Atomistry » Manganese » PDB 2ypq-3au8 » 3a6k
Atomistry »
  Manganese »
    PDB 2ypq-3au8 »
      3a6k »

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: Tue Dec 15 04:07:30 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy