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Manganese in PDB 3a6d: Creatininase Complexed with 1-Methylguanidine

Enzymatic activity of Creatininase Complexed with 1-Methylguanidine

All present enzymatic activity of Creatininase Complexed with 1-Methylguanidine:
3.5.2.10;

Protein crystallography data

The structure of Creatininase Complexed with 1-Methylguanidine, PDB code: 3a6d 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 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 102.400, 152.700, 167.500, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 20.7

Other elements in 3a6d:

The structure of Creatininase Complexed with 1-Methylguanidine also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Creatininase Complexed with 1-Methylguanidine (pdb code 3a6d). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Creatininase Complexed with 1-Methylguanidine, PDB code: 3a6d:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3a6d

Go back to Manganese Binding Sites List in 3a6d
Manganese binding site 1 out of 6 in the Creatininase Complexed with 1-Methylguanidine


Mono view


Stereo pair view

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

b:23.9
occ:1.00
 OE2 A:GLU34 2.1 23.1 1.0
OD2 A:ASP45 2.1 20.3 1.0
O A:HOH2087 2.2 22.3 1.0
O A:HOH2083 2.3 24.2 1.0
ND1 A:HIS120 2.3 19.4 1.0
CE1 A:HIS120 3.0 20.0 1.0
CD A:GLU34 3.1 20.9 1.0
O A:HOH1205 3.1 29.7 1.0
CG A:ASP45 3.3 21.5 1.0
ZN A:ZN301 3.5 26.5 1.0
OE1 A:GLU34 3.5 21.9 1.0
CG A:HIS120 3.5 22.0 1.0
OD1 A:ASP45 3.8 22.0 1.0
CA A:HIS120 4.0 21.8 1.0
NH2 A:MGX302 4.1 35.5 1.0
ND1 A:HIS178 4.1 24.9 1.0
CB A:HIS120 4.1 20.9 1.0
CE1 A:HIS178 4.1 23.8 1.0
OE1 A:GLU122 4.2 22.0 1.0
NE2 A:HIS120 4.3 22.5 1.0
N A:TYR121 4.4 22.6 1.0
CG A:GLU34 4.5 22.3 1.0
CE1 A:HIS36 4.5 23.8 1.0
NE2 A:HIS36 4.5 24.5 1.0
CB A:ASP45 4.5 21.4 1.0
CD2 A:HIS120 4.5 19.4 1.0
CB A:GLU34 4.6 21.7 1.0
C A:HIS120 4.7 22.0 1.0
O A:GLY119 4.7 22.3 1.0

Manganese binding site 2 out of 6 in 3a6d

Go back to Manganese Binding Sites List in 3a6d
Manganese binding site 2 out of 6 in the Creatininase Complexed with 1-Methylguanidine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Creatininase Complexed with 1-Methylguanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn300

b:23.6
occ:1.00
 OE2 B:GLU34 2.1 22.6 1.0
OD2 B:ASP45 2.1 22.1 1.0
O B:HOH2084 2.2 22.7 1.0
O B:HOH2088 2.2 21.9 1.0
ND1 B:HIS120 2.3 19.8 1.0
CE1 B:HIS120 3.0 22.8 1.0
CD B:GLU34 3.1 21.1 1.0
CG B:ASP45 3.2 21.3 1.0
O B:HOH1167 3.4 28.3 1.0
OE1 B:GLU34 3.5 22.0 1.0
CG B:HIS120 3.5 23.6 1.0
ZN B:ZN301 3.5 26.7 1.0
OD1 B:ASP45 3.7 21.9 1.0
CA B:HIS120 4.0 22.2 1.0
CB B:HIS120 4.0 23.4 1.0
ND1 B:HIS178 4.1 23.8 1.0
NH2 B:MGX303 4.1 36.8 1.0
CE1 B:HIS178 4.2 22.7 1.0
NE2 B:HIS120 4.2 22.6 1.0
OE1 B:GLU122 4.2 24.3 1.0
CG B:GLU34 4.4 22.1 1.0
NE2 B:HIS36 4.4 24.7 1.0
N B:TYR121 4.5 23.3 1.0
CE1 B:HIS36 4.5 25.4 1.0
CD2 B:HIS120 4.5 21.1 1.0
CB B:ASP45 4.5 20.4 1.0
CB B:GLU34 4.6 21.2 1.0
C B:HIS120 4.7 22.9 1.0
O B:GLY119 4.7 22.1 1.0
CB B:ALA32 5.0 17.8 1.0

