NE2 E:GLN122 4.0 57.0 1.0
CA E:HIS120 4.1 37.4 1.0
CB E:HIS120 4.1 38.1 1.0
NE2 E:HIS120 4.2 39.7 1.0
ND1 E:HIS178 4.4 47.8 1.0
CE1 E:HIS178 4.4 46.2 1.0
CG E:GLU34 4.5 32.5 1.0
CD2 E:HIS120 4.5 39.6 1.0
N E:TYR121 4.5 41.7 1.0
CB E:ASP45 4.6 29.0 1.0
NE2 E:HIS36 4.6 27.5 1.0
CE1 E:HIS36 4.7 30.3 1.0
O E:GLY119 4.7 35.2 1.0
C E:HIS120 4.7 39.0 1.0
CB E:GLU34 4.8 30.1 1.0

Manganese binding site 6 out of 6 in 3a6k

Go back to Manganese Binding Sites List in 3a6k
Manganese binding site 6 out of 6 in the The E122Q Mutant Creatininase, Mn-Zn Type


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The E122Q Mutant Creatininase, Mn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn300

b:39.0
occ:1.00
 OD2 F:ASP45 2.2 26.1 1.0
OE1 F:GLU34 2.2 35.9 1.0
ND1 F:HIS120 2.3 36.5 1.0
CL F:CL302 2.9 46.2 1.0
CE1 F:HIS120 3.0 35.6 1.0
CD F:GLU34 3.2 35.6 1.0
CG F:ASP45 3.3 27.2 1.0
OE2 F:GLU34 3.5 38.2 1.0
CG F:HIS120 3.5 36.8 1.0
ZN F:ZN301 3.6 32.4 1.0
OD1 F:ASP45 3.9 30.5 1.0
CA F:HIS120 4.0 36.9 1.0
NE2 F:GLN122 4.0 49.3 1.0
CB F:HIS120 4.1 36.2 1.0
CE1 F:HIS178 4.1 36.2 1.0
ND1 F:HIS178 4.2 36.3 1.0
NE2 F:HIS120 4.2 39.1 1.0
N F:TYR121 4.4 39.0 1.0
CD2 F:HIS120 4.5 37.7 1.0
CG F:GLU34 4.5 33.7 1.0
CB F:ASP45 4.5 27.7 1.0
C F:HIS120 4.6 37.5 1.0
O F:GLY119 4.7 35.3 1.0
NE2 F:HIS36 4.7 28.5 1.0
CE1 F:HIS36 4.7 30.8 1.0
CB F:GLU34 4.8 30.5 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 15:41:40 2024

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