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Manganese in PDB 1j2t: Creatininase Mn

Enzymatic activity of Creatininase Mn

All present enzymatic activity of Creatininase Mn:
3.5.2.10;

Protein crystallography data

The structure of Creatininase Mn, PDB code: 1j2t was solved by T.Yoshimoto, N.Tanaka, N.Kanada, T.Inoue, Y.Nakajima, M.Haratake, K.T.Nakamura, Y.Xu, K.Ito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.989, 150.742, 167.066, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.3

Other elements in 1j2t:

The structure of Creatininase Mn also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Creatininase Mn (pdb code 1j2t). 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 Mn, PDB code: 1j2t:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 1j2t

Go back to Manganese Binding Sites List in 1j2t
Manganese binding site 1 out of 6 in the Creatininase Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Creatininase Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:15.0
occ:1.00
 OD2 A:ASP45 2.0 14.6 1.0
OE2 A:GLU34 2.1 15.3 1.0
O A:HOH7009 2.2 17.3 1.0
O A:HOH7008 2.2 14.4 1.0
ND1 A:HIS120 2.3 11.8 1.0
CE1 A:HIS120 3.0 13.1 1.0
CD A:GLU34 3.0 14.3 1.0
O A:HOH7010 3.2 20.9 1.0
CG A:ASP45 3.2 14.5 1.0
OE1 A:GLU34 3.3 13.1 1.0
CG A:HIS120 3.4 13.4 1.0
ZN A:ZN302 3.5 16.9 1.0
OD1 A:ASP45 3.6 14.6 1.0
CA A:HIS120 3.9 13.6 1.0
CB A:HIS120 3.9 13.3 1.0
ND1 A:HIS178 4.1 17.7 1.0
CE1 A:HIS178 4.2 15.3 1.0
OE1 A:GLU122 4.2 14.2 1.0
NE2 A:HIS120 4.2 12.6 1.0
N A:TYR121 4.3 13.4 1.0
CG A:GLU34 4.4 13.6 1.0
CE1 A:HIS36 4.4 14.0 1.0
NE2 A:HIS36 4.4 15.3 1.0
CD2 A:HIS120 4.4 14.5 1.0
CB A:ASP45 4.5 13.9 1.0
C A:HIS120 4.5 14.0 1.0
CB A:GLU34 4.6 13.3 1.0
O A:GLY119 4.7 14.5 1.0
CB A:ALA32 4.9 13.2 1.0

Manganese binding site 2 out of 6 in 1j2t

Go back to Manganese Binding Sites List in 1j2t
Manganese binding site 2 out of 6 in the Creatininase Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Creatininase Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:17.9
occ:1.00
 OE2 B:GLU34 2.0 17.6 1.0
OD2 B:ASP45 2.1 18.1 1.0
O B:HOH7010 2.2 19.2 1.0
ND1 B:HIS120 2.2 13.1 1.0
O B:HOH7009 2.3 17.6 1.0
CE1 B:HIS120 3.0 14.7 1.0
CD B:GLU34 3.1 14.7 1.0
CG B:ASP45 3.2 17.3 1.0
O B:HOH7011 3.2 26.2 1.0
CG B:HIS120 3.4 16.1 1.0
OE1 B:GLU34 3.4 17.5 1.0
ZN B:ZN302 3.5 20.6 1.0
OD1 B:ASP45 3.7 17.5 1.0
CB B:HIS120 3.9 16.7 1.0
CA B:HIS120 3.9 16.9 1.0
OE1 B:GLU122 4.2 16.2 1.0
ND1 B:HIS178 4.2 22.0 1.0
CE1 B:HIS178 4.2 20.4 1.0
NE2 B:HIS120 4.2 15.6 1.0
CG B:GLU34 4.4 16.8 1.0
CD2 B:HIS120 4.4 14.0 1.0
CE1 B:HIS36 4.4 16.6 1.0
NE2 B:HIS36 4.5 19.3 1.0
CB B:ASP45 4.5 17.3 1.0
N B:TYR121 4.5 18.3 1.0
CB B:GLU34 4.6 16.1 1.0
O B:GLY119 4.7 17.3 1.0
C B:HIS120 4.7 17.8 1.0
CB B:ALA32 4.9 14.2 1.0

Manganese binding site 3 out of 6 in 1j2t

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Manganese binding site 3 out of 6 in the Creatininase Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Creatininase Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:17.6
occ:1.00
 OE2 C:GLU34 2.0 15.6 1.0
OD2 C:ASP45 2.1 16.0 1.0
O C:HOH7011 2.1 16.8 1.0
O C:HOH7010 2.2 16.1 1.0
ND1 C:HIS120 2.3 15.4 1.0
CE1 C:HIS120 3.0 15.9 1.0
CD C:GLU34 3.1 15.2 1.0
CG C:ASP45 3.2 18.7 1.0
O C:HOH7012 3.3 29.7 1.0
CG C:HIS120 3.4 15.5 1.0
OE1 C:GLU34 3.5 16.0 1.0
ZN C:ZN302 3.5 20.1 1.0
OD1 C:ASP45 3.7 19.8 1.0
CB C:HIS120 3.9 16.7 1.0
CA C:HIS120 4.0 16.9 1.0
CE1 C:HIS178 4.1 18.0 1.0
ND1 C:HIS178 4.1 19.2 1.0
OE1 C:GLU122 4.2 17.1 1.0
NE2 C:HIS120 4.2 14.5 1.0
CG C:GLU34 4.4 15.4 1.0
CE1 C:HIS36 4.4 17.4 1.0
NE2 C:HIS36 4.4 17.0 1.0
CD2 C:HIS120 4.4 13.6 1.0
CB C:ASP45 4.5 17.4 1.0
CB C:GLU34 4.7 15.9 1.0
N C:TYR121 4.7 18.1 1.0
O C:GLY119 4.7 16.9 1.0
C C:HIS120 4.8 17.4 1.0
CB C:ALA32 5.0 15.5 1.0
O C:SER78 5.0 23.7 1.0

Manganese binding site 4 out of 6 in 1j2t

Go back to Manganese Binding Sites List in 1j2t
Manganese binding site 4 out of 6 in the Creatininase Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Creatininase Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:18.8
occ:1.00
 OE2 D:GLU34 1.9 18.2 1.0
OD2 D:ASP45 2.1 19.5 1.0
O D:HOH7003 2.2 18.1 1.0
O D:HOH7002 2.2 19.7 1.0
ND1 D:HIS120 2.3 15.2 1.0
CD D:GLU34 3.0 17.4 1.0
CE1 D:HIS120 3.1 17.3 1.0
CG D:ASP45 3.3 19.8 1.0
O D:HOH7004 3.3 24.8 1.0
OE1 D:GLU34 3.4 17.0 1.0
CG D:HIS120 3.4 17.7 1.0
ZN D:ZN302 3.5 21.1 1.0
OD1 D:ASP45 3.7 19.4 1.0
CB D:HIS120 3.9 17.5 1.0
CA D:HIS120 3.9 17.1 1.0
ND1 D:HIS178 4.1 17.5 1.0
CE1 D:HIS178 4.1 16.1 1.0
OE1 D:GLU122 4.2 17.7 1.0
NE2 D:HIS120 4.3 16.7 1.0
CE1 D:HIS36 4.3 20.0 1.0
CG D:GLU34 4.3 17.8 1.0
NE2 D:HIS36 4.3 20.1 1.0
N D:TYR121 4.3 16.6 1.0
CD2 D:HIS120 4.5 16.0 1.0
CB D:ASP45 4.5 18.3 1.0
C D:HIS120 4.5 16.9 1.0
CB D:GLU34 4.6 18.2 1.0
O D:GLY119 4.7 17.2 1.0
O D:SER78 4.9 25.7 1.0
CB D:ALA32 4.9 17.0 1.0

Manganese binding site 5 out of 6 in 1j2t

Go back to Manganese Binding Sites List in 1j2t
Manganese binding site 5 out of 6 in the Creatininase Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Creatininase Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn301

b:18.2
occ:1.00
 OE2 E:GLU34 1.9 15.8 1.0
OD2 E:ASP45 2.1 17.4 1.0
O E:HOH7004 2.2 18.8 1.0
O E:HOH7005 2.2 17.2 1.0
ND1 E:HIS120 2.3 14.4 1.0
CE1 E:HIS120 3.0 16.1 1.0
CD E:GLU34 3.0 16.0 1.0
CG E:ASP45 3.3 18.1 1.0
O E:HOH7006 3.3 25.5 1.0
OE1 E:GLU34 3.4 16.4 1.0
CG E:HIS120 3.4 16.7 1.0
ZN E:ZN302 3.5 20.8 1.0
OD1 E:ASP45 3.7 18.4 1.0
CB E:HIS120 3.9 17.4 1.0
CA E:HIS120 3.9 17.0 1.0
ND1 E:HIS178 4.1 19.4 1.0
OE1 E:GLU122 4.1 17.1 1.0
CE1 E:HIS178 4.1 17.1 1.0
NE2 E:HIS120 4.2 15.1 1.0
CG E:GLU34 4.3 16.8 1.0
CE1 E:HIS36 4.3 19.1 1.0
N E:TYR121 4.4 16.2 1.0
NE2 E:HIS36 4.4 19.5 1.0
CD2 E:HIS120 4.4 14.7 1.0
CB E:ASP45 4.5 18.2 1.0
C E:HIS120 4.6 17.1 1.0
CB E:GLU34 4.6 16.4 1.0
O E:GLY119 4.8 17.3 1.0
O E:SER78 4.9 22.5 1.0
CB E:ALA32 4.9 16.9 1.0

Manganese binding site 6 out of 6 in 1j2t

Go back to Manganese Binding Sites List in 1j2t
Manganese binding site 6 out of 6 in the Creatininase Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Creatininase Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn301

b:16.8
occ:1.00
 OD2 F:ASP45 2.1 14.9 1.0
OE2 F:GLU34 2.1 16.8 1.0
O F:HOH7011 2.2 15.7 1.0
O F:HOH7012 2.2 17.7 1.0
ND1 F:HIS120 2.3 13.4 1.0
CE1 F:HIS120 3.1 14.4 1.0
CD F:GLU34 3.1 15.4 1.0
CG F:ASP45 3.2 15.2 1.0
O F:HOH7013 3.3 28.6 1.0
CG F:HIS120 3.4 14.1 1.0
ZN F:ZN302 3.5 19.2 1.0
OE1 F:GLU34 3.5 14.9 1.0
OD1 F:ASP45 3.6 14.9 1.0
CB F:HIS120 3.9 15.6 1.0
CA F:HIS120 4.0 15.6 1.0
ND1 F:HIS178 4.2 17.6 1.0
OE1 F:GLU122 4.2 16.4 1.0
CE1 F:HIS178 4.2 17.8 1.0
NE2 F:HIS120 4.3 12.8 1.0
NE2 F:HIS36 4.4 18.9 1.0
CE1 F:HIS36 4.4 17.8 1.0
CG F:GLU34 4.4 15.1 1.0
CD2 F:HIS120 4.4 12.7 1.0
CB F:ASP45 4.5 14.9 1.0
N F:TYR121 4.6 16.7 1.0
CB F:GLU34 4.7 15.2 1.0
O F:GLY119 4.7 15.7 1.0
C F:HIS120 4.7 16.1 1.0
CB F:ALA32 4.9 14.2 1.0

Reference:

T.Yoshimoto, N.Tanaka, N.Kanada, T.Inoue, Y.Nakajima, M.Haratake, K.T.Nakamura, Y.Xu, K.Ito. Crystal Structures of Creatininase Reveal the Substrate Binding Site and Provide An Insight Into the Catalytic Mechanism J.Mol.Biol. V. 337 399 2004.
ISSN: ISSN 0022-2836
PubMed: 15003455
DOI: 10.1016/J.JMB.2004.01.022
Page generated: Sat Oct 5 11:06:39 2024

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