Manganese binding site 3 out of 6 in 3a6d

Go back to Manganese Binding Sites List in 3a6d
Manganese binding site 3 out of 6 in the Creatininase Complexed with 1-Methylguanidine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Creatininase Complexed with 1-Methylguanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn300

b:24.9
occ:1.00
 OE2 C:GLU34 2.1 22.9 1.0
OD2 C:ASP45 2.1 22.5 1.0
O C:HOH1324 2.2 21.1 1.0
ND1 C:HIS120 2.3 20.8 1.0
O C:HOH2085 2.3 25.4 1.0
CE1 C:HIS120 3.0 21.0 1.0
CD C:GLU34 3.1 24.5 1.0
O C:HOH1242 3.3 37.4 1.0
CG C:ASP45 3.3 24.2 1.0
ZN C:ZN301 3.5 27.6 1.0
OE1 C:GLU34 3.5 25.2 1.0
CG C:HIS120 3.5 22.6 1.0
OD1 C:ASP45 3.7 22.6 1.0
CA C:HIS120 4.0 22.6 1.0
CB C:HIS120 4.0 21.8 1.0
NH2 C:MGX304 4.1 45.3 1.0
ND1 C:HIS178 4.1 24.4 1.0
OE1 C:GLU122 4.2 25.4 1.0
CE1 C:HIS178 4.2 24.7 1.0
NE2 C:HIS120 4.2 20.9 1.0
CG C:GLU34 4.5 24.5 1.0
CD2 C:HIS120 4.5 21.3 1.0
CB C:ASP45 4.5 21.9 1.0
CE1 C:HIS36 4.5 22.7 1.0
N C:TYR121 4.5 24.5 1.0
NE2 C:HIS36 4.5 21.6 1.0
C C:HIS120 4.7 22.7 1.0
CB C:GLU34 4.7 23.7 1.0
O C:GLY119 4.7 21.6 1.0

Manganese binding site 4 out of 6 in 3a6d

Go back to Manganese Binding Sites List in 3a6d
Manganese binding site 4 out of 6 in the Creatininase Complexed with 1-Methylguanidine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Creatininase Complexed with 1-Methylguanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn300

b:28.1
occ:1.00
 OE2 D:GLU34 2.1 24.7 1.0
OD2 D:ASP45 2.2 23.3 1.0
O D:HOH1657 2.2 23.0 1.0
O D:HOH1028 2.3 24.0 1.0
ND1 D:HIS120 2.4 22.8 1.0
O D:HOH1129 3.1 30.5 1.0
CE1 D:HIS120 3.1 26.1 1.0
CD D:GLU34 3.1 25.8 1.0
CG D:ASP45 3.2 26.4 1.0
ZN D:ZN301 3.4 29.5 1.0
CG D:HIS120 3.5 23.3 1.0
OE1 D:GLU34 3.6 24.0 1.0
OD1 D:ASP45 3.7 25.2 1.0
NH2 D:MGX305 3.9 49.5 1.0
CA D:HIS120 4.0 24.6 1.0
CB D:HIS120 4.0 23.2 1.0
ND1 D:HIS178 4.1 28.1 1.0
OE1 D:GLU122 4.3 25.5 1.0
NE2 D:HIS120 4.3 22.4 1.0
CE1 D:HIS178 4.3 25.1 1.0
NE2 D:HIS36 4.4 25.7 1.0
N D:TYR121 4.4 23.3 1.0
CE1 D:HIS36 4.4 27.5 1.0
CG D:GLU34 4.4 24.9 1.0
CB D:ASP45 4.5 23.5 1.0
CD2 D:HIS120 4.5 22.1 1.0
CB D:GLU34 4.6 23.9 1.0
C D:HIS120 4.6 24.5 1.0
O D:GLY119 4.7 25.5 1.0
CZ D:MGX305 4.9 48.4 1.0

Manganese binding site 5 out of 6 in 3a6d

Go back to Manganese Binding Sites List in 3a6d
Manganese binding site 5 out of 6 in the Creatininase Complexed with 1-Methylguanidine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Creatininase Complexed with 1-Methylguanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn300

b:26.8
occ:1.00
 OE2 E:GLU34 2.1 22.8 1.0
OD2 E:ASP45 2.1 22.0 1.0
O E:HOH1326 2.3 22.7 1.0
O E:HOH1076 2.3 25.8 1.0
ND1 E:HIS120 2.4 22.7 1.0
O E:HOH1477 3.0 40.0 1.0
CE1 E:HIS120 3.1 24.1 1.0
CD E:GLU34 3.2 22.8 1.0
CG E:ASP45 3.2 24.5 1.0
ZN E:ZN301 3.4 27.6 1.0
OE1 E:GLU34 3.5 22.3 1.0
CG E:HIS120 3.5 22.5 1.0
OD1 E:ASP45 3.7 24.2 1.0
NH2 E:MGX306 3.7 49.3 1.0
CA E:HIS120 3.9 21.7 1.0
CB E:HIS120 4.0 21.8 1.0
ND1 E:HIS178 4.1 24.1 1.0
OE1 E:GLU122 4.2 23.3 1.0
CE1 E:HIS178 4.2 21.7 1.0
NE2 E:HIS120 4.3 22.0 1.0
N E:TYR121 4.4 21.3 1.0
NE2 E:HIS36 4.4 24.6 1.0
CE1 E:HIS36 4.4 22.6 1.0
CG E:GLU34 4.5 22.5 1.0
CB E:ASP45 4.5 22.0 1.0
CD2 E:HIS120 4.6 20.4 1.0
C E:HIS120 4.6 21.8 1.0
O E:GLY119 4.6 21.7 1.0
CB E:GLU34 4.6 23.7 1.0
CZ E:MGX306 4.9 46.7 1.0

Manganese binding site 6 out of 6 in 3a6d

Go back to Manganese Binding Sites List in 3a6d
Manganese binding site 6 out of 6 in the Creatininase Complexed with 1-Methylguanidine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Creatininase Complexed with 1-Methylguanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn300

b:24.6
occ:1.00
 OD2 F:ASP45 2.1 20.6 1.0
OE2 F:GLU34 2.2 23.1 1.0
O F:HOH2089 2.3 22.2 1.0
ND1 F:HIS120 2.3 20.1 1.0
O F:HOH2086 2.3 27.7 1.0
CE1 F:HIS120 3.0 18.1 1.0
CD F:GLU34 3.2 22.2 1.0
CG F:ASP45 3.2 22.3 1.0
O F:HOH1469 3.3 39.2 1.0
ZN F:ZN301 3.5 27.0 1.0
OE1 F:GLU34 3.5 23.1 1.0
CG F:HIS120 3.5 19.7 1.0
OD1 F:ASP45 3.7 20.9 1.0
CA F:HIS120 4.0 21.3 1.0
CB F:HIS120 4.0 20.5 1.0
ND1 F:HIS178 4.1 23.6 1.0
NH2 F:MGX307 4.2 43.3 1.0
CE1 F:HIS178 4.2 23.4 1.0
OE1 F:GLU122 4.2 25.1 1.0
NE2 F:HIS120 4.2 21.5 1.0
CE1 F:HIS36 4.4 21.0 1.0
NE2 F:HIS36 4.4 20.7 1.0
CG F:GLU34 4.5 22.4 1.0
N F:TYR121 4.5 23.2 1.0
CD2 F:HIS120 4.5 19.5 1.0
CB F:ASP45 4.5 20.4 1.0
O F:GLY119 4.7 23.4 1.0
CB F:GLU34 4.7 20.4 1.0
C F:HIS120 4.7 21.8 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 Aug 16 11:18:48 2025

